b1ar_analysis-sparse.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Couldn't import dot_parser, loading of dot files will not be possible.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/enf/software/anaconda/lib/python2.7/site-packages/matplotlib/__init__.py:1318: UserWarning:  This call to matplotlib.use() has no effect\n",
      "because the backend has already been chosen;\n",
      "matplotlib.use() must be called *before* pylab, matplotlib.pyplot,\n",
      "or matplotlib.backends is imported for the first time.\n",
      "\n",
      "  warnings.warn(_use_error_msg)\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import matplotlib\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "# changing matplotlib the default style\n",
    "matplotlib.style.use('ggplot')\n",
    "\n",
    "from PDB_Order_Fixer import PDB_Order_Fixer\n",
    "import mdtraj as md\n",
    "import os\n",
    "import numpy as np\n",
    "import h5py\n",
    "\n",
    "import datetime\n",
    "import glob\n",
    "import copy\n",
    "from functools import partial \n",
    "import operator\n",
    "import time\n",
    "\n",
    "import random \n",
    "import subprocess\n",
    "from subprocess import Popen\n",
    "import sys\n",
    "from io_functions import *\n",
    "from custom_clusterer import *\n",
    "from custom_tica import *\n",
    "from custom_featurizer import *\n",
    "from pdb_editing import *\n",
    "from analysis import *\n",
    "from io_functions import *\n",
    "#from topology_fixing import *\n",
    "from subsampling import *\n",
    "from conversions import *\n",
    "from custom_msm import *\n",
    "from grids import *\n",
    "from docking_analysis import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from operator import itemgetter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import warnings\n",
    "warnings.filterwarnings('ignore')\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false
   },
   "source": [
    "In this iPython notebook, we will featurize MOR ligand binding simulation by pairwise distances between the ligand and different receptor residues. We will then perform tICA and prospectively build an MSM. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "we are operating on biox3\n"
     ]
    }
   ],
   "source": [
    "from detect_intermediates import *\n",
    "from interpret_tICs import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273]\n",
      "There are 271 common residues between input structures\n"
     ]
    }
   ],
   "source": [
    "from b1ar_feature_types import *\n",
    "from get_variable_names import *\n",
    "from b1ar_tica_config import *\n",
    "from residue import Residue, Atom\n",
    "ori_feature_name = copy.deepcopy(feature_name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA\n",
      "/home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA\n"
     ]
    }
   ],
   "source": [
    "rho = 0.1\n",
    "rho_string = \"0pt1\"\n",
    "lag_time = 5\n",
    "n_components = 10\n",
    "n_clusters = 1000\n",
    "\n",
    "rho = 0.01\n",
    "rho_string = \"0pt01\"\n",
    "lag_time=50\n",
    "schemes = [\"closest-heavy\", \"CA\"]\n",
    "feature_name = \"%s-CA\" %ori_feature_name\n",
    "#feature_name = \"%s_phi_psi_chi2\" %feature_name\n",
    "(active_ref_dir, inactive_ref_dir, simulation_ref_dir, scripts_dir,\n",
    "          ligand_dir, agonist_dir, inverse_agonist_dir, biased_agonist_dir, ref_receptors_dir, whole_trajectory_pnas,\n",
    "          sasa_file) = get_base_files(base)\n",
    "\n",
    "tica_dir = get_tica_dir(base, is_sparse, lag_time, n_components, feature_name, \n",
    "                                 wolf_string, shrinkage_string, rho_string)\n",
    "ori_tica_dir = copy.deepcopy(tica_dir)\n",
    "#tica_dir = \"%s-normalized\" % ori_tica_dir\n",
    "features_dir = get_features_dir(base, feature_name)\n",
    "\n",
    "landmarks_dir = get_landmarks_dir(tica_dir)\n",
    "analysis_dir = get_analysis_dir(tica_dir, n_clusters, sampling_method)\n",
    "gmm_dir = get_gmm_dir(tica_dir)\n",
    "rf_dir = get_rf_dir(tica_dir)\n",
    "\n",
    "\n",
    "ref_tica_dir, ref_tica_coords = get_ref_tica_dirs(tica_dir)\n",
    "\n",
    "graph_file = get_graph_file(tica_dir, msm_lag_time, n_clusters)\n",
    "\n",
    "pnas_titles =  [\"tm6_tm3_dist\", \"rmsd_npxxy_inactive\", \"rmsd_npxxy_active\", \"rmsd_connector_inactive\", \"rmsd_connector_active\"]\n",
    "pnas_features_dir = analysis_dir\n",
    "\n",
    "\n",
    "(clusterer_dir, msm_model_dir, macrostate_dir, features_known, model_dir, projected_features_dir,\n",
    "         projection_operator_dir, ktica_fit_model_filename, ktica_projected_data_filename, nystroem_data_filename,\n",
    "         mutual_information_csv, pearson_csv) = get_tica_files(base, tica_dir, n_clusters, msm_lag_time, n_macrostates)\n",
    "\n",
    "(standardized_features_dir, feature_residues_csv, feature_residues_pkl,\n",
    "          contact_csv, ref_features_dir) = get_feature_files(features_dir)\n",
    "\n",
    "(kmeans_csv, tica_coords_csv, features_csv, active_rmsd_dir, inactive_rmsd_dir, active_pnas_dir, inactive_pnas_joined, active_pnas_joined,\n",
    "        clusters_map_file, ktica_clusters_map_file, analysis_file, combined_file, docking_summary, docking_joined, docking_z_scores_csv,\n",
    "        aggregate_docking, aggregate_docking_joined, docking_pnas_joined, aggregate_docking_pnas, aggregate_docking_pnas_joined, docking_multiple_ligands,\n",
    "        docking_distances_file, docking_pdf, mmgbsa_docking_distances, pnas_coords, mmgbsa_dir, mmgbsa_csv, mmgbsa_pdf, aggregate_mmgbsa,\n",
    "        aggregate_mmgbsa_joined, aggregate_mmgbsa_pnas_joined, mmgbsa_z_scores_csv, active_clusters_csv, intermediate_clusters_csv,\n",
    "        inactive_clusters_csv, pnas_clusters_averages, tica_clusters_averages, tica_classes_csv, tica_samples_csv, subgraph_save_base,\n",
    "        degree_save_base, degree_map_csv, degree_z_map_csv, aggregate_docking_pnas_degree_z_joined, tic_residue_csv, feature_coefs_csv,\n",
    "        duplicated_feature_coefs_csv) = get_analysis_files(analysis_dir, n_clusters, tica_dir, tica_dir, sampling_method, n_samples, precision,\n",
    "                                                           msm_lag_time)\n",
    "\n",
    "(inactive_pnas_distances_dir, active_pnas_distances_dir, active_pnas_all_distances_dir,\n",
    "          inactive_pnas_distances_new_csv, active_pnas_distances_new_csv, active_pnas_joined, active_pnas_means, pnas_coords_dir,\n",
    "          pnas_coords_csv, pnas_all_coords_csv, pnas_coords_hexbin_dir, pnas_coords_co_crystallized_docking_dir,\n",
    "          pnas_coords_active_colors_dir, user_defined_features_file, reaction_coordinates_trajs_file) = get_pnas_files(whole_trajectory_pnas, pnas_features_dir)\n",
    "\n",
    "features_dir = get_features_dir(base, feature_name)\n",
    "\n",
    "\n",
    "\n",
    "graph_file = get_graph_file(tica_dir, msm_lag_time, n_clusters)\n",
    "(scripts_dir, pymol_fixpdb_dir) = get_script_dir(scripts_dir)\n",
    "(save_dir, reimaged_dir, mae_dir, combined_reimaged_dir, grid_dir, docking_dir) = get_docking_dirs(tica_dir, n_clusters, n_components, n_samples, sampling_method, precision)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "134\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<AsyncMapResult: chdir>"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from ipyparallel import Client\n",
    "rc = Client()\n",
    "print(len(rc.ids))\n",
    "dview = rc[:]\n",
    "dview.map(os.chdir, ['/home/enf/b2ar_analysis/conformation']*len(rc.ids))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import custom_featurizer\n",
    "reload (custom_featurizer)\n",
    "from custom_featurizer import *\n",
    "suf_trajectories = [t for t in get_trajectory_files(traj_dir, \".h5\")]\n",
    "#fix_chain_names(suf_trajectories, dview)\n",
    "#featurize_contacts_custom(traj_dir, features_dir = features_dir, traj_ext = traj_ext, contact_residue_pairs_file = feature_residues_pkl, structures=[inactive_dir, active_dir], contact_residues=contact_residues,\n",
    "#                          residues_map = None, contact_cutoff = cutoff, parallel = False, exacycle = exacycle, traj_top_structure = None, iterative=False,\n",
    "#                          user_specified_atom_residue_pairs = [], load_from_file=False, worker_pool=None, schemes=schemes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "traj_dir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_featurizer\n",
    "reload(custom_featurizer)\n",
    "from custom_featurizer import *\n",
    "user_defined_features_dir = \"%s/user_defined_features\" %traj_dir\n",
    "if not os.path.exists(user_defined_features_dir):\n",
    "    os.makedirs(user_defined_features_dir)\n",
    "compute_user_defined_features_wrapper(traj_dir, traj_ext, inactive_dir, active_dir, None,\n",
    "                                        feature_name_residues_dict, user_defined_features_file, worker_pool=dview, \n",
    "                                        save_dir=user_defined_features_dir, parallel=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_featurizer\n",
    "reload(custom_featurizer)\n",
    "from custom_featurizer import *\n",
    "featurize_contacts_custom(traj_dir, features_dir = features_dir, traj_ext = traj_ext, contact_residue_pairs_file = feature_residues_pkl, structures=[inactive_dir, active_dir], contact_residues=contact_residues,\n",
    "                          residues_map = None, contact_cutoff = cutoff, parallel = False, exacycle = exacycle, traj_top_structure = None, iterative=False,\n",
    "                          user_specified_atom_residue_pairs = [], load_from_file=False, worker_pool=None, schemes=schemes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "fit_normalizer(features_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import pickle\n",
    "with open(feature_residues_pkl, \"rb\") as f:\n",
    "    feature_residues = pickle.load(f)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "feature_residues"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import custom_tica\n",
    "reload(custom_tica)\n",
    "from custom_tica import *\n",
    "fit_and_transform(features_directory = features_dir, model_dir = tica_dir, stride=5, lag_time = lag_time, n_components = n_components, sparse = sparse, wolf = wolf, rho = rho, shrinkage = shrinkage, parallel=True, traj_ext = traj_ext, normalize=True, partial_fit=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_featurizer\n",
    "reload(custom_featurizer)\n",
    "from custom_featurizer import *\n",
    "\n",
    "featurize_contacts_custom(ref_receptors_dir, features_dir = ref_features_dir, traj_ext = \".pdb\", contact_residue_pairs_file = feature_residues_pkl, structures=[inactive_dir, active_dir], contact_residues=contact_residues,\n",
    "                          residues_map = None, contact_cutoff = cutoff, parallel = False, exacycle = exacycle, traj_top_structure = None, iterative=False,\n",
    "                          user_specified_atom_residue_pairs = [], load_from_file=False, worker_pool=None, schemes=schemes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/home/enf/md_simulations/B1AR/reference_receptors'"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ref_receptors_dir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "transform(existing_model = projection_operator_dir, features_directory = ref_features_dir, tica_dir = ref_tica_dir, normalizer=verboseload(\"%s/normalizer.h5\" %features_dir))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_tica\n",
    "reload(custom_tica)\n",
    "from custom_tica import *\n",
    "transform_to_h5(projection_operator_dir, features_dir, projected_features_dir, worker_pool=None, parallel=True, normalizer=verboseload(\"%s/normalizer.h5\" %features_dir))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/phi_psi_chi2_allprot_tica_coords.h5\"...\n"
     ]
    }
   ],
   "source": [
    "tica_object = verboseload(projection_operator_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "#all_tica = verboseload(projected_features_dir)\n",
    "#all_tica = [x[:,range(1,10)] for x in all_tica]\n",
    "#print(all_tica[0].shape)\n",
    "#print(len(all_tica))\n",
    "#verbosedump(all_tica, projected_features_dir)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#n_components=9"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([ 1807.27577207,   930.82557327,   715.12014423,   577.5271037 ,\n",
       "         552.90096526,   471.41700734,   429.5572142 ,   418.77614562,\n",
       "         389.1365181 ,   374.5275853 ])"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tica_object.timescales_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_columns(tica_dir, projected_features_dir, titles = [\"tIC%d\" %j for j in range(1,11)], tICA = True, scale = 1.0, refcoords_file = None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/phi_psi_chi2_allprot_projected.h5\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/all_pnas_features/user_defined_features.h5\"...\n"
     ]
    }
   ],
   "source": [
    "feature_indices = []\n",
    "traj_basenames = get_trajectory_files(traj_dir, \".h5\")\n",
    "traj_basenames = [os.path.splitext(os.path.basename(t))[0] for t in traj_basenames]\n",
    "feature_basenames = get_trajectory_files(features_dir, \".dataset\")\n",
    "feature_basenames = [os.path.splitext(os.path.basename(t))[0] for t in feature_basenames]\n",
    "for i, traj_basename in enumerate(traj_basenames):\n",
    "    if traj_basename in feature_basenames:\n",
    "        feature_indices.append(int(i))\n",
    "\n",
    "tica_coords = verboseload(projected_features_dir)\n",
    "pnas_coords = verboseload(user_defined_features_file)\n",
    "pnas_coords = [pnas_coords[i] for i in feature_indices]\n",
    "tica_names = [\"tIC.%d\" %i for i in range(1,n_components+1)]\n",
    "pnas_names = sorted(feature_name_residues_dict.keys())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(29570, 5)\n",
      "(29570, 10)\n"
     ]
    }
   ],
   "source": [
    "print(np.concatenate(pnas_coords).shape)\n",
    "print(np.concatenate(tica_coords).shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plt.hist(np.concatenate(pnas_coords)[:,0], bins=50)\n",
    "plt.xlabel(\"tm6 to tm3 packing\")\n",
    "plt.ylabel(\"counts\")\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from plots import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_data_vs_data(np.concatenate(tica_coords), np.concatenate(pnas_coords), tica_names, pnas_names, analysis_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "subsampled_features_dir = os.path.join(tica_dir, \"subsampled_features\")\n",
    "if not os.path.exists(subsampled_features_dir): os.makedirs(subsampled_features_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ILE210 to ILE211\n"
     ]
    }
   ],
   "source": [
    "with open(feature_residues_pkl) as f:\n",
    "    feature_names = pickle.load(f)\n",
    "print(feature_names[0].__repr__())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n"
     ]
    },
    {
     "ename": "IndexError",
     "evalue": "list index out of range",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mIndexError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-18-0affd4cb8184>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[0mref_features\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;33m[\u001b[0m\u001b[0mload_file\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mf\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mf\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mget_trajectory_files\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mref_features_dir\u001b[0m\u001b[1;33m,\u001b[0m \u001b[1;34m\".dataset\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      2\u001b[0m \u001b[1;32mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mref_features\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 3\u001b[1;33m \u001b[1;32mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mref_features\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m0\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      4\u001b[0m \u001b[1;32mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mref_features\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mshape\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m \u001b[1;32mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mfeature_names\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mIndexError\u001b[0m: list index out of range"
     ]
    }
   ],
   "source": [
    "ref_features = [load_file(f) for f in get_trajectory_files(ref_features_dir, \".dataset\")]\n",
    "print(len(ref_features))\n",
    "print(ref_features[0].shape)\n",
    "print(ref_features[1].shape)\n",
    "print(len(feature_names))\n",
    "ref_features = pd.DataFrame(ref_features[0], columns=[str(f) for f in feature_names])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Interpreting tIC 1\n",
      "feature_importances_df.shape\n",
      "(12, 7)\n",
      "residue_importances_df.shape\n",
      "(13, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "5   Thr166_Ca To Ala171_Ca  Thr166_Ca  Ala171_Ca      166      171   \n",
      "2   Thr166_Ca To Ala169_Ca  Thr166_Ca  Ala169_Ca      166      169   \n",
      "6   Asn167_Ca To Ala171_Ca  Asn167_Ca  Ala171_Ca      167      171   \n",
      "7   Trp145_Ca To Thr166_Ca  Trp145_Ca  Thr166_Ca      145      166   \n",
      "9   Phe164_Ca To Thr166_Ca  Phe164_Ca  Thr166_Ca      164      166   \n",
      "8   Trp145_Ca To Asp163_Ca  Trp145_Ca  Asp163_Ca      145      163   \n",
      "11  Val165_Ca To Asn167_Ca  Val165_Ca  Asn167_Ca      165      167   \n",
      "3   Asn167_Ca To Ala169_Ca  Asn167_Ca  Ala169_Ca      167      169   \n",
      "4   Phe164_Ca To Tyr170_Ca  Phe164_Ca  Tyr170_Ca      164      170   \n",
      "0          Phe265 To Leu35     Phe265      Leu35      265       35   \n",
      "1         Asp147 To Ala169     Asp147     Ala169      147      169   \n",
      "10  Thr166_Ca To Asn167_Ca  Thr166_Ca  Asn167_Ca      166      167   \n",
      "\n",
      "    importance                 feature  \n",
      "5     0.408828  THR166_CA to ALA171_CA  \n",
      "2    -0.342735  THR166_CA to ALA169_CA  \n",
      "6    -0.181767  ASN167_CA to ALA171_CA  \n",
      "7     0.151778  TRP145_CA to THR166_CA  \n",
      "9     0.141651  PHE164_CA to THR166_CA  \n",
      "8    -0.129163  TRP145_CA to ASP163_CA  \n",
      "11   -0.123869  VAL165_CA to ASN167_CA  \n",
      "3     0.123849  ASN167_CA to ALA169_CA  \n",
      "4    -0.120513  PHE164_CA to TYR170_CA  \n",
      "0     0.087573         PHE265 to LEU35  \n",
      "1     0.066886        ASP147 to ALA169  \n",
      "10    0.045889  THR166_CA to ASN167_CA  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Ala171_Ca  Ala171_Ca    0.379298    171\n",
      "Thr166_Ca  Thr166_Ca    0.357418    166\n",
      "Trp145_Ca  Trp145_Ca    0.137731    145\n",
      "Asp163_Ca  Asp163_Ca   -0.129163    163\n",
      "Phe164_Ca  Phe164_Ca    0.128542    164\n",
      "Val165_Ca  Val165_Ca   -0.123869    165\n",
      "Tyr170_Ca  Tyr170_Ca   -0.120513    170\n",
      "Asn167_Ca  Asn167_Ca    0.112155    167\n",
      "Ala169_Ca  Ala169_Ca    0.100520    169\n",
      "Leu35          Leu35    0.087573     35\n",
      "Phe265        Phe265    0.087573    265\n",
      "Ala169        Ala169    0.066886    169\n",
      "Asp147        Asp147    0.066886    147\n",
      "Using dark_background\n",
      "Interpreting tIC 2\n",
      "feature_importances_df.shape\n",
      "(22, 7)\n",
      "residue_importances_df.shape\n",
      "(40, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "13  Thr207_Ca To Ser262_Ca  Thr207_Ca  Ser262_Ca      207      262   \n",
      "8    Arg118_Ca To Leu38_Ca  Arg118_Ca   Leu38_Ca      118       38   \n",
      "12   Ala119_Ca To Leu38_Ca  Ala119_Ca   Leu38_Ca      119       38   \n",
      "17  Arg200_Ca To Pro263_Ca  Arg200_Ca  Pro263_Ca      200      263   \n",
      "19  Leu208_Ca To Ile258_Ca  Leu208_Ca  Ile258_Ca      208      258   \n",
      "9   Ala197_Ca To Ile106_Ca  Ala197_Ca  Ile106_Ca      197      106   \n",
      "20  Asp147_Ca To Ala169_Ca  Asp147_Ca  Ala169_Ca      147      169   \n",
      "0         Arg195 To Ile106     Arg195     Ile106      195      106   \n",
      "10  Leu205_Ca To Ile106_Ca  Leu205_Ca  Ile106_Ca      205      106   \n",
      "15  Val193_Ca To Lys198_Ca  Val193_Ca  Lys198_Ca      193      198   \n",
      "6          Arg261 To Ile43     Arg261      Ile43      261       43   \n",
      "2         Asp147 To Arg168     Asp147     Arg168      147      168   \n",
      "18  Arg233_Ca To Ala152_Ca  Arg233_Ca  Ala152_Ca      233      152   \n",
      "1           Phe60 To Leu64      Phe60      Leu64       60       64   \n",
      "16  Glu196_Ca To Tyr103_Ca  Glu196_Ca  Tyr103_Ca      196      103   \n",
      "4         Leu208 To Asp101     Leu208     Asp101      208      101   \n",
      "14  Arg233_Ca To Arg168_Ca  Arg233_Ca  Arg168_Ca      233      168   \n",
      "5         Arg233 To Val165     Arg233     Val165      233      165   \n",
      "7   Met186_Ca To Ile211_Ca  Met186_Ca  Ile211_Ca      186      211   \n",
      "3         Phe215 To Asn255     Phe215     Asn255      215      255   \n",
      "21  Tyr194_Ca To Leu208_Ca  Tyr194_Ca  Leu208_Ca      194      208   \n",
      "11  Lys206_Ca To Gly209_Ca  Lys206_Ca  Gly209_Ca      206      209   \n",
      "\n",
      "    importance                 feature  \n",
      "13    0.196151  THR207_CA to SER262_CA  \n",
      "8     0.192010   ARG118_CA to LEU38_CA  \n",
      "12   -0.153973   ALA119_CA to LEU38_CA  \n",
      "17   -0.151188  ARG200_CA to PRO263_CA  \n",
      "19   -0.143850  LEU208_CA to ILE258_CA  \n",
      "9     0.129536  ALA197_CA to ILE106_CA  \n",
      "20    0.124314  ASP147_CA to ALA169_CA  \n",
      "0    -0.121472        ARG195 to ILE106  \n",
      "10    0.112779  LEU205_CA to ILE106_CA  \n",
      "15   -0.108429  VAL193_CA to LYS198_CA  \n",
      "6    -0.107066         ARG261 to ILE43  \n",
      "2     0.098926        ASP147 to ARG168  \n",
      "18   -0.097746  ARG233_CA to ALA152_CA  \n",
      "1     0.089462          PHE60 to LEU64  \n",
      "16    0.084919  GLU196_CA to TYR103_CA  \n",
      "4     0.084041        LEU208 to ASP101  \n",
      "14    0.078333  ARG233_CA to ARG168_CA  \n",
      "5    -0.076466        ARG233 to VAL165  \n",
      "7     0.073061  MET186_CA to ILE211_CA  \n",
      "3    -0.072389        PHE215 to ASN255  \n",
      "21   -0.072340  TYR194_CA to LEU208_CA  \n",
      "11    0.068995  LYS206_CA to GLY209_CA  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Ser262_Ca  Ser262_Ca    0.196151    262\n",
      "Thr207_Ca  Thr207_Ca    0.196151    207\n",
      "Arg118_Ca  Arg118_Ca    0.192010    118\n",
      "Leu38_Ca    Leu38_Ca    0.174711     38\n",
      "Ala119_Ca  Ala119_Ca   -0.153973    119\n",
      "Pro263_Ca  Pro263_Ca   -0.151188    263\n",
      "Arg200_Ca  Arg200_Ca   -0.151188    200\n",
      "Ile258_Ca  Ile258_Ca   -0.143850    258\n",
      "Ala197_Ca  Ala197_Ca    0.129536    197\n",
      "Ile106_Ca  Ile106_Ca    0.128698    106\n",
      "Asp147_Ca  Asp147_Ca    0.124314    147\n",
      "Ala169_Ca  Ala169_Ca    0.124314    169\n",
      "Ile106        Ile106   -0.121472    106\n",
      "Arg195        Arg195   -0.121472    195\n",
      "Leu205_Ca  Leu205_Ca    0.112779    205\n",
      "Lys198_Ca  Lys198_Ca   -0.108429    198\n",
      "Val193_Ca  Val193_Ca   -0.108429    193\n",
      "Arg261        Arg261   -0.107066    261\n",
      "Ile43          Ile43   -0.107066     43\n",
      "Arg168        Arg168    0.098926    168\n",
      "Asp147        Asp147    0.098926    147\n",
      "Ala152_Ca  Ala152_Ca   -0.097746    152\n",
      "Leu64          Leu64    0.089462     64\n",
      "Phe60          Phe60    0.089462     60\n",
      "Glu196_Ca  Glu196_Ca    0.084919    196\n",
      "Tyr103_Ca  Tyr103_Ca    0.084919    103\n",
      "Asp101        Asp101    0.084041    101\n",
      "Leu208        Leu208    0.084041    208\n",
      "Arg168_Ca  Arg168_Ca    0.078333    168\n",
      "Val165        Val165   -0.076466    165\n",
      "Arg233        Arg233   -0.076466    233\n",
      "Leu208_Ca  Leu208_Ca   -0.075915    208\n",
      "Ile211_Ca  Ile211_Ca    0.073061    211\n",
      "Met186_Ca  Met186_Ca    0.073061    186\n",
      "Asn255        Asn255   -0.072389    255\n",
      "Phe215        Phe215   -0.072389    215\n",
      "Tyr194_Ca  Tyr194_Ca   -0.072340    194\n",
      "Arg233_Ca  Arg233_Ca    0.069529    233\n",
      "Lys206_Ca  Lys206_Ca    0.068995    206\n",
      "Gly209_Ca  Gly209_Ca    0.068995    209\n",
      "Using dark_background\n",
      "Interpreting tIC 3\n",
      "feature_importances_df.shape\n",
      "(19, 7)\n",
      "residue_importances_df.shape\n",
      "(35, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "16  Val193_Ca To Glu196_Ca  Val193_Ca  Glu196_Ca      193      196   \n",
      "8         Arg233 To Val165     Arg233     Val165      233      165   \n",
      "3         Tyr194 To Lys198     Tyr194     Lys198      194      198   \n",
      "4         Asn232 To Val236     Asn232     Val236      232      236   \n",
      "13  Arg192_Ca To Ala197_Ca  Arg192_Ca  Ala197_Ca      192      197   \n",
      "2         Leu191 To Glu196     Leu191     Glu196      191      196   \n",
      "6          Phe164 To Trp80     Phe164      Trp80      164       80   \n",
      "14  Asn232_Ca To Leu235_Ca  Asn232_Ca  Leu235_Ca      232      235   \n",
      "10        Tyr259 To Arg102     Tyr259     Arg102      259      102   \n",
      "17  Ile140_Ca To Phe164_Ca  Ile140_Ca  Phe164_Ca      140      164   \n",
      "5         Phe164 To Tyr170     Phe164     Tyr170      164      170   \n",
      "15  Val214_Ca To Ile258_Ca  Val214_Ca  Ile258_Ca      214      258   \n",
      "9          Ser132 To Thr94     Ser132      Thr94      132       94   \n",
      "7          Trp246 To Trp80     Trp246      Trp80      246       80   \n",
      "0          Val128 To Ser91     Val128      Ser91      128       91   \n",
      "11        Val214 To Ala250     Val214     Ala250      214      250   \n",
      "12        Ser178 To Phe215     Ser178     Phe215      178      215   \n",
      "1          Val128 To Ser45     Val128      Ser45      128       45   \n",
      "18    Leu51_Ca To Ala20_Ca   Leu51_Ca   Ala20_Ca       51       20   \n",
      "\n",
      "    importance                 feature  \n",
      "16    0.257155  VAL193_CA to GLU196_CA  \n",
      "8     0.168118        ARG233 to VAL165  \n",
      "3     0.156343        TYR194 to LYS198  \n",
      "4     0.136903        ASN232 to VAL236  \n",
      "13   -0.134776  ARG192_CA to ALA197_CA  \n",
      "2     0.134676        LEU191 to GLU196  \n",
      "6     0.126414         PHE164 to TRP80  \n",
      "14   -0.118911  ASN232_CA to LEU235_CA  \n",
      "10   -0.117187        TYR259 to ARG102  \n",
      "17    0.108267  ILE140_CA to PHE164_CA  \n",
      "5    -0.107298        PHE164 to TYR170  \n",
      "15   -0.106633  VAL214_CA to ILE258_CA  \n",
      "9     0.100674         SER132 to THR94  \n",
      "7    -0.097189         TRP246 to TRP80  \n",
      "0     0.095869         VAL128 to SER91  \n",
      "11   -0.091547        VAL214 to ALA250  \n",
      "12   -0.075165        SER178 to PHE215  \n",
      "1    -0.074851         VAL128 to SER45  \n",
      "18    0.073991    LEU51_CA to ALA20_CA  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Glu196_Ca  Glu196_Ca    0.257155    196\n",
      "Val193_Ca  Val193_Ca    0.257155    193\n",
      "Arg233        Arg233    0.168118    233\n",
      "Val165        Val165    0.168118    165\n",
      "Lys198        Lys198    0.156343    198\n",
      "Tyr194        Tyr194    0.156343    194\n",
      "Asn232        Asn232    0.136903    232\n",
      "Val236        Val236    0.136903    236\n",
      "Ala197_Ca  Ala197_Ca   -0.134776    197\n",
      "Arg192_Ca  Arg192_Ca   -0.134776    192\n",
      "Glu196        Glu196    0.134676    196\n",
      "Leu191        Leu191    0.134676    191\n",
      "Leu235_Ca  Leu235_Ca   -0.118911    235\n",
      "Asn232_Ca  Asn232_Ca   -0.118911    232\n",
      "Arg102        Arg102   -0.117187    102\n",
      "Tyr259        Tyr259   -0.117187    259\n",
      "Trp80          Trp80    0.115234     80\n",
      "Phe164        Phe164    0.114728    164\n",
      "Ile140_Ca  Ile140_Ca    0.108267    140\n",
      "Phe164_Ca  Phe164_Ca    0.108267    164\n",
      "Tyr170        Tyr170   -0.107298    170\n",
      "Val214_Ca  Val214_Ca   -0.106633    214\n",
      "Ile258_Ca  Ile258_Ca   -0.106633    258\n",
      "Thr94          Thr94    0.100674     94\n",
      "Ser132        Ser132    0.100674    132\n",
      "Trp246        Trp246   -0.097189    246\n",
      "Ser91          Ser91    0.095869     91\n",
      "Val214        Val214   -0.091547    214\n",
      "Ala250        Ala250   -0.091547    250\n",
      "Val128        Val128    0.087333    128\n",
      "Ser178        Ser178   -0.075165    178\n",
      "Phe215        Phe215   -0.075165    215\n",
      "Ser45          Ser45   -0.074851     45\n",
      "Leu51_Ca    Leu51_Ca    0.073991     51\n",
      "Ala20_Ca    Ala20_Ca    0.073991     20\n",
      "Using dark_background\n",
      "Interpreting tIC 4\n",
      "feature_importances_df.shape\n",
      "(23, 7)\n",
      "residue_importances_df.shape\n",
      "(41, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "22  Val214_Ca To Tyr259_Ca  Val214_Ca  Tyr259_Ca      214      259   \n",
      "16  Val214_Ca To Ile258_Ca  Val214_Ca  Ile258_Ca      214      258   \n",
      "19  Ile140_Ca To Phe164_Ca  Ile140_Ca  Phe164_Ca      140      164   \n",
      "9         Trp145 To Asp163     Trp145     Asp163      145      163   \n",
      "11        Lys206 To Arg261     Lys206     Arg261      206      261   \n",
      "5          Tyr259 To Ala47     Tyr259      Ala47      259       47   \n",
      "21  Phe164_Ca To Asn245_Ca  Phe164_Ca  Asn245_Ca      164      245   \n",
      "1          Met141 To Phe75     Met141      Phe75      141       75   \n",
      "6         Asn232 To Val236     Asn232     Val236      232      236   \n",
      "7         Phe164 To Tyr170     Phe164     Tyr170      164      170   \n",
      "18   Phe215_Ca To Leu46_Ca  Phe215_Ca   Leu46_Ca      215       46   \n",
      "17    Ile98_Ca To Leu46_Ca   Ile98_Ca   Leu46_Ca       98       46   \n",
      "0            Gly6 To Leu10       Gly6      Leu10        6       10   \n",
      "2          Met212 To Ile98     Met212      Ile98      212       98   \n",
      "3          Phe265 To Ile29     Phe265      Ile29      265       29   \n",
      "13  Arg192_Ca To Ala197_Ca  Arg192_Ca  Ala197_Ca      192      197   \n",
      "8          Tyr259 To Phe42     Tyr259      Phe42      259       42   \n",
      "10        Arg233 To Thr166     Arg233     Thr166      233      166   \n",
      "20    Ala27_Ca To Gly30_Ca   Ala27_Ca   Gly30_Ca       27       30   \n",
      "14  Val230_Ca To Arg233_Ca  Val230_Ca  Arg233_Ca      230      233   \n",
      "4          Trp246 To Val14     Trp246      Val14      246       14   \n",
      "12        Val193 To Leu208     Val193     Leu208      193      208   \n",
      "15  Arg233_Ca To Val236_Ca  Arg233_Ca  Val236_Ca      233      236   \n",
      "\n",
      "    importance                 feature  \n",
      "22   -0.474578  VAL214_CA to TYR259_CA  \n",
      "16    0.315415  VAL214_CA to ILE258_CA  \n",
      "19   -0.191896  ILE140_CA to PHE164_CA  \n",
      "9     0.164193        TRP145 to ASP163  \n",
      "11   -0.147850        LYS206 to ARG261  \n",
      "5     0.130938         TYR259 to ALA47  \n",
      "21    0.121008  PHE164_CA to ASN245_CA  \n",
      "1     0.113602         MET141 to PHE75  \n",
      "6    -0.109280        ASN232 to VAL236  \n",
      "7     0.102632        PHE164 to TYR170  \n",
      "18    0.101606   PHE215_CA to LEU46_CA  \n",
      "17   -0.093378    ILE98_CA to LEU46_CA  \n",
      "0     0.091240           GLY6 to LEU10  \n",
      "2     0.082569         MET212 to ILE98  \n",
      "3    -0.081823         PHE265 to ILE29  \n",
      "13    0.076606  ARG192_CA to ALA197_CA  \n",
      "8     0.075332         TYR259 to PHE42  \n",
      "10    0.075112        ARG233 to THR166  \n",
      "20   -0.071305    ALA27_CA to GLY30_CA  \n",
      "14   -0.070133  VAL230_CA to ARG233_CA  \n",
      "4    -0.068630         TRP246 to VAL14  \n",
      "12   -0.064642        VAL193 to LEU208  \n",
      "15    0.060267  ARG233_CA to VAL236_CA  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Tyr259_Ca  Tyr259_Ca   -0.474578    259\n",
      "Ile258_Ca  Ile258_Ca    0.315415    258\n",
      "Val214_Ca  Val214_Ca    0.275915    214\n",
      "Ile140_Ca  Ile140_Ca   -0.191896    140\n",
      "Asp163        Asp163    0.164193    163\n",
      "Trp145        Trp145    0.164193    145\n",
      "Arg261        Arg261   -0.147850    261\n",
      "Lys206        Lys206   -0.147850    206\n",
      "Ala47          Ala47    0.130938     47\n",
      "Tyr259        Tyr259    0.128158    259\n",
      "Asn245_Ca  Asn245_Ca    0.121008    245\n",
      "Met141        Met141    0.113602    141\n",
      "Phe75          Phe75    0.113602     75\n",
      "Asn232        Asn232   -0.109280    232\n",
      "Val236        Val236   -0.109280    236\n",
      "Phe164_Ca  Phe164_Ca    0.105363    164\n",
      "Phe164        Phe164    0.102632    164\n",
      "Tyr170        Tyr170    0.102632    170\n",
      "Phe215_Ca  Phe215_Ca    0.101606    215\n",
      "Ile98_Ca    Ile98_Ca   -0.093378     98\n",
      "Leu46_Ca    Leu46_Ca    0.091857     46\n",
      "Leu10          Leu10    0.091240     10\n",
      "Gly6            Gly6    0.091240      6\n",
      "Met212        Met212    0.082569    212\n",
      "Ile98          Ile98    0.082569     98\n",
      "Phe265        Phe265   -0.081823    265\n",
      "Ile29          Ile29   -0.081823     29\n",
      "Arg192_Ca  Arg192_Ca    0.076606    192\n",
      "Ala197_Ca  Ala197_Ca    0.076606    197\n",
      "Phe42          Phe42    0.075332     42\n",
      "Arg233        Arg233    0.075112    233\n",
      "Thr166        Thr166    0.075112    166\n",
      "Ala27_Ca    Ala27_Ca   -0.071305     27\n",
      "Gly30_Ca    Gly30_Ca   -0.071305     30\n",
      "Val230_Ca  Val230_Ca   -0.070133    230\n",
      "Val14          Val14   -0.068630     14\n",
      "Trp246        Trp246   -0.068630    246\n",
      "Leu208        Leu208   -0.064642    208\n",
      "Val193        Val193   -0.064642    193\n",
      "Val236_Ca  Val236_Ca    0.060267    236\n",
      "Arg233_Ca  Arg233_Ca    0.053747    233\n",
      "Using dark_background\n",
      "Interpreting tIC 5\n",
      "feature_importances_df.shape\n",
      "(26, 7)\n",
      "residue_importances_df.shape\n",
      "(45, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "23    Trp239_Ca To Trp3_Ca  Trp239_Ca    Trp3_Ca      239        3   \n",
      "10        Phe215 To Tyr259     Phe215     Tyr259      215      259   \n",
      "0         Trp144 To Ala169     Trp144     Ala169      144      169   \n",
      "17  Thr207_Ca To Ile258_Ca  Thr207_Ca  Ile258_Ca      207      258   \n",
      "1          Met141 To Leu79     Met141      Leu79      141       79   \n",
      "16  Val230_Ca To Arg233_Ca  Val230_Ca  Arg233_Ca      230      233   \n",
      "9          Trp239 To Val65     Trp239      Val65      239       65   \n",
      "5         Arg200 To Pro263     Arg200     Pro263      200      263   \n",
      "12   Ser178_Ca To Val85_Ca  Ser178_Ca   Val85_Ca      178       85   \n",
      "18  Ile140_Ca To Trp145_Ca  Ile140_Ca  Trp145_Ca      140      145   \n",
      "21   Tyr180_Ca To Ile92_Ca  Tyr180_Ca   Ile92_Ca      180       92   \n",
      "22  Phe231_Ca To Arg168_Ca  Phe231_Ca  Arg168_Ca      231      168   \n",
      "13  Val135_Ca To Leu138_Ca  Val135_Ca  Leu138_Ca      135      138   \n",
      "8          Asp101 To Asn40     Asp101      Asn40      101       40   \n",
      "20  Arg233_Ca To Asn167_Ca  Arg233_Ca  Asn167_Ca      233      167   \n",
      "25  Ala197_Ca To Thr107_Ca  Ala197_Ca  Thr107_Ca      197      107   \n",
      "2         Met141 To Trp145     Met141     Trp145      141      145   \n",
      "24  Phe222_Ca To Phe164_Ca  Phe222_Ca  Phe164_Ca      222      164   \n",
      "15  Val230_Ca To Thr166_Ca  Val230_Ca  Thr166_Ca      230      166   \n",
      "19  Val193_Ca To Lys198_Ca  Val193_Ca  Lys198_Ca      193      198   \n",
      "6         Met141 To Arg146     Met141     Arg146      141      146   \n",
      "14  Val135_Ca To Ile140_Ca  Val135_Ca  Ile140_Ca      135      140   \n",
      "4          Trp246 To Trp80     Trp246      Trp80      246       80   \n",
      "7         Arg120 To Tyr112     Arg120     Tyr112      120      112   \n",
      "3          Phe164 To Trp80     Phe164      Trp80      164       80   \n",
      "11  Ala121_Ca To Arg118_Ca  Ala121_Ca  Arg118_Ca      121      118   \n",
      "\n",
      "    importance                 feature  \n",
      "23    0.402394    TRP239_CA to TRP3_CA  \n",
      "10   -0.206398        PHE215 to TYR259  \n",
      "0     0.198240        TRP144 to ALA169  \n",
      "17   -0.161906  THR207_CA to ILE258_CA  \n",
      "1    -0.155979         MET141 to LEU79  \n",
      "16    0.146713  VAL230_CA to ARG233_CA  \n",
      "9    -0.138441         TRP239 to VAL65  \n",
      "5     0.136176        ARG200 to PRO263  \n",
      "12   -0.124653   SER178_CA to VAL85_CA  \n",
      "18    0.124257  ILE140_CA to TRP145_CA  \n",
      "21    0.098100   TYR180_CA to ILE92_CA  \n",
      "22    0.092938  PHE231_CA to ARG168_CA  \n",
      "13    0.092055  VAL135_CA to LEU138_CA  \n",
      "8    -0.091600         ASP101 to ASN40  \n",
      "20   -0.090098  ARG233_CA to ASN167_CA  \n",
      "25   -0.088099  ALA197_CA to THR107_CA  \n",
      "2    -0.087962        MET141 to TRP145  \n",
      "24   -0.086676  PHE222_CA to PHE164_CA  \n",
      "15    0.085429  VAL230_CA to THR166_CA  \n",
      "19    0.081564  VAL193_CA to LYS198_CA  \n",
      "6    -0.068907        MET141 to ARG146  \n",
      "14   -0.068591  VAL135_CA to ILE140_CA  \n",
      "4     0.065543         TRP246 to TRP80  \n",
      "7     0.059687        ARG120 to TYR112  \n",
      "3    -0.048118         PHE164 to TRP80  \n",
      "11   -0.046677  ALA121_CA to ARG118_CA  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Trp3_Ca      Trp3_Ca    0.402394      3\n",
      "Trp239_Ca  Trp239_Ca    0.402394    239\n",
      "Phe215        Phe215   -0.206398    215\n",
      "Tyr259        Tyr259   -0.206398    259\n",
      "Trp144        Trp144    0.198240    144\n",
      "Ala169        Ala169    0.198240    169\n",
      "Ile258_Ca  Ile258_Ca   -0.161906    258\n",
      "Thr207_Ca  Thr207_Ca   -0.161906    207\n",
      "Leu79          Leu79   -0.155979     79\n",
      "Val230_Ca  Val230_Ca    0.143648    230\n",
      "Trp239        Trp239   -0.138441    239\n",
      "Val65          Val65   -0.138441     65\n",
      "Arg200        Arg200    0.136176    200\n",
      "Pro263        Pro263    0.136176    263\n",
      "Arg233_Ca  Arg233_Ca    0.134872    233\n",
      "Ser178_Ca  Ser178_Ca   -0.124653    178\n",
      "Val85_Ca    Val85_Ca   -0.124653     85\n",
      "Trp145_Ca  Trp145_Ca    0.124257    145\n",
      "Ile140_Ca  Ile140_Ca    0.114615    140\n",
      "Ile92_Ca    Ile92_Ca    0.098100     92\n",
      "Tyr180_Ca  Tyr180_Ca    0.098100    180\n",
      "Arg168_Ca  Arg168_Ca    0.092938    168\n",
      "Phe231_Ca  Phe231_Ca    0.092938    231\n",
      "Leu138_Ca  Leu138_Ca    0.092055    138\n",
      "Asp101        Asp101   -0.091600    101\n",
      "Asn40          Asn40   -0.091600     40\n",
      "Asn167_Ca  Asn167_Ca   -0.090098    167\n",
      "Thr107_Ca  Thr107_Ca   -0.088099    107\n",
      "Ala197_Ca  Ala197_Ca   -0.088099    197\n",
      "Trp145        Trp145   -0.087962    145\n",
      "Phe164_Ca  Phe164_Ca   -0.086676    164\n",
      "Phe222_Ca  Phe222_Ca   -0.086676    222\n",
      "Thr166_Ca  Thr166_Ca    0.085429    166\n",
      "Val135_Ca  Val135_Ca    0.084022    135\n",
      "Val193_Ca  Val193_Ca    0.081564    193\n",
      "Lys198_Ca  Lys198_Ca    0.081564    198\n",
      "Met141        Met141   -0.070812    141\n",
      "Arg146        Arg146   -0.068907    146\n",
      "Trp246        Trp246    0.065543    246\n",
      "Trp80          Trp80    0.059860     80\n",
      "Arg120        Arg120    0.059687    120\n",
      "Tyr112        Tyr112    0.059687    112\n",
      "Phe164        Phe164   -0.048118    164\n",
      "Ala121_Ca  Ala121_Ca   -0.046677    121\n",
      "Arg118_Ca  Arg118_Ca   -0.046677    118\n",
      "Using dark_background\n",
      "Interpreting tIC 6\n",
      "feature_importances_df.shape\n",
      "(35, 7)\n",
      "residue_importances_df.shape\n",
      "(59, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "7          Phe164 To Trp80     Phe164      Trp80      164       80   \n",
      "23  Val214_Ca To Ile258_Ca  Val214_Ca  Ile258_Ca      214      258   \n",
      "33  Val214_Ca To Tyr259_Ca  Val214_Ca  Tyr259_Ca      214      259   \n",
      "5         Trp145 To Asp163     Trp145     Asp163      145      163   \n",
      "24  Trp145_Ca To Phe164_Ca  Trp145_Ca  Phe164_Ca      145      164   \n",
      "9         Ile140 To Phe164     Ile140     Phe164      140      164   \n",
      "8          Asp163 To Trp80     Asp163      Trp80      163       80   \n",
      "27  Arg146_Ca To Thr166_Ca  Arg146_Ca  Thr166_Ca      146      166   \n",
      "11          Leu56 To Trp72      Leu56      Trp72       56       72   \n",
      "31   Ala250_Ca To Val14_Ca  Ala250_Ca   Val14_Ca      250       14   \n",
      "6         Val193 To Glu196     Val193     Glu196      193      196   \n",
      "22   Trp246_Ca To Gly61_Ca  Trp246_Ca   Gly61_Ca      246       61   \n",
      "3         Asn232 To Val236     Asn232     Val236      232      236   \n",
      "2          Phe265 To Ile29     Phe265      Ile29      265       29   \n",
      "10        Phe188 To Glu196     Phe188     Glu196      188      196   \n",
      "13  Arg195_Ca To Lys198_Ca  Arg195_Ca  Lys198_Ca      195      198   \n",
      "18  Trp144_Ca To Thr166_Ca  Trp144_Ca  Thr166_Ca      144      166   \n",
      "4          Phe137 To Leu79     Phe137      Leu79      137       79   \n",
      "26   Ser178_Ca To Thr89_Ca  Ser178_Ca   Thr89_Ca      178       89   \n",
      "25  Asn255_Ca To Cys260_Ca  Asn255_Ca  Cys260_Ca      255      260   \n",
      "29  Ser136_Ca To Trp145_Ca  Ser136_Ca  Trp145_Ca      136      145   \n",
      "32    Leu56_Ca To Leu79_Ca   Leu56_Ca   Leu79_Ca       56       79   \n",
      "34  Ala197_Ca To Thr107_Ca  Ala197_Ca  Thr107_Ca      197      107   \n",
      "16   Arg118_Ca To Thr37_Ca  Arg118_Ca   Thr37_Ca      118       37   \n",
      "21  Asn232_Ca To Leu235_Ca  Asn232_Ca  Leu235_Ca      232      235   \n",
      "15  Ala121_Ca To Arg118_Ca  Ala121_Ca  Arg118_Ca      121      118   \n",
      "14  Thr166_Ca To Ala169_Ca  Thr166_Ca  Ala169_Ca      166      169   \n",
      "17    Phe60_Ca To Thr63_Ca   Phe60_Ca   Thr63_Ca       60       63   \n",
      "20    Trp72_Ca To Cys77_Ca   Trp72_Ca   Cys77_Ca       72       77   \n",
      "12  Cys155_Ca To Phe164_Ca  Cys155_Ca  Phe164_Ca      155      164   \n",
      "0            Gly6 To Leu10       Gly6      Leu10        6       10   \n",
      "19   Arg102_Ca To Thr39_Ca  Arg102_Ca   Thr39_Ca      102       39   \n",
      "1           Trp72 To Phe75      Trp72      Phe75       72       75   \n",
      "30  Leu115_Ca To Leu104_Ca  Leu115_Ca  Leu104_Ca      115      104   \n",
      "28  Asp147_Ca To Ala152_Ca  Asp147_Ca  Ala152_Ca      147      152   \n",
      "\n",
      "    importance                 feature  \n",
      "7    -0.260143         PHE164 to TRP80  \n",
      "23   -0.245627  VAL214_CA to ILE258_CA  \n",
      "33    0.211893  VAL214_CA to TYR259_CA  \n",
      "5     0.194903        TRP145 to ASP163  \n",
      "24   -0.166317  TRP145_CA to PHE164_CA  \n",
      "9     0.156598        ILE140 to PHE164  \n",
      "8     0.156347         ASP163 to TRP80  \n",
      "27    0.152381  ARG146_CA to THR166_CA  \n",
      "11    0.149572          LEU56 to TRP72  \n",
      "31    0.136694   ALA250_CA to VAL14_CA  \n",
      "6    -0.136252        VAL193 to GLU196  \n",
      "22   -0.134326   TRP246_CA to GLY61_CA  \n",
      "3     0.133670        ASN232 to VAL236  \n",
      "2    -0.131502         PHE265 to ILE29  \n",
      "10   -0.122539        PHE188 to GLU196  \n",
      "13   -0.121131  ARG195_CA to LYS198_CA  \n",
      "18   -0.120567  TRP144_CA to THR166_CA  \n",
      "4     0.115700         PHE137 to LEU79  \n",
      "26    0.113777   SER178_CA to THR89_CA  \n",
      "25    0.107533  ASN255_CA to CYS260_CA  \n",
      "29    0.107500  SER136_CA to TRP145_CA  \n",
      "32    0.091860    LEU56_CA to LEU79_CA  \n",
      "34   -0.086000  ALA197_CA to THR107_CA  \n",
      "16    0.085137   ARG118_CA to THR37_CA  \n",
      "21   -0.084133  ASN232_CA to LEU235_CA  \n",
      "15    0.078166  ALA121_CA to ARG118_CA  \n",
      "14    0.072721  THR166_CA to ALA169_CA  \n",
      "17    0.070694    PHE60_CA to THR63_CA  \n",
      "20   -0.062528    TRP72_CA to CYS77_CA  \n",
      "12    0.059825  CYS155_CA to PHE164_CA  \n",
      "0    -0.058937           GLY6 to LEU10  \n",
      "19   -0.057358   ARG102_CA to THR39_CA  \n",
      "1     0.055132          TRP72 to PHE75  \n",
      "30   -0.051211  LEU115_CA to LEU104_CA  \n",
      "28   -0.047088  ASP147_CA to ALA152_CA  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Ile258_Ca  Ile258_Ca   -0.245627    258\n",
      "Tyr259_Ca  Tyr259_Ca    0.211893    259\n",
      "Trp145        Trp145    0.194903    145\n",
      "Asp163        Asp163    0.192975    163\n",
      "Val214_Ca  Val214_Ca    0.189017    214\n",
      "Ile140        Ile140    0.156598    140\n",
      "Arg146_Ca  Arg146_Ca    0.152381    146\n",
      "Leu56          Leu56    0.149572     56\n",
      "Trp72          Trp72    0.144850     72\n",
      "Thr166_Ca  Thr166_Ca    0.144415    166\n",
      "Ala250_Ca  Ala250_Ca    0.136694    250\n",
      "Val14_Ca    Val14_Ca    0.136694     14\n",
      "Val193        Val193   -0.136252    193\n",
      "Phe164        Phe164    0.135761    164\n",
      "Trp80          Trp80    0.135522     80\n",
      "Gly61_Ca    Gly61_Ca   -0.134326     61\n",
      "Trp246_Ca  Trp246_Ca   -0.134326    246\n",
      "Asn232        Asn232    0.133670    232\n",
      "Val236        Val236    0.133670    236\n",
      "Ile29          Ile29   -0.131502     29\n",
      "Phe265        Phe265   -0.131502    265\n",
      "Glu196        Glu196   -0.123224    196\n",
      "Phe188        Phe188   -0.122539    188\n",
      "Arg195_Ca  Arg195_Ca   -0.121131    195\n",
      "Lys198_Ca  Lys198_Ca   -0.121131    198\n",
      "Trp144_Ca  Trp144_Ca   -0.120567    144\n",
      "Phe137        Phe137    0.115700    137\n",
      "Leu79          Leu79    0.115700     79\n",
      "Thr89_Ca    Thr89_Ca    0.113777     89\n",
      "Ser178_Ca  Ser178_Ca    0.113777    178\n",
      "Asn255_Ca  Asn255_Ca    0.107533    255\n",
      "Cys260_Ca  Cys260_Ca    0.107533    260\n",
      "Ser136_Ca  Ser136_Ca    0.107500    136\n",
      "Trp145_Ca  Trp145_Ca    0.093810    145\n",
      "Leu56_Ca    Leu56_Ca    0.091860     56\n",
      "Leu79_Ca    Leu79_Ca    0.091860     79\n",
      "Thr107_Ca  Thr107_Ca   -0.086000    107\n",
      "Ala197_Ca  Ala197_Ca   -0.086000    197\n",
      "Thr37_Ca    Thr37_Ca    0.085137     37\n",
      "Arg118_Ca  Arg118_Ca    0.084788    118\n",
      "Asn232_Ca  Asn232_Ca   -0.084133    232\n",
      "Leu235_Ca  Leu235_Ca   -0.084133    235\n",
      "Ala121_Ca  Ala121_Ca    0.078166    121\n",
      "Ala169_Ca  Ala169_Ca    0.072721    169\n",
      "Thr63_Ca    Thr63_Ca    0.070694     63\n",
      "Phe60_Ca    Phe60_Ca    0.070694     60\n",
      "Trp72_Ca    Trp72_Ca   -0.062528     72\n",
      "Cys77_Ca    Cys77_Ca   -0.062528     77\n",
      "Cys155_Ca  Cys155_Ca    0.059825    155\n",
      "Leu10          Leu10   -0.058937     10\n",
      "Gly6            Gly6   -0.058937      6\n",
      "Arg102_Ca  Arg102_Ca   -0.057358    102\n",
      "Thr39_Ca    Thr39_Ca   -0.057358     39\n",
      "Phe75          Phe75    0.055132     75\n",
      "Leu115_Ca  Leu115_Ca   -0.051211    115\n",
      "Leu104_Ca  Leu104_Ca   -0.051211    104\n",
      "Phe164_Ca  Phe164_Ca    0.048518    164\n",
      "Asp147_Ca  Asp147_Ca   -0.047088    147\n",
      "Ala152_Ca  Ala152_Ca   -0.047088    152\n",
      "Using dark_background\n",
      "Interpreting tIC 7\n",
      "feature_importances_df.shape\n",
      "(25, 7)\n",
      "residue_importances_df.shape\n",
      "(46, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "18  Phe215_Ca To Leu220_Ca  Phe215_Ca  Leu220_Ca      215      220   \n",
      "10         Trp145 To Thr81     Trp145      Thr81      145       81   \n",
      "5           Phe60 To Leu76      Phe60      Leu76       60       76   \n",
      "17        Phe231 To Arg168     Phe231     Arg168      231      168   \n",
      "24  Asp147_Ca To Ala169_Ca  Asp147_Ca  Ala169_Ca      147      169   \n",
      "8          Phe215 To Cys87     Phe215      Cys87      215       87   \n",
      "16         Trp246 To Val15     Trp246      Val15      246       15   \n",
      "14          Pro59 To Met11      Pro59      Met11       59       11   \n",
      "9          Met141 To Ser82     Met141      Ser82      141       82   \n",
      "15        Cys260 To Arg102     Cys260     Arg102      260      102   \n",
      "3          Trp145 To Glu78     Trp145      Glu78      145       78   \n",
      "7          Tyr259 To Ile43     Tyr259      Ile43      259       43   \n",
      "21  Arg233_Ca To Arg168_Ca  Arg233_Ca  Arg168_Ca      233      168   \n",
      "11         Phe164 To Trp80     Phe164      Trp80      164       80   \n",
      "4          Phe164 To Val85     Phe164      Val85      164       85   \n",
      "23  Asn226_Ca To Phe164_Ca  Asn226_Ca  Phe164_Ca      226      164   \n",
      "22   Asn255_Ca To Val25_Ca  Asn255_Ca   Val25_Ca      255       25   \n",
      "20  Pro256_Ca To Phe269_Ca  Pro256_Ca  Phe269_Ca      256      269   \n",
      "12         Cys260 To Leu24     Cys260      Leu24      260       24   \n",
      "0         Arg195 To Lys198     Arg195     Lys198      195      198   \n",
      "1         Val230 To Ala169     Val230     Ala169      230      169   \n",
      "6          Leu183 To Ile92     Leu183      Ile92      183       92   \n",
      "19  Ile187_Ca To Thr216_Ca  Ile187_Ca  Thr216_Ca      187      216   \n",
      "2           Thr63 To Met11      Thr63      Met11       63       11   \n",
      "13        Arg120 To Ser114     Arg120     Ser114      120      114   \n",
      "\n",
      "    importance                 feature  \n",
      "18    0.207851  PHE215_CA to LEU220_CA  \n",
      "10   -0.200912         TRP145 to THR81  \n",
      "5    -0.172325          PHE60 to LEU76  \n",
      "17    0.169484        PHE231 to ARG168  \n",
      "24    0.154442  ASP147_CA to ALA169_CA  \n",
      "8    -0.153394         PHE215 to CYS87  \n",
      "16    0.148823         TRP246 to VAL15  \n",
      "14    0.133750          PRO59 to MET11  \n",
      "9     0.133355         MET141 to SER82  \n",
      "15    0.123814        CYS260 to ARG102  \n",
      "3     0.121569         TRP145 to GLU78  \n",
      "7     0.104073         TYR259 to ILE43  \n",
      "21   -0.102581  ARG233_CA to ARG168_CA  \n",
      "11   -0.101270         PHE164 to TRP80  \n",
      "4     0.097519         PHE164 to VAL85  \n",
      "23    0.096534  ASN226_CA to PHE164_CA  \n",
      "22    0.096070   ASN255_CA to VAL25_CA  \n",
      "20   -0.090418  PRO256_CA to PHE269_CA  \n",
      "12    0.084753         CYS260 to LEU24  \n",
      "0    -0.082835        ARG195 to LYS198  \n",
      "1    -0.070316        VAL230 to ALA169  \n",
      "6    -0.069122         LEU183 to ILE92  \n",
      "19    0.066571  ILE187_CA to THR216_CA  \n",
      "2     0.066061          THR63 to MET11  \n",
      "13   -0.060143        ARG120 to SER114  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Phe215_Ca  Phe215_Ca    0.207851    215\n",
      "Leu220_Ca  Leu220_Ca    0.207851    220\n",
      "Thr81          Thr81   -0.200912     81\n",
      "Phe60          Phe60   -0.172325     60\n",
      "Leu76          Leu76   -0.172325     76\n",
      "Phe231        Phe231    0.169484    231\n",
      "Arg168        Arg168    0.169484    168\n",
      "Asp147_Ca  Asp147_Ca    0.154442    147\n",
      "Ala169_Ca  Ala169_Ca    0.154442    169\n",
      "Cys87          Cys87   -0.153394     87\n",
      "Phe215        Phe215   -0.153394    215\n",
      "Val15          Val15    0.148823     15\n",
      "Trp246        Trp246    0.148823    246\n",
      "Pro59          Pro59    0.133750     59\n",
      "Ser82          Ser82    0.133355     82\n",
      "Met141        Met141    0.133355    141\n",
      "Met11          Met11    0.130365     11\n",
      "Arg102        Arg102    0.123814    102\n",
      "Cys260        Cys260    0.121861    260\n",
      "Glu78          Glu78    0.121569     78\n",
      "Trp145        Trp145    0.105445    145\n",
      "Ile43          Ile43    0.104073     43\n",
      "Tyr259        Tyr259    0.104073    259\n",
      "Arg233_Ca  Arg233_Ca   -0.102581    233\n",
      "Arg168_Ca  Arg168_Ca   -0.102581    168\n",
      "Trp80          Trp80   -0.101270     80\n",
      "Val85          Val85    0.097519     85\n",
      "Asn226_Ca  Asn226_Ca    0.096534    226\n",
      "Phe164_Ca  Phe164_Ca    0.096534    164\n",
      "Val25_Ca    Val25_Ca    0.096070     25\n",
      "Asn255_Ca  Asn255_Ca    0.096070    255\n",
      "Phe269_Ca  Phe269_Ca   -0.090418    269\n",
      "Pro256_Ca  Pro256_Ca   -0.090418    256\n",
      "Phe164        Phe164    0.087579    164\n",
      "Leu24          Leu24    0.084753     24\n",
      "Lys198        Lys198   -0.082835    198\n",
      "Arg195        Arg195   -0.082835    195\n",
      "Ala169        Ala169   -0.070316    169\n",
      "Val230        Val230   -0.070316    230\n",
      "Ile92          Ile92   -0.069122     92\n",
      "Leu183        Leu183   -0.069122    183\n",
      "Thr216_Ca  Thr216_Ca    0.066571    216\n",
      "Ile187_Ca  Ile187_Ca    0.066571    187\n",
      "Thr63          Thr63    0.066061     63\n",
      "Ser114        Ser114   -0.060143    114\n",
      "Arg120        Arg120   -0.060143    120\n",
      "Using dark_background\n",
      "Interpreting tIC 8\n",
      "feature_importances_df.shape\n",
      "(35, 7)\n",
      "residue_importances_df.shape\n",
      "(65, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "20   Met142_Ca To Glu78_Ca  Met142_Ca   Glu78_Ca      142       78   \n",
      "34    Trp239_Ca To Trp3_Ca  Trp239_Ca    Trp3_Ca      239        3   \n",
      "28  Val193_Ca To Ala197_Ca  Val193_Ca  Ala197_Ca      193      197   \n",
      "19  Arg192_Ca To Ala197_Ca  Arg192_Ca  Ala197_Ca      192      197   \n",
      "15        Leu205 To Tyr103     Leu205     Tyr103      205      103   \n",
      "9          Asp101 To Thr39     Asp101      Thr39      101       39   \n",
      "21   Cys162_Ca To Leu64_Ca  Cys162_Ca   Leu64_Ca      162       64   \n",
      "24   Trp145_Ca To Cys77_Ca  Trp145_Ca   Cys77_Ca      145       77   \n",
      "16        Arg120 To Tyr112     Arg120     Tyr112      120      112   \n",
      "6             Gln2 To Gly6       Gln2       Gly6        2        6   \n",
      "1         Pro109 To Gln113     Pro109     Gln113      109      113   \n",
      "18         Asp101 To Asn40     Asp101      Asn40      101       40   \n",
      "11        Glu196 To His202     Glu196     His202      196      202   \n",
      "3         Lys198 To Ile106     Lys198     Ile106      198      106   \n",
      "22   Arg102_Ca To Thr39_Ca  Arg102_Ca   Thr39_Ca      102       39   \n",
      "27   Asp101_Ca To Phe42_Ca  Asp101_Ca   Phe42_Ca      101       42   \n",
      "29  Arg200_Ca To Pro263_Ca  Arg200_Ca  Pro263_Ca      200      263   \n",
      "32  Arg120_Ca To Tyr112_Ca  Arg120_Ca  Tyr112_Ca      120      112   \n",
      "26  Cys218_Ca To Met254_Ca  Cys218_Ca  Met254_Ca      218      254   \n",
      "7         Val230 To Ile172     Val230     Ile172      230      172   \n",
      "31  Phe179_Ca To Phe215_Ca  Phe179_Ca  Phe215_Ca      179      215   \n",
      "30   Phe164_Ca To Thr81_Ca  Phe164_Ca   Thr81_Ca      164       81   \n",
      "0          Tyr112 To Thr39     Tyr112      Thr39      112       39   \n",
      "12        Met141 To Arg146     Met141     Arg146      141      146   \n",
      "5         Val135 To Phe137     Val135     Phe137      135      137   \n",
      "13        Phe222 To Phe241     Phe222     Phe241      222      241   \n",
      "4         Ile185 To Ile100     Ile185     Ile100      185      100   \n",
      "33  Ala190_Ca To Leu208_Ca  Ala190_Ca  Leu208_Ca      190      208   \n",
      "2          Trp246 To Val14     Trp246      Val14      246       14   \n",
      "17        Ser108 To Leu115     Ser108     Leu115      108      115   \n",
      "10           Arg67 To Trp3      Arg67       Trp3       67        3   \n",
      "14        Arg233 To Asp147     Arg233     Asp147      233      147   \n",
      "8          Trp246 To Gly61     Trp246      Gly61      246       61   \n",
      "23  Gly248_Ca To Asn251_Ca  Gly248_Ca  Asn251_Ca      248      251   \n",
      "25  Val135_Ca To Ile140_Ca  Val135_Ca  Ile140_Ca      135      140   \n",
      "\n",
      "    importance                 feature  \n",
      "20   -0.336529   MET142_CA to GLU78_CA  \n",
      "34   -0.243783    TRP239_CA to TRP3_CA  \n",
      "28   -0.211870  VAL193_CA to ALA197_CA  \n",
      "19    0.169093  ARG192_CA to ALA197_CA  \n",
      "15    0.165052        LEU205 to TYR103  \n",
      "9     0.148647         ASP101 to THR39  \n",
      "21    0.139895   CYS162_CA to LEU64_CA  \n",
      "24    0.127956   TRP145_CA to CYS77_CA  \n",
      "16   -0.122396        ARG120 to TYR112  \n",
      "6     0.121710            GLN2 to GLY6  \n",
      "1     0.119666        PRO109 to GLN113  \n",
      "18    0.115631         ASP101 to ASN40  \n",
      "11    0.112140        GLU196 to HIS202  \n",
      "3     0.108577        LYS198 to ILE106  \n",
      "22   -0.103057   ARG102_CA to THR39_CA  \n",
      "27    0.102821   ASP101_CA to PHE42_CA  \n",
      "29    0.101271  ARG200_CA to PRO263_CA  \n",
      "32    0.098505  ARG120_CA to TYR112_CA  \n",
      "26   -0.097806  CYS218_CA to MET254_CA  \n",
      "7    -0.089085        VAL230 to ILE172  \n",
      "31   -0.080062  PHE179_CA to PHE215_CA  \n",
      "30    0.080004   PHE164_CA to THR81_CA  \n",
      "0    -0.076452         TYR112 to THR39  \n",
      "12   -0.075495        MET141 to ARG146  \n",
      "5     0.073739        VAL135 to PHE137  \n",
      "13    0.072686        PHE222 to PHE241  \n",
      "4     0.070462        ILE185 to ILE100  \n",
      "33   -0.070120  ALA190_CA to LEU208_CA  \n",
      "2     0.069799         TRP246 to VAL14  \n",
      "17   -0.067535        SER108 to LEU115  \n",
      "10    0.066994           ARG67 to TRP3  \n",
      "14    0.060582        ARG233 to ASP147  \n",
      "8    -0.060461         TRP246 to GLY61  \n",
      "23    0.053966  GLY248_CA to ASN251_CA  \n",
      "25   -0.051281  VAL135_CA to ILE140_CA  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Met142_Ca  Met142_Ca   -0.336529    142\n",
      "Glu78_Ca    Glu78_Ca   -0.336529     78\n",
      "Trp3_Ca      Trp3_Ca   -0.243783      3\n",
      "Trp239_Ca  Trp239_Ca   -0.243783    239\n",
      "Val193_Ca  Val193_Ca   -0.211870    193\n",
      "Arg192_Ca  Arg192_Ca    0.169093    192\n",
      "Leu205        Leu205    0.165052    205\n",
      "Tyr103        Tyr103    0.165052    103\n",
      "Ala197_Ca  Ala197_Ca    0.150045    197\n",
      "Asp101        Asp101    0.146996    101\n",
      "Cys162_Ca  Cys162_Ca    0.139895    162\n",
      "Leu64_Ca    Leu64_Ca    0.139895     64\n",
      "Thr39          Thr39    0.137392     39\n",
      "Cys77_Ca    Cys77_Ca    0.127956     77\n",
      "Trp145_Ca  Trp145_Ca    0.127956    145\n",
      "Arg120        Arg120   -0.122396    120\n",
      "Gln2            Gln2    0.121710      2\n",
      "Gly6            Gly6    0.121710      6\n",
      "Gln113        Gln113    0.119666    113\n",
      "Pro109        Pro109    0.119666    109\n",
      "Asn40          Asn40    0.115631     40\n",
      "Glu196        Glu196    0.112140    196\n",
      "His202        His202    0.112140    202\n",
      "Ile106        Ile106    0.108577    106\n",
      "Lys198        Lys198    0.108577    198\n",
      "Thr39_Ca    Thr39_Ca   -0.103057     39\n",
      "Arg102_Ca  Arg102_Ca   -0.103057    102\n",
      "Phe42_Ca    Phe42_Ca    0.102821     42\n",
      "Asp101_Ca  Asp101_Ca    0.102821    101\n",
      "Arg200_Ca  Arg200_Ca    0.101271    200\n",
      "...              ...         ...    ...\n",
      "Val230        Val230   -0.089085    230\n",
      "Ile172        Ile172   -0.089085    172\n",
      "Phe215_Ca  Phe215_Ca   -0.080062    215\n",
      "Phe179_Ca  Phe179_Ca   -0.080062    179\n",
      "Thr81_Ca    Thr81_Ca    0.080004     81\n",
      "Phe164_Ca  Phe164_Ca    0.080004    164\n",
      "Tyr112        Tyr112   -0.078749    112\n",
      "Met141        Met141   -0.075495    141\n",
      "Arg146        Arg146   -0.075495    146\n",
      "Val135        Val135    0.073739    135\n",
      "Phe137        Phe137    0.073739    137\n",
      "Phe222        Phe222    0.072686    222\n",
      "Phe241        Phe241    0.072686    241\n",
      "Ile100        Ile100    0.070462    100\n",
      "Ile185        Ile185    0.070462    185\n",
      "Leu208_Ca  Leu208_Ca   -0.070120    208\n",
      "Ala190_Ca  Ala190_Ca   -0.070120    190\n",
      "Val14          Val14    0.069799     14\n",
      "Leu115        Leu115   -0.067535    115\n",
      "Ser108        Ser108   -0.067535    108\n",
      "Trp3            Trp3    0.066994      3\n",
      "Arg67          Arg67    0.066994     67\n",
      "Trp246        Trp246    0.063286    246\n",
      "Asp147        Asp147    0.060582    147\n",
      "Arg233        Arg233    0.060582    233\n",
      "Gly61          Gly61   -0.060461     61\n",
      "Gly248_Ca  Gly248_Ca    0.053966    248\n",
      "Asn251_Ca  Asn251_Ca    0.053966    251\n",
      "Val135_Ca  Val135_Ca   -0.051281    135\n",
      "Ile140_Ca  Ile140_Ca   -0.051281    140\n",
      "\n",
      "[65 rows x 3 columns]\n",
      "Using dark_background\n",
      "Interpreting tIC 9\n",
      "feature_importances_df.shape\n",
      "(25, 7)\n",
      "residue_importances_df.shape\n",
      "(44, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "13  Arg192_Ca To Ala197_Ca  Arg192_Ca  Ala197_Ca      192      197   \n",
      "3         Leu205 To Ile106     Leu205     Ile106      205      106   \n",
      "16  Ala197_Ca To Ile106_Ca  Ala197_Ca  Ile106_Ca      197      106   \n",
      "24  Tyr194_Ca To His202_Ca  Tyr194_Ca  His202_Ca      194      202   \n",
      "18   Leu208_Ca To Ile43_Ca  Leu208_Ca   Ile43_Ca      208       43   \n",
      "21  Val193_Ca To Ala197_Ca  Val193_Ca  Ala197_Ca      193      197   \n",
      "22  Val193_Ca To Lys198_Ca  Val193_Ca  Lys198_Ca      193      198   \n",
      "23  Glu196_Ca To His202_Ca  Glu196_Ca  His202_Ca      196      202   \n",
      "0         Trp144 To Ala169     Trp144     Ala169      144      169   \n",
      "11          Trp239 To Trp3     Trp239       Trp3      239        3   \n",
      "7         Glu196 To His202     Glu196     His202      196      202   \n",
      "5         Val193 To Leu205     Val193     Leu205      193      205   \n",
      "2         Pro109 To Gln113     Pro109     Gln113      109      113   \n",
      "10         Ser132 To Thr94     Ser132      Thr94      132       94   \n",
      "12        Phe215 To Tyr259     Phe215     Tyr259      215      259   \n",
      "19   Pro256_Ca To Leu24_Ca  Pro256_Ca   Leu24_Ca      256       24   \n",
      "9         Ala197 To His202     Ala197     His202      197      202   \n",
      "20  Val214_Ca To Trp219_Ca  Val214_Ca  Trp219_Ca      214      219   \n",
      "6          Asp163 To Trp80     Asp163      Trp80      163       80   \n",
      "8         Arg233 To Thr166     Arg233     Thr166      233      166   \n",
      "1           Ile26 To Ser31      Ile26      Ser31       26       31   \n",
      "4         Val135 To Tyr170     Val135     Tyr170      135      170   \n",
      "17  Lys154_Ca To Cys161_Ca  Lys154_Ca  Cys161_Ca      154      161   \n",
      "14   Arg102_Ca To Thr39_Ca  Arg102_Ca   Thr39_Ca      102       39   \n",
      "15   Tyr170_Ca To Val85_Ca  Tyr170_Ca   Val85_Ca      170       85   \n",
      "\n",
      "    importance                 feature  \n",
      "13   -0.444589  ARG192_CA to ALA197_CA  \n",
      "3     0.244977        LEU205 to ILE106  \n",
      "16    0.221879  ALA197_CA to ILE106_CA  \n",
      "24    0.220214  TYR194_CA to HIS202_CA  \n",
      "18    0.220096   LEU208_CA to ILE43_CA  \n",
      "21    0.199602  VAL193_CA to ALA197_CA  \n",
      "22    0.179695  VAL193_CA to LYS198_CA  \n",
      "23   -0.162698  GLU196_CA to HIS202_CA  \n",
      "0    -0.158712        TRP144 to ALA169  \n",
      "11    0.155139          TRP239 to TRP3  \n",
      "7    -0.145759        GLU196 to HIS202  \n",
      "5     0.145486        VAL193 to LEU205  \n",
      "2     0.143045        PRO109 to GLN113  \n",
      "10   -0.129563         SER132 to THR94  \n",
      "12    0.123944        PHE215 to TYR259  \n",
      "19   -0.123454   PRO256_CA to LEU24_CA  \n",
      "9     0.112560        ALA197 to HIS202  \n",
      "20    0.111348  VAL214_CA to TRP219_CA  \n",
      "6    -0.084819         ASP163 to TRP80  \n",
      "8     0.078583        ARG233 to THR166  \n",
      "1    -0.076382          ILE26 to SER31  \n",
      "4    -0.071479        VAL135 to TYR170  \n",
      "17   -0.068539  LYS154_CA to CYS161_CA  \n",
      "14   -0.067136   ARG102_CA to THR39_CA  \n",
      "15   -0.057450   TYR170_CA to VAL85_CA  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Arg192_Ca  Arg192_Ca   -0.444589    192\n",
      "Ile106        Ile106    0.244977    106\n",
      "Leu205        Leu205    0.240003    205\n",
      "Ile106_Ca  Ile106_Ca    0.221879    106\n",
      "Tyr194_Ca  Tyr194_Ca    0.220214    194\n",
      "Ile43_Ca    Ile43_Ca    0.220096     43\n",
      "Leu208_Ca  Leu208_Ca    0.220096    208\n",
      "Ala197_Ca  Ala197_Ca    0.219651    197\n",
      "His202_Ca  His202_Ca    0.201069    202\n",
      "Val193_Ca  Val193_Ca    0.198607    193\n",
      "Lys198_Ca  Lys198_Ca    0.179695    198\n",
      "Glu196_Ca  Glu196_Ca   -0.162698    196\n",
      "Ala169        Ala169   -0.158712    169\n",
      "Trp144        Trp144   -0.158712    144\n",
      "Trp3            Trp3    0.155139      3\n",
      "Trp239        Trp239    0.155139    239\n",
      "Glu196        Glu196   -0.145759    196\n",
      "Val193        Val193    0.145486    193\n",
      "Pro109        Pro109    0.143045    109\n",
      "Gln113        Gln113    0.143045    113\n",
      "Thr94          Thr94   -0.129563     94\n",
      "Ser132        Ser132   -0.129563    132\n",
      "Tyr259        Tyr259    0.123944    259\n",
      "Phe215        Phe215    0.123944    215\n",
      "Pro256_Ca  Pro256_Ca   -0.123454    256\n",
      "Leu24_Ca    Leu24_Ca   -0.123454     24\n",
      "Ala197        Ala197    0.112560    197\n",
      "Trp219_Ca  Trp219_Ca    0.111348    219\n",
      "Val214_Ca  Val214_Ca    0.111348    214\n",
      "His202        His202    0.099644    202\n",
      "Trp80          Trp80   -0.084819     80\n",
      "Asp163        Asp163   -0.084819    163\n",
      "Arg233        Arg233    0.078583    233\n",
      "Thr166        Thr166    0.078583    166\n",
      "Ser31          Ser31   -0.076382     31\n",
      "Ile26          Ile26   -0.076382     26\n",
      "Tyr170        Tyr170   -0.071479    170\n",
      "Val135        Val135   -0.071479    135\n",
      "Cys161_Ca  Cys161_Ca   -0.068539    161\n",
      "Lys154_Ca  Lys154_Ca   -0.068539    154\n",
      "Arg102_Ca  Arg102_Ca   -0.067136    102\n",
      "Thr39_Ca    Thr39_Ca   -0.067136     39\n",
      "Tyr170_Ca  Tyr170_Ca   -0.057450    170\n",
      "Val85_Ca    Val85_Ca   -0.057450     85\n",
      "Using dark_background\n",
      "Interpreting tIC 10\n",
      "feature_importances_df.shape\n",
      "(31, 7)\n",
      "residue_importances_df.shape\n",
      "(49, 3)\n",
      "              feature_name      res_i      res_j  resid_i  resid_j  \\\n",
      "28  Val193_Ca To Lys198_Ca  Val193_Ca  Lys198_Ca      193      198   \n",
      "22  Val230_Ca To Arg168_Ca  Val230_Ca  Arg168_Ca      230      168   \n",
      "30  Asn229_Ca To Arg168_Ca  Asn229_Ca  Arg168_Ca      229      168   \n",
      "21  Arg195_Ca To Lys198_Ca  Arg195_Ca  Lys198_Ca      195      198   \n",
      "7         His202 To Ile106     His202     Ile106      202      106   \n",
      "20  Arg195_Ca To Ala197_Ca  Arg195_Ca  Ala197_Ca      195      197   \n",
      "19        Asn229 To Thr166     Asn229     Thr166      229      166   \n",
      "4          Phe137 To Leu86     Phe137      Leu86      137       86   \n",
      "18          Trp239 To Trp3     Trp239       Trp3      239        3   \n",
      "27  Val193_Ca To Ala197_Ca  Val193_Ca  Ala197_Ca      193      197   \n",
      "25  Trp145_Ca To Ala171_Ca  Trp145_Ca  Ala171_Ca      145      171   \n",
      "5           Leu64 To Trp72      Leu64      Trp72       64       72   \n",
      "17          Leu56 To Trp72      Leu56      Trp72       56       72   \n",
      "16          Arg67 To Trp72      Arg67      Trp72       67       72   \n",
      "13         Phe164 To Trp80     Phe164      Trp80      164       80   \n",
      "8         Tyr180 To Leu224     Tyr180     Leu224      180      224   \n",
      "9         Tyr180 To Leu220     Tyr180     Leu220      180      220   \n",
      "0         Ile210 To Arg261     Ile210     Arg261      210      261   \n",
      "26  Phe164_Ca To Ala171_Ca  Phe164_Ca  Ala171_Ca      164      171   \n",
      "3           Thr69 To Trp72      Thr69      Trp72       69       72   \n",
      "29   Trp246_Ca To Trp80_Ca  Trp246_Ca   Trp80_Ca      246       80   \n",
      "23  Val230_Ca To Arg233_Ca  Val230_Ca  Arg233_Ca      230      233   \n",
      "10         Phe137 To Ser82     Phe137      Ser82      137       82   \n",
      "6          Cys162 To Trp80     Cys162      Trp80      162       80   \n",
      "24  Ile140_Ca To Tyr170_Ca  Ile140_Ca  Tyr170_Ca      140      170   \n",
      "1         Arg192 To Thr107     Arg192     Thr107      192      107   \n",
      "14         Trp129 To Ser45     Trp129      Ser45      129       45   \n",
      "2         Tyr112 To Arg102     Tyr112     Arg102      112      102   \n",
      "12        Tyr156 To Asp163     Tyr156     Asp163      156      163   \n",
      "15          Pro59 To Met11      Pro59      Met11       59       11   \n",
      "11        Cys218 To Tyr249     Cys218     Tyr249      218      249   \n",
      "\n",
      "    importance                 feature  \n",
      "28    0.324964  VAL193_CA to LYS198_CA  \n",
      "22    0.270502  VAL230_CA to ARG168_CA  \n",
      "30   -0.261828  ASN229_CA to ARG168_CA  \n",
      "21   -0.231208  ARG195_CA to LYS198_CA  \n",
      "7     0.199252        HIS202 to ILE106  \n",
      "20    0.186911  ARG195_CA to ALA197_CA  \n",
      "19   -0.182690        ASN229 to THR166  \n",
      "4     0.170032         PHE137 to LEU86  \n",
      "18   -0.169519          TRP239 to TRP3  \n",
      "27   -0.158913  VAL193_CA to ALA197_CA  \n",
      "25    0.152705  TRP145_CA to ALA171_CA  \n",
      "5     0.128307          LEU64 to TRP72  \n",
      "17   -0.123524          LEU56 to TRP72  \n",
      "16   -0.110098          ARG67 to TRP72  \n",
      "13    0.108591         PHE164 to TRP80  \n",
      "8     0.108116        TYR180 to LEU224  \n",
      "9     0.107715        TYR180 to LEU220  \n",
      "0    -0.097853        ILE210 to ARG261  \n",
      "26    0.095355  PHE164_CA to ALA171_CA  \n",
      "3     0.094620          THR69 to TRP72  \n",
      "29    0.094157   TRP246_CA to TRP80_CA  \n",
      "23    0.089456  VAL230_CA to ARG233_CA  \n",
      "10    0.083029         PHE137 to SER82  \n",
      "6    -0.081682         CYS162 to TRP80  \n",
      "24   -0.078369  ILE140_CA to TYR170_CA  \n",
      "1    -0.077691        ARG192 to THR107  \n",
      "14   -0.072307         TRP129 to SER45  \n",
      "2    -0.067189        TYR112 to ARG102  \n",
      "12   -0.066400        TYR156 to ASP163  \n",
      "15   -0.063031          PRO59 to MET11  \n",
      "11    0.058330        CYS218 to TYR249  \n",
      "Using dark_background\n",
      "             residue  importance  resid\n",
      "Val193_Ca  Val193_Ca    0.300771    193\n",
      "Lys198_Ca  Lys198_Ca    0.297156    198\n",
      "Asn229_Ca  Asn229_Ca   -0.261828    229\n",
      "Val230_Ca  Val230_Ca    0.261450    230\n",
      "Arg168_Ca  Arg168_Ca    0.243886    168\n",
      "Ile106        Ile106    0.199252    106\n",
      "His202        His202    0.199252    202\n",
      "Asn229        Asn229   -0.182690    229\n",
      "Thr166        Thr166   -0.182690    166\n",
      "Leu86          Leu86    0.170032     86\n",
      "Ala197_Ca  Ala197_Ca    0.169620    197\n",
      "Trp3            Trp3   -0.169519      3\n",
      "Trp239        Trp239   -0.169519    239\n",
      "Arg195_Ca  Arg195_Ca    0.166005    195\n",
      "Phe137        Phe137    0.165682    137\n",
      "Trp145_Ca  Trp145_Ca    0.152705    145\n",
      "Ala171_Ca  Ala171_Ca    0.149837    171\n",
      "Leu64          Leu64    0.128307     64\n",
      "Leu56          Leu56   -0.123524     56\n",
      "Trp72          Trp72    0.123254     72\n",
      "Arg67          Arg67   -0.110098     67\n",
      "Phe164        Phe164    0.108591    164\n",
      "Leu224        Leu224    0.108116    224\n",
      "Tyr180        Tyr180    0.108096    180\n",
      "Leu220        Leu220    0.107715    220\n",
      "Trp80          Trp80    0.099077     80\n",
      "Arg261        Arg261   -0.097853    261\n",
      "Ile210        Ile210   -0.097853    210\n",
      "Phe164_Ca  Phe164_Ca    0.095355    164\n",
      "Thr69          Thr69    0.094620     69\n",
      "Trp246_Ca  Trp246_Ca    0.094157    246\n",
      "Trp80_Ca    Trp80_Ca    0.094157     80\n",
      "Arg233_Ca  Arg233_Ca    0.089456    233\n",
      "Ser82          Ser82    0.083029     82\n",
      "Cys162        Cys162   -0.081682    162\n",
      "Ile140_Ca  Ile140_Ca   -0.078369    140\n",
      "Tyr170_Ca  Tyr170_Ca   -0.078369    170\n",
      "Arg192        Arg192   -0.077691    192\n",
      "Thr107        Thr107   -0.077691    107\n",
      "Trp129        Trp129   -0.072307    129\n",
      "Ser45          Ser45   -0.072307     45\n",
      "Arg102        Arg102   -0.067189    102\n",
      "Tyr112        Tyr112   -0.067189    112\n",
      "Asp163        Asp163   -0.066400    163\n",
      "Tyr156        Tyr156   -0.066400    156\n",
      "Met11          Met11   -0.063031     11\n",
      "Pro59          Pro59   -0.063031     59\n",
      "Cys218        Cys218    0.058330    218\n",
      "Tyr249        Tyr249    0.058330    249\n",
      "Using dark_background\n"
     ]
    }
   ],
   "source": [
    "import interpret_tICs\n",
    "reload(interpret_tICs)\n",
    "from interpret_tICs import *\n",
    "tic_components_dir = tica_dir\n",
    "important_contact_features = interpret_tIC_components(projection_operator_dir, tic_components_dir, feature_residues_pkl, n_tica_components=n_components, percentile=95)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN0.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM1.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM4.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R1.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R12.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM7.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R15.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R4.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R7.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR1.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR12.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR15.dataset\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUNFAH.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM2.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM5.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R10.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R13.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM8.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R2.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R5.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R8.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR10.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR13.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR16.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM00.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM3.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM6.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R11.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R14.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_Active_GP_LigandXAM9.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R3.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R6.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_R9.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR11.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR14.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR17.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR37.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR31.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR20.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR18.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR23.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR26.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR29.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR38.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR32.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR21.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR3.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR27.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR19.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR24.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR39.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR33.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR22.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR30.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR28.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR2.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR25.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR56.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR50.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR4.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR45.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR42.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR34.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR48.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR57.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR51.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR40.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR46.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR43.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR35.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR49.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR58.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR52.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR41.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR47.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR44.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR36.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR5.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF20.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF15.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR59.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF12.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR7.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR53.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF1.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF3.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF16.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR6.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF13.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR8.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR54.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF10.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF4.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF17.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR60.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF14.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR9.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RR55.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF11.dataset\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF18.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF5.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF8.dataset\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF9.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF19.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF6.dataset\n",
      "\n",
      "\n",
      "loading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF2.datasetloading /home/enf/md_simulations/B1AR/featuresall_residues_5f8u_hom_under_cutoff6A-CA/RUN_RSF7.dataset\n",
      "\n"
     ]
    }
   ],
   "source": [
    "import interpret_tICs\n",
    "reload(interpret_tICs)\n",
    "from interpret_tICs import *\n",
    "tic_subsampled_features_file = \"%s/features_subsampled.pkl\" % tica_dir\n",
    "subsampled_features_dir = os.path.join(tica_dir, \"subsampled_features\")\n",
    "if not os.path.exists(subsampled_features_dir): os.makedirs(subsampled_features_dir)\n",
    "important_contact_features_pruned, important_contact_features_indices = find_non_zero_features(important_contact_features[0], feature_names)\n",
    "subsample_features(features_dir, important_contact_features_indices, important_contact_features_pruned, tic_subsampled_features_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "protein_top_features = load_file(tic_subsampled_features_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "140\n"
     ]
    }
   ],
   "source": [
    "from ipyparallel import Client\n",
    "rc = Client()\n",
    "dview = rc[:]\n",
    "dview.map(os.chdir, ['/home/enf/b2ar_analysis/conformation']*len(rc.ids))\n",
    "\n",
    "print(len(rc.ids))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "trajs = []\n",
    "apo_trajs = []\n",
    "oxy_trajs = []\n",
    "suf_trajs = []\n",
    "trv_trajs = []\n",
    "trajs = get_trajectory_files(features_dir, \".dataset\")\n",
    "#trajs = [t for t in get_trajectory_files(traj_dir, traj_ext) if \"apo_reimaged\" not in t and \"oxy\" not in t]\n",
    "all_trajs = []\n",
    "for i, traj in enumerate(trajs):\n",
    "    all_trajs.append(i)\n",
    "\n",
    "user_defined_coords = load_file(user_defined_features_file)\n",
    "\n",
    "            "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "n_clusters = 1000\n",
    "clusterer_dir = \"%s/clusterer_%dclusters.h5\" %(tica_dir, n_clusters)\n",
    "if not os.path.exists(clusterer_dir):\n",
    "    cluster_minikmeans(tica_dir, projected_features_dir, traj_dir, n_clusters=n_clusters, clusterer_dir=clusterer_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "clusterer = verboseload(clusterer_dir)\n",
    "cluster_labels = clusterer.labels_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cluster_tica_averages = calculate_cluster_averages_per_feature(clusterer, tica_coords)\n",
    "cluster_tica_averages = pd.DataFrame(cluster_tica_averages, columns=[\"tIC.%d\" %i for i in range(1, n_components+1)])\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "intermediate_actives = cluster_tica_averages.loc[(cluster_tica_averages[\"tIC.2\"] > 0.7) & (cluster_tica_averages[\"tIC.2\"] < 1.2) & (cluster_tica_averages[\"tIC.5\"] > 0.) & (cluster_tica_averages[\"tIC.2\"] < 0.8)]\n",
    "intermediate_actives"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import custom_msm\n",
    "reload(custom_msm)\n",
    "from custom_msm import *\n",
    "from msm_resampled import *"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "clusters_map = make_clusters_map(clusterer)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "\n",
    "plt.clf()\n",
    "plot_timescales(clusterer_dir, n_clusters, tica_dir, main=\"MSM Timescales\", lag_times=list(range(1,31,6)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import msmbui"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "lag_time=1\n",
    "prior_counts = 0.0\n",
    "msm_dir = os.path.join(tica_dir, \"msm_lag-time%d_prior-counts%s_clusters%d.h5\" %(lag_time, str(prior_counts), n_clusters))\n",
    "if not os.path.exists(msm_dir):\n",
    "    msm_object = build_msm(clusterer_dir, lag_time, msm_dir, prior_counts)\n",
    "else:\n",
    "    msm_object = verboseload(msm_dir)\n",
    "\n",
    "import msm_resampled\n",
    "reload(msm_resampled)\n",
    "from msm_resampled import *\n",
    "total_samples = 20000\n",
    "num_trajs = len(trajs)\n",
    "prior_counts = 0.\n",
    "resampled_traj_to_frames_file = os.path.join(tica_dir, \"msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "#if not os.path.exists(resampled_traj_to_frames_file):\n",
    "resampled_traj_to_frames = resample_by_msm(total_samples, msm_object, clusters_map, num_trajs, resampled_traj_to_frames_file)\n",
    "#else:\n",
    "resampled_traj_to_frames = verboseload(resampled_traj_to_frames_file)\n",
    "\n",
    "pnas = pnas_coords\n",
    "pnas_resampled_file = os.path.join(tica_dir, \"pnas_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(pnas, resampled_traj_to_frames, pnas_resampled_file)\n",
    "pnas_resampled = verboseload(pnas_resampled_file)\n",
    "\n",
    "tica_concatenated = np.concatenate(verboseload(projected_features_dir))\n",
    "tica_axes = [(np.min(tica_concatenated[:,i]), np.max(tica_concatenated[:,i])) for i in range(0, np.shape(tica_concatenated)[1])]\n",
    "\n",
    "tica = tica_coords\n",
    "tica_resampled_file = os.path.join(tica_dir, \"tica_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(tica, resampled_traj_to_frames, tica_resampled_file)\n",
    "tica_resampled = verboseload(tica_resampled_file)\n",
    "\n",
    "clusterer = verboseload(clusterer_dir)\n",
    "msm_object = verboseload(msm_dir)\n",
    "\n",
    "cluster_id_proportion_tuples = []\n",
    "\n",
    "equilibrium_populations = msm_object.populations_\n",
    "\n",
    "for cluster_id in msm_object.mapping_.keys():\n",
    "    state_id = msm_object.mapping_[cluster_id]\n",
    "    cluster_id_proportion_tuples.append((cluster_id,equilibrium_populations[state_id]))\n",
    "cluster_id_proportion_tuples = sorted(cluster_id_proportion_tuples, key=itemgetter(1), reverse=True)\n",
    "\n",
    "#plot_all_tics_and_clusters(tica_dir, tica_resampled_file, clusterer_file, lag_time, tic_range=range(0,n_components), main = \"MSM_Reweighted\", label = \"cluster_id\", active_cluster_ids = [c[0] for c in cluster_id_proportion_tuples[0:100]], intermediate_cluster_ids = [], inactive_cluster_ids = [], concatenate=False, axes=tica_axes)\n",
    "\n",
    "#plot_columns(tica_dir, tica_resampled_file, titles = [\"tIC.%d\" %i for i in range(1,n_components+1)], main = \"mOR_MSM_\", tICA = False, scale = 1.0, refcoords_file = ref_tica_coords, axes=tica_axes, concatenate=False, reshape=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "graph_file = \"%s/msm_lag_time%d_graph.graphml\" % (tica_dir, lag_time)\n",
    "tica_averages = calculate_cluster_averages_per_feature(clusterer, tica)\n",
    "cluster_attributes = {}\n",
    "for i, title in enumerate([\"tIC.%d\" %i for i in range(1,n_components+1)]):\n",
    "    cluster_attributes[title] = tica_averages[:,i]\n",
    "construct_graph(msm_dir, clusterer_file, n_clusters, 5, 5, graph_file, inactive = None, active = None, pnas_clusters_averages = None, tica_clusters_averages = None, docking=None, macrostate = None, cluster_attributes=cluster_attributes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_columns(tica_dir, apo_pnas_resampled_file, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_Apo_MSM_\", tICA = False, scale = 1.0, refcoords_file = None, axes=None, concatenate=False, reshape=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "lag_time=25\n",
    "prior_counts = 0.0\n",
    "msm_dir = os.path.join(tica_dir, \"msm_lag-time%d_prior-counts%s_clusters%d.h5\" %(lag_time, str(prior_counts), n_clusters))\n",
    "if not os.path.exists(msm_dir):\n",
    "    msm = build_msm(clusterer_file, lag_time, msm_dir, prior_counts)\n",
    "else:\n",
    "    msm = verboseload(msm_dir)\n",
    "msm.timescales_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "total_samples = 20000\n",
    "num_trajs = len(trajs)\n",
    "resampled_traj_to_frames_file = os.path.join(tica_dir, \"msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "if not os.path.exists(resampled_traj_to_frames_file):\n",
    "    resampled_traj_to_frames = resample_by_msm(total_samples, msm, clusters_map, num_trajs, resampled_traj_to_frames_file)\n",
    "else:\n",
    "    resampled_traj_to_frames = verboseload(resampled_traj_to_frames_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "resampled_traj_to_frames_file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "pnas = pnas_coords\n",
    "pnas_resampled_file = os.path.join(tica_dir, \"pnas_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(pnas, resampled_traj_to_frames, pnas_resampled_file)\n",
    "pnas_resampled = verboseload(pnas_resampled_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tica = tica_coords\n",
    "tica_resampled_file = os.path.join(tica_dir, \"tica_msm_lag-time%d_prior-counts%s_clusters%d_resampled_%d.h5\" %(lag_time, str(prior_counts), n_clusters, total_samples))\n",
    "resample_features_by_msm_equilibirum_pop(tica, resampled_traj_to_frames, tica_resampled_file)\n",
    "tica_resampled = verboseload(tica_resampled_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tica_resampled = np.vstack([verboseload(pnas_resampled_file)[::1,]])\n",
    "mins = np.min(tica_resampled, axis=0)\n",
    "maxs = np.max(tica_resampled, axis=0)\n",
    "stds = np.std(tica_resampled, axis=0)\n",
    "custom_lims = [[mins[i] - 1.*stds[i], maxs[i] + 1.*stds[i]] for i in range(0,len(mins))]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ref_pnas = load_file(\"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/ref_coords.h5\")\n",
    "ref_pnas = np.hstack([np.array(x).T for x in ref_pnas])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "def get_features(features_dir):\n",
    "    feature_files = get_trajectory_files(features_dir, \".dataset\")\n",
    "    features = np.vstack([load_file(f) for f in feature_files])\n",
    "    print(features.shape)\n",
    "    return features\n",
    "\n",
    "ref_pp_features = pd.DataFrame(get_features(ref_features_dir), columns=feature_names)\n",
    "\n",
    "ref_pp_tica = pd.read_csv(ref_tica_coords, header=None).values\n",
    "#ref_pp_tica.columns = [\"mOR tIC.%d\" %i for i in range(1,ref_pp_tica.shape[1])]\n",
    "\n",
    "ref_pnas = load_file(\"/home/enf/md_simulations/MOR/h8_reimaged/all_pnas_features/ref_coords.h5\")\n",
    "ref_pnas = np.hstack([np.array(x).T for x in ref_pnas])\n",
    "print(ref_pnas)\n",
    "\n",
    "#ref_pnas = pd.DataFrame(ref_pnas, columns=sorted(feature_name_residues_dict.keys()))\n",
    "\n",
    "#ref_features = pd.concat([ref_pp_features*10., ref_lp_features*10., ref_pp_tica, ref_lp_tica, ref_pnas], axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ref_pp_tica"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import jointplot_d3\n",
    "reload(jointplot_d3)\n",
    "from jointplot_d3 import *\n",
    "jointplots(pnas_resampled[::1,:], analysis_dir, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_MSM_\", refcoords = ref_pnas, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=20, min_density=None, max_diff=3., custom_lims=custom_lims, n_levels=15, n_pts=200j, parallel=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "ref_pnas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "jointplots(apo_pnas_resampled[::1,:], analysis_dir, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_APO_MSM_\", refcoords=ref_pnas, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=20, min_density=None, max_diff=3., custom_lims=custom_lims, n_levels=10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "jointplots(suf_pnas_resampled[::1,:], analysis_dir, titles = sorted(feature_name_residues_dict.keys()), main = \"mOR_SUF_MSM_\", refcoords=ref_pnas, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=20, min_density=None, max_diff=3., custom_lims=custom_lims, n_levels=10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tica_resampled = np.vstack([verboseload(tica_resampled_file)[::1,]])\n",
    "mins = np.min(tica_resampled, axis=0)\n",
    "maxs = np.max(tica_resampled, axis=0)\n",
    "stds = np.std(tica_resampled, axis=0)\n",
    "custom_lims = [[mins[i] - 1.*stds[i], maxs[i] + 1.*stds[i]] for i in range(0,len(mins))]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "print(custom_lims)\n",
    "print(custom_lims[3][1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import jointplot_d3\n",
    "reload(jointplot_d3)\n",
    "from jointplot_d3 import *\n",
    "refcoords_jointplots_dir = \"%s/refcoords_jointplots\" %analysis_dir\n",
    "if not os.path.exists(refcoords_jointplots_dir):\n",
    "    os.makedirs(refcoords_jointplots_dir)\n",
    "jointplots(verboseload(tica_resampled_file)[::1,:], refcoords_jointplots_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"BU72 MSM\", refcoords=ref_pp_tica, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=10, min_density=None, max_diff=5., custom_lims=custom_lims, n_pts=200j, n_levels=15)\n",
    "#jointplots(verboseload(apo_tica_resampled_file)[::1,:], refcoords_jointplots_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"Apo MSM\", refcoords=ref_pp_tica, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=10, min_density=None, max_diff=5., custom_lims=custom_lims, n_pts=200j, n_levels=15)\n",
    "\n",
    "\n",
    "#jointplots(verboseload(suf_tica_resampled_file)[::1,:], refcoords_jointplots_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"Sufentanil MSM\", refcoords=ref_pp_tica, axes=None, data_j=None, titles_j=None, reshape=False, max_tIC=10, min_density=None, max_diff=5., custom_lims=custom_lims, n_pts=200j, n_levels=15)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import jointplot_d3\n",
    "reload(jointplot_d3)\n",
    "from jointplot_d3 import *\n",
    "jointplots(verboseload(tica_resampled_file)[::1,:], analysis_dir, titles = [\"tIC%d\" %j for j in range(1,n_components+1)], main = \"BU72 MSM\", refcoords=None, axes=None, data_j=pnas_resampled, titles_j=sorted(feature_name_residues_dict.keys()), reshape=False, max_tIC=10, min_density=None, max_diff=5., custom_lims=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer_25clusters_1samples_samples_kdtree\n"
     ]
    }
   ],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters=300\n",
    "samples_dir = \"%s/clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(clusterer_file, tica_file, [traj_files[i] for i in trajs], \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"NON\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "get_trajectory_files(traj_dir, traj_ext)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 5\n",
    "n_clusters=1000\n",
    "samples_dir = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "\n",
    "sample_from_clusterer(apo_clusterer_file, apo_tica_file, [traj_files[i] for i in apo_trajs],\n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"LIG\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "traj_files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "feature_name_residues_dict.keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "\n",
    "np.shape(apo_pnas_resampled)\n",
    "msm_dir = os.path.join(tica_dir, \"msm_lag-time%d_prior-counts%s_clusters%d_analysis\" %(lag_time, str(prior_counts), n_clusters))\n",
    "if not os.path.exists(msm_dir): os.makedirs(msm_dir)\n",
    "\n",
    "#plot_columns(msm_dir, apo_pnas_resampled_file, titles = feature_name_residues_dict.keys(), main = \"Apo-mOR\", tICA = False, scale = 1.0, refcoords_file = None, axes=None, concatenate=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import pip\n",
    "\n",
    "def install(package):\n",
    "    pip.main(['install', package])\n",
    "    \n",
    "install(\"moviepy\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import jointplot_d3\n",
    "reload(jointplot_d3)\n",
    "from jointplot_d3 import *\n",
    "\n",
    "for i, traj in enumerate(get_trajectory_files(traj_dir, traj_ext)):\n",
    "    if \"apo_rep_68.\" in traj:\n",
    "        index=i\n",
    "        break\n",
    "\n",
    "jointplot(apo_pnas_resampled[::10,[6,3]], \"%s/test.pdf\" %msm_dir, trajectory=apo_pnas[index][::1,[6,3]], \n",
    "          titles=[\"TM6 to TM3 distance\", \"RMSD of NPxxY to Inactive\"], main = \"mOR Activation Pathway\", \n",
    "          video_file = \"%s/apo_68.mp4\" %msm_dir, custom_xlim=[4.0, 16.0], custom_ylim= [0.0, 1.0])\n",
    "#test(\"%s/test2.mp4\" %msm_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "build_msm(clusterer_file, lag_time, msm_model_dir)\n",
    "build_msm(apo_clusterer_file, lag_time, msm_model_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "tics_1_5_file = os.path.join(tica_dir, \"tICs_1_5.h5\")\n",
    "tics = load_file(projected_features_dir)\n",
    "tics_1_5 = [x[:,range(1,5)] for x in tics]\n",
    "verbosedump(tics_1_5, tics_1_5_file)\n",
    "\n",
    "clusterer300_clusters = os.path.join(tica_dir, \"clusterer300_clusters_tICs1_5.h5\")\n",
    "cluster_minikmeans(tica_dir, tics_1_5_file, traj_dir, n_clusters=300, clusterer_dir=clusterer300_clusters)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading /home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/phi_psi_chi2_allprot_projected.h5\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/phi_psi_chi2_allprot_projected.h5\"...\n",
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/tICs_2_3.h5\"... (<type 'list'>)\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer25_clusters_tICs2_3.h5\"...\n",
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/reduced_tica.h5\"... (<type 'list'>)\n",
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/reduced_clusterer.h5\"... (<class 'msmbuilder.cluster.MiniBatchKMeans'>)\n",
      "/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer_25clusters_1samples_samples_kdtree\n"
     ]
    }
   ],
   "source": [
    "\n",
    "tics_2_3_file = os.path.join(tica_dir, \"tICs_2_3.h5\")\n",
    "tics = load_file(projected_features_dir)\n",
    "tics_2_3 = [x[:,range(2,4)] for x in tics]\n",
    "verbosedump(tics_2_3, tics_2_3_file)\n",
    "\n",
    "clusterer25_clusters = os.path.join(tica_dir, \"clusterer25_clusters_tICs2_3.h5\")\n",
    "if not os.path.exists(clusterer25_clusters):\n",
    "    cluster_minikmeans(tica_dir, tics_2_3_file, traj_dir, n_clusters=25, clusterer_dir=clusterer25_clusters)\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters = 25\n",
    "\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "featurized_trajectories = [traj_files[i] for i in feature_indices]\n",
    "traj_files = [t for t in featurized_trajectories if \"bu72\" in t]\n",
    "reduced_clusterer = verboseload(clusterer25_clusters)\n",
    "reduced_clusterer_file = \"%s/reduced_clusterer.h5\" %tica_dir\n",
    "\n",
    "reduced_tica_file = \"%s/reduced_tica.h5\" %tica_dir\n",
    "reduced_tica = [x[:,[2,3]] for x in tica_coords]\n",
    "reseeded_dir = \"%s/reseeded_samples\" %tica_dir\n",
    "if not os.path.exists(reseeded_dir):\n",
    "    os.makedirs(reseeded_dir)\n",
    "verbosedump(reduced_tica, reduced_tica_file)\n",
    "\n",
    "reduced_clusters = reduced_clusterer.labels_\n",
    "reduced_clusterer = copy.deepcopy(reduced_clusterer)\n",
    "reduced_clusterer.labels_ = reduced_clusters\n",
    "verbosedump(reduced_clusterer, reduced_clusterer_file)\n",
    "#reseed_from_clusterer(reduced_clusterer_file, \"bu72\", reseeded_dir, reduced_tica_file, traj_files)\n",
    "\n",
    "\n",
    "samples_dir = \"%s/clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "\n",
    "\n",
    "reseed_dir = \"%s/clusterer_%dclusters_%dsamples_samples_kdtree_reseed\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "if not os.path.exists(reseed_dir): os.makedirs(reseed_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "#sample_from_clusterer(reduced_clusterer_file, reduced_tica_file, traj_files, \n",
    "#                      n_samples, samples_dir, samples_indices_file,\n",
    "#                      worker_pool=None, parallel=True, lig_name=\"NON\", reseed_dir = reseed_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "25\n",
      "['/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer_25clusters_1samples_samples_kdtree/cluster0_sample0.pdb', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer_25clusters_1samples_samples_kdtree/cluster10_sample0.pdb', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer_25clusters_1samples_samples_kdtree/cluster11_sample0.pdb']\n",
      "Done prepping proteins\n",
      "/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/grids_clusterer_25clusters_1samples_samples_kdtree\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "ligands\n",
      "['/home/enf/b2ar_analysis/all_ligands/3p0g_lig-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Ici118551-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Ici215001-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Ici89406-out.maegz', '/home/enf/b2ar_analysis/all_ligands/MAPE-out.maegz', '/home/enf/b2ar_analysis/all_ligands/N-Cyclopentylbutanephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Structure2D_CID_3343-out.maegz', '/home/enf/b2ar_analysis/all_ligands/TERBSN-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Tulobuterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ZINC_results-single-out.maegz', '/home/enf/b2ar_analysis/all_ligands/acebutolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/adrenalone-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ah3021-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ah3474-out.maegz', '/home/enf/b2ar_analysis/all_ligands/alprenalol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/bevantolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/bisoprolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/broxaterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/bucindolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/bupranolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/cgp12177-out.maegz', '/home/enf/b2ar_analysis/all_ligands/cicloprolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/cimaterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/clenbuterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/clenproperol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/dichloroisopreterenol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/dobutamine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/dopamine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/du211117-out.maegz', '/home/enf/b2ar_analysis/all_ligands/du28663-out.maegz', '/home/enf/b2ar_analysis/all_ligands/epinine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ethylnorepinephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/fenoterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/formoterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/hexoprenaline-out.maegz', '/home/enf/b2ar_analysis/all_ligands/isoetharine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/isoetharine_prep-out.maegz', '/home/enf/b2ar_analysis/all_ligands/isopropylnorsynephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/labetalol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/metoprolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/nadolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/nebivolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/nipradilol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/nor-metanephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/norepinephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/olodaterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/orciprenaline-out.maegz', '/home/enf/b2ar_analysis/all_ligands/pindolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/practolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/procaterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/pronethalol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/propranolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/r_epinephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/r_isopreterenol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ritrodine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/s-atenolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/s-carazolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/s-carvedilol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/s-carvedilol_prep-out.maegz', '/home/enf/b2ar_analysis/all_ligands/salbutamol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/salmeterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/skf42469-out.maegz', '/home/enf/b2ar_analysis/all_ligands/skf56301-out.maegz', '/home/enf/b2ar_analysis/all_ligands/sotalol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/sulfonterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/t-0509-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ta-2005-out.maegz', '/home/enf/b2ar_analysis/all_ligands/terbutaline-out.maegz', '/home/enf/b2ar_analysis/all_ligands/timolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/xamoterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/zinterol-out.maegz']\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "completed grid generation job\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "completed grid generation jobalready generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "completed grid generation job\n",
      "already generated grid; skipping\n",
      "\n",
      "\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "['/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster19_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster1_sample0.in', 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'/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/t-0509/cluster6_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/ta-2005/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/ta-2005/cluster10_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/ta-2005/cluster11_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/ta-2005/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/ta-2005/cluster19_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/ta-2005/cluster1_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/ta-2005/cluster4_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/ta-2005/cluster6_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/terbutaline/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/terbutaline/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/terbutaline/cluster19_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/terbutaline/cluster1_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/terbutaline/cluster4_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/terbutaline/cluster6_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/timolol/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/timolol/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/timolol/cluster19_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/timolol/cluster1_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/timolol/cluster4_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/timolol/cluster6_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster10_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster11_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster19_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster1_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster21_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster4_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/xamoterol/cluster6_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/zinterol/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/zinterol/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/zinterol/cluster19_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/zinterol/cluster1_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/zinterol/cluster4_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/zinterol/cluster6_sample0.in']\n"
     ]
    }
   ],
   "source": [
    "grid_center = \"19., 4.5, -9.3\"\n",
    "n_samples=1\n",
    "active_ref_dir = active_dir\n",
    "\n",
    "precision = \"XP\"\n",
    "docking_dir = \"%s/docking_%s_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, precision, n_clusters, n_samples)\n",
    "if not os.path.exists(docking_dir):\n",
    "    os.makedirs(docking_dir)\n",
    "grid_dir = \"%s/grids_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(grid_dir):\n",
    "    os.makedirs(grid_dir)\n",
    "\n",
    "indices = [0, n_clusters]\n",
    "chosen_receptors = []\n",
    "for i in range(indices[0], indices[1]):\n",
    "  for j in range(0, n_samples):\n",
    "    chosen_receptors.append(\"cluster%d_sample%d\" %(i, j))\n",
    "\n",
    "reimaged_dir = samples_dir\n",
    "mae_dir = reimaged_dir\n",
    "#remove_ter(reimaged_dir)\n",
    "#reorder(reimaged_dir)\n",
    "\n",
    "all_ligands_dir = \"/home/enf/b2ar_analysis/all_ligands\"\n",
    "\n",
    "\n",
    "#agonist_ligands = [a for a in agonist_ligands if \"TA\" not in a]\n",
    "\n",
    "pprep(mae_dir, ref = active_ref_dir, chosen_receptors = chosen_receptors, worker_pool=None, parallel=True)\n",
    "generate_grids(mae_dir, grid_center, grid_dir, remove_lig = \"LIG\", chosen_receptors = chosen_receptors, worker_pool=None, outer_box=30.)\n",
    "\n",
    "\n",
    "dock_ligands_and_receptors(grid_dir, docking_dir, all_ligands_dir, precision = precision, ext = \"-out.maegz\", chosen_ligands = False, chosen_receptors = False, parallel = None, grid_ext = \".zip\", worker_pool=dview)\n",
    "\n",
    "#dock_ligands_and_receptors(grid_dir, docking_dir,  biased_agonist_dir, precision = precision, ext = \"-out.maegz\", chosen_ligands = biased_ligands, chosen_receptors = chosen_receptors, parallel = None, grid_ext = \".grd\", worker_pool=dview)\n",
    "#dock_ligands_and_receptors(grid_dir, docking_dir, agonist_dir, precision = precision, ext = \"-out.maegz\", chosen_ligands = agonist_ligands, chosen_receptors = chosen_receptors, parallel = None, grid_ext = \".grd\", worker_pool=dview)\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "25\n",
      "['/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer_25clusters_1samples_samples_kdtree/cluster0_sample0.pdb', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer_25clusters_1samples_samples_kdtree/cluster10_sample0.pdb', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/clusterer_25clusters_1samples_samples_kdtree/cluster11_sample0.pdb']\n",
      "Done prepping proteins\n",
      "/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/grids_clusterer_25clusters_1samples_samples_kdtree\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "already prepped and mae'd protein\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "Already created that grid job, skipping\n",
      "ligands\n",
      "['/home/enf/b2ar_analysis/all_ligands/3p0g_lig-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Ici118551-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Ici215001-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Ici89406-out.maegz', '/home/enf/b2ar_analysis/all_ligands/MAPE-out.maegz', '/home/enf/b2ar_analysis/all_ligands/N-Cyclopentylbutanephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Structure2D_CID_3343-out.maegz', '/home/enf/b2ar_analysis/all_ligands/TERBSN-out.maegz', '/home/enf/b2ar_analysis/all_ligands/Tulobuterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ZINC_results-single-out.maegz', '/home/enf/b2ar_analysis/all_ligands/acebutolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/adrenalone-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ah3021-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ah3474-out.maegz', '/home/enf/b2ar_analysis/all_ligands/alprenalol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/bevantolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/bisoprolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/broxaterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/bucindolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/bupranolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/cgp12177-out.maegz', '/home/enf/b2ar_analysis/all_ligands/cicloprolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/cimaterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/clenbuterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/clenproperol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/dichloroisopreterenol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/dobutamine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/dopamine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/du211117-out.maegz', '/home/enf/b2ar_analysis/all_ligands/du28663-out.maegz', '/home/enf/b2ar_analysis/all_ligands/epinine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ethylnorepinephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/fenoterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/formoterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/hexoprenaline-out.maegz', '/home/enf/b2ar_analysis/all_ligands/isoetharine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/isoetharine_prep-out.maegz', '/home/enf/b2ar_analysis/all_ligands/isopropylnorsynephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/labetalol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/metoprolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/nadolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/nebivolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/nipradilol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/nor-metanephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/norepinephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/olodaterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/orciprenaline-out.maegz', '/home/enf/b2ar_analysis/all_ligands/pindolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/practolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/procaterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/pronethalol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/propranolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/r_epinephrine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/r_isopreterenol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ritrodine-out.maegz', '/home/enf/b2ar_analysis/all_ligands/s-atenolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/s-carazolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/s-carvedilol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/s-carvedilol_prep-out.maegz', '/home/enf/b2ar_analysis/all_ligands/salbutamol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/salmeterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/skf42469-out.maegz', '/home/enf/b2ar_analysis/all_ligands/skf56301-out.maegz', '/home/enf/b2ar_analysis/all_ligands/sotalol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/sulfonterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/t-0509-out.maegz', '/home/enf/b2ar_analysis/all_ligands/ta-2005-out.maegz', '/home/enf/b2ar_analysis/all_ligands/terbutaline-out.maegz', '/home/enf/b2ar_analysis/all_ligands/timolol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/xamoterol-out.maegz', '/home/enf/b2ar_analysis/all_ligands/zinterol-out.maegz']\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "completed grid generation job\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "completed grid generation jobalready generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "already generated grid; skipping\n",
      "completed grid generation job\n",
      "\n",
      "\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
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      "already docked cluster20_sample0\n",
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      "already docked cluster22_sample0\n",
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      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
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      "already docked cluster18_sample0\n",
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      "already docked cluster20_sample0\n",
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      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
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      "already docked cluster1_sample0\n",
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      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster1_sample0\n",
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      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
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      "already docked cluster23_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
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      "already docked cluster20_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
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      "already docked cluster20_sample0\n",
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      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
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      "already docked cluster20_sample0\n",
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      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
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      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
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      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
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      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
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      "already docked cluster3_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
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      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
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      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
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      "already docked cluster18_sample0\n",
      "already docked cluster1_sample0\n",
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      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
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      "already docked cluster18_sample0\n",
      "already docked cluster19_sample0\n",
      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
      "already docked cluster21_sample0\n",
      "already docked cluster22_sample0\n",
      "already docked cluster23_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
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      "already docked cluster21_sample0\n",
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      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster6_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
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      "already docked cluster15_sample0\n",
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      "already docked cluster1_sample0\n",
      "already docked cluster20_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
      "already docked cluster13_sample0\n",
      "already docked cluster14_sample0\n",
      "already docked cluster15_sample0\n",
      "already docked cluster17_sample0\n",
      "already docked cluster18_sample0\n",
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      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster21_sample0\n",
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      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
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      "already docked cluster15_sample0\n",
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      "already docked cluster21_sample0\n",
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      "already docked cluster3_sample0\n",
      "already docked cluster4_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster6_sample0\n",
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      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster12_sample0\n",
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      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster1_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
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      "already docked cluster20_sample0\n",
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      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
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      "already docked cluster24_sample0\n",
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      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster11_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
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      "already docked cluster3_sample0\n",
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      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
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      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster3_sample0\n",
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      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster2_sample0\n",
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      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster12_sample0\n",
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      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster0_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
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      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster12_sample0\n",
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      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "already docked cluster10_sample0\n",
      "already docked cluster11_sample0\n",
      "already docked cluster12_sample0\n",
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      "already docked cluster23_sample0\n",
      "already docked cluster24_sample0\n",
      "already docked cluster2_sample0\n",
      "already docked cluster3_sample0\n",
      "already docked cluster8_sample0\n",
      "already docked cluster9_sample0\n",
      "Written all docking job input files\n",
      "['/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster19_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster1_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster22_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster3_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster4_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/3p0g_lig/cluster6_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/Ici118551/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/Ici118551/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/Ici118551/cluster19_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/Ici118551/cluster1_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/Ici118551/cluster6_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/Ici215001/cluster0_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/Ici215001/cluster13_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/Ici215001/cluster15_sample0.in', 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'/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/zinterol/cluster4_sample0.in', '/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/docking_XP_clusterer_25clusters_1samples_samples_kdtree/zinterol/cluster6_sample0.in']\n",
      "got stale result: 68932e38-141b-428d-a6bc-cdcac4b5c2cc\n",
      "{}\n",
      "{'parent_header': {u'username': u'enf', u'version': u'5.0', u'msg_type': u'apply_request', u'msg_id': u'68932e38-141b-428d-a6bc-cdcac4b5c2cc', u'session': u'9bb8c302-234a-41aa-b146-c67829db814b', u'date': datetime.datetime(2016, 7, 13, 17, 52, 26, 302795)}, 'msg_type': u'apply_reply', 'msg_id': u'0e05f74d-2068-42b5-ae68-21abd8b47e57', 'content': {u'status': u'ok'}, 'header': {u'username': u'enf', u'version': u'5.0', u'msg_type': u'apply_reply', u'msg_id': u'0e05f74d-2068-42b5-ae68-21abd8b47e57', u'session': u'56eec24b-bd52-4b7a-884e-6745d195465c', u'date': datetime.datetime(2016, 7, 13, 18, 8, 18, 573934)}, 'buffers': [<memory at 0x7f7b5a506218>], 'metadata': {u'started': u'2016-07-13T17:52:27.066773', u'dependencies_met': True, u'status': u'ok', u'engine': u'56eec24b-bd52-4b7a-884e-6745d195465c'}}\n",
      "got stale result: 6d3e4b0f-da2a-4c4c-b980-3d26bb1ef58f\n",
      "{}\n",
      "{'parent_header': {u'username': u'enf', u'version': u'5.0', u'msg_type': u'apply_request', u'msg_id': u'6d3e4b0f-da2a-4c4c-b980-3d26bb1ef58f', u'session': u'9bb8c302-234a-41aa-b146-c67829db814b', u'date': datetime.datetime(2016, 7, 13, 17, 52, 26, 245644)}, 'msg_type': u'apply_reply', 'msg_id': u'97bed9f5-5d01-4ace-91ff-fe2721be00a0', 'content': {u'status': u'ok'}, 'header': {u'username': u'enf', u'version': u'5.0', u'msg_type': u'apply_reply', u'msg_id': u'97bed9f5-5d01-4ace-91ff-fe2721be00a0', u'session': u'1b158e5a-79b8-4005-9c7e-f7f4994c2e00', u'date': datetime.datetime(2016, 7, 13, 18, 13, 56, 459089)}, 'buffers': [<memory at 0x7f7b5a63e6d8>], 'metadata': {u'started': u'2016-07-13T17:52:27.309368', u'dependencies_met': True, u'status': u'ok', u'engine': u'1b158e5a-79b8-4005-9c7e-f7f4994c2e00'}}\n"
     ]
    },
    {
     "ename": "CompositeError",
     "evalue": "one or more exceptions from call to method: dock\n[Engine Exception]EngineError: Engine 15 died while running task '6d3e4b0f-da2a-4c4c-b980-3d26bb1ef58f'\n[Engine Exception]EngineError: Engine 40 died while running task '68932e38-141b-428d-a6bc-cdcac4b5c2cc'",
     "output_type": "error",
     "traceback": [
      "[Engine Exception]",
      "Traceback (most recent call last):",
      "  File \"/home/enf/software/anaconda/lib/python2.7/site-packages/ipyparallel/client/client.py\", line 713, in _handle_stranded_msgs",
      "    raise error.EngineError(\"Engine %r died while running task %r\"%(eid, msg_id))",
      "EngineError: Engine 15 died while running task '6d3e4b0f-da2a-4c4c-b980-3d26bb1ef58f'",
      "",
      "[Engine Exception]",
      "Traceback (most recent call last):",
      "  File \"/home/enf/software/anaconda/lib/python2.7/site-packages/ipyparallel/client/client.py\", line 713, in _handle_stranded_msgs",
      "    raise error.EngineError(\"Engine %r died while running task %r\"%(eid, msg_id))",
      "EngineError: Engine 40 died while running task '68932e38-141b-428d-a6bc-cdcac4b5c2cc'",
      ""
     ]
    }
   ],
   "source": [
    "grid_center = \"19., 4.5, -9.3\"\n",
    "n_samples=1\n",
    "active_ref_dir = active_dir\n",
    "\n",
    "precision = \"XP\"\n",
    "docking_dir = \"%s/docking_%s_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, precision, n_clusters, n_samples)\n",
    "if not os.path.exists(docking_dir):\n",
    "    os.makedirs(docking_dir)\n",
    "grid_dir = \"%s/grids_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(grid_dir):\n",
    "    os.makedirs(grid_dir)\n",
    "\n",
    "indices = [0, n_clusters]\n",
    "chosen_receptors = []\n",
    "for i in range(indices[0], indices[1]):\n",
    "  for j in range(0, n_samples):\n",
    "    chosen_receptors.append(\"cluster%d_sample%d\" %(i, j))\n",
    "\n",
    "reimaged_dir = samples_dir\n",
    "mae_dir = reimaged_dir\n",
    "#remove_ter(reimaged_dir)\n",
    "#reorder(reimaged_dir)\n",
    "\n",
    "all_ligands_dir = \"/home/enf/b2ar_analysis/all_ligands\"\n",
    "\n",
    "\n",
    "#agonist_ligands = [a for a in agonist_ligands if \"TA\" not in a]\n",
    "\n",
    "pprep(mae_dir, ref = active_ref_dir, chosen_receptors = chosen_receptors, worker_pool=None, parallel=True)\n",
    "generate_grids(mae_dir, grid_center, grid_dir, remove_lig = \"LIG\", chosen_receptors = chosen_receptors, worker_pool=None, outer_box=30.)\n",
    "\n",
    "\n",
    "dock_ligands_and_receptors(grid_dir, docking_dir, all_ligands_dir, precision = precision, ext = \"-out.maegz\", chosen_ligands = False, chosen_receptors = False, parallel = None, grid_ext = \".zip\", worker_pool=dview)\n",
    "\n",
    "#dock_ligands_and_receptors(grid_dir, docking_dir,  biased_agonist_dir, precision = precision, ext = \"-out.maegz\", chosen_ligands = biased_ligands, chosen_receptors = chosen_receptors, parallel = None, grid_ext = \".grd\", worker_pool=dview)\n",
    "#dock_ligands_and_receptors(grid_dir, docking_dir, agonist_dir, precision = precision, ext = \"-out.maegz\", chosen_ligands = agonist_ligands, chosen_receptors = chosen_receptors, parallel = None, grid_ext = \".grd\", worker_pool=dview)\n",
    "\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/home/enf/md_simulations/B1AR/reference_receptors/5f8u_hm_P_for_conformation.pdb'"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "active_dir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'dview' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-11-14235323d3a1>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdview\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m: name 'dview' is not defined"
     ]
    }
   ],
   "source": [
    "len(dview)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters = 300\n",
    "\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "featurized_trajectories = [traj_files[i] for i in feature_indices]\n",
    "suf_traj_files = [t for t in featurized_trajectories if \"suf\" in t]\n",
    "reduced_clusterer = verboseload(clusterer300_clusters)\n",
    "suf_reduced_clusterer_file = \"%s/suf_reduced_clusterer.h5\" %tica_dir\n",
    "\n",
    "suf_reduced_tica_file = \"%s/suf_reduced_tica.h5\" %tica_dir\n",
    "suf_reduced_tica = [x[:,range(1,5)] for x in suf_tica]\n",
    "suf_reseeded_dir = \"%s/suf_reseeded_samples\" %tica_dir\n",
    "if not os.path.exists(suf_reseeded_dir):\n",
    "    os.makedirs(suf_reseeded_dir)\n",
    "verbosedump(suf_reduced_tica, suf_reduced_tica_file)\n",
    "\n",
    "suf_reduced_clusters = [reduced_clusterer.labels_[i] for i in suf_trajs]\n",
    "suf_reduced_clusterer = copy.deepcopy(reduced_clusterer)\n",
    "suf_reduced_clusterer.labels_ = suf_reduced_clusters\n",
    "verbosedump(suf_reduced_clusterer, suf_reduced_clusterer_file)\n",
    "#reseed_from_clusterer(suf_reduced_clusterer_file, \"suf\", suf_reseeded_dir, suf_reduced_tica_file, suf_traj_files)\n",
    "\n",
    "\n",
    "samples_dir = \"%s/suf_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "reseed_dir = \"%s/suf_clusterer_%dclusters_%dsamples_samples_kdtree_reseed\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/suf_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "if not os.path.exists(reseed_dir): os.makedirs(reseed_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(suf_reduced_clusterer_file, suf_reduced_tica_file, [traj_files[i] for i in suf_trajs], \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"LIG\", reseed_dir = reseed_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/phi_psi_chi2_allprot_projected.h5\"...\n"
     ]
    }
   ],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters = 300\n",
    "\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "receptor_only_trajs = []\n",
    "gp_trajs = []\n",
    "gp_traj_files = []\n",
    "receptor_traj_files = []\n",
    "for i, traj_file in enumerate(traj_files):\n",
    "    if \"GP\" in traj_file:\n",
    "        gp_trajs.append(i)\n",
    "        gp_traj_files.append(traj_file)\n",
    "    else:\n",
    "        receptor_only_trajs.append(i)\n",
    "        receptor_traj_files.append(traj_file)\n",
    "\n",
    "tica_coords = verboseload(projected_features_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/phi_psi_chi2_allprot_projected.h5\"...\n",
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_tica.h5\"... (<type 'list'>)\n",
      "Clustering by KMeans\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_tica.h5\"...\n",
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer300\"... (<class 'msmbuilder.cluster.MiniBatchKMeans'>)\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer300\"...\n",
      "300\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer300\"...\n",
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      "[127, 99, 130, 212, 250, 283, 129, 192, 215, 60, 125, 299, 57, 18, 258, 141]\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_tica.h5\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer300\"...\n",
      "[[-0.30683416  0.32714542  0.66983086 ...,  0.65359669 -1.04779347\n",
      "  -0.4763977 ]\n",
      " [-0.21657969 -0.17612369  0.4933075  ..., -0.37198585 -0.47001549\n",
      "  -0.77060915]\n",
      " [-0.12202967  0.32755473  0.01882709 ..., -0.81269731 -0.64499276\n",
      "   0.47277766]\n",
      " ..., \n",
      " [-0.24387081  0.08252424  0.70366943 ..., -0.21895616  0.42626555\n",
      "  -0.27370782]\n",
      " [-0.28131932 -0.37490051 -2.08287035 ...,  3.01777008 -0.48046148\n",
      "  -1.61309573]\n",
      " [-0.26515211 -1.00811235 -2.47499805 ..., -0.69855587 -0.24754939\n",
      "  -0.14628413]]\n",
      "Printed all tICA coords and all requested clusters\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_tica.h5\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer300\"...\n",
      "Looking at cluster 18\n",
      "Snapshot in: (15, 273)\n",
      "Looking at cluster 57\n",
      "Snapshot in: (69, 50)\n",
      "Looking at cluster 60\n",
      "Snapshot in: (16, 326)\n",
      "Looking at cluster 99\n",
      "Snapshot in: (5, 863)\n",
      "Looking at cluster 125\n",
      "Snapshot in: (5, 480)\n",
      "Looking at cluster 127\n",
      "Snapshot in: (15, 165)\n",
      "Looking at cluster 129\n",
      "Snapshot in: (4, 550)\n",
      "Looking at cluster 130\n",
      "Snapshot in: (32, 141)\n",
      "Looking at cluster 141\n",
      "Snapshot in: (96, 350)\n",
      "Looking at cluster 192\n",
      "Snapshot in: (10, 28)\n",
      "Looking at cluster 212\n",
      "Snapshot in: (17, 33)\n",
      "Looking at cluster 215\n",
      "Snapshot in: (4, 15)\n",
      "Looking at cluster 250\n",
      "Snapshot in: (13, 364)\n",
      "Looking at cluster 258\n",
      "Snapshot in: (5, 581)\n",
      "Looking at cluster 283\n",
      "Snapshot in: (52, 96)\n",
      "Looking at cluster 299\n",
      "Snapshot in: (4, 505)\n",
      "/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer_300clusters_1samples_samples_kdtree\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer300\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_tica.h5\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer300\"...\n",
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      "300\n",
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/receptor_clusterer_300clusters_1samples_samples_kdtree_indices.h5\"... (<type 'numpy.ndarray'>)\n"
     ]
    }
   ],
   "source": [
    "\n",
    "gp_tica = [tica_coords[i] for i in gp_trajs]\n",
    "receptor_tica = [tica_coords[i] for i in receptor_only_trajs]\n",
    "\n",
    "gp_clusterer = \"%s/gp_clusterer%d\" %(tica_dir, n_clusters)\n",
    "receptor_clusterer_file = \"%s/receptor_clusterer%d\" %(tica_dir, n_clusters)\n",
    "\n",
    "receptor_tica_file = \"%s/receptor_tica.h5\" %tica_dir\n",
    "reseeded_dir = \"%s/receptor_reseeded_samples_%dclusters\" %(tica_dir, n_clusters)\n",
    "if not os.path.exists(reseeded_dir):\n",
    "    os.makedirs(reseeded_dir)\n",
    "verbosedump(receptor_tica, receptor_tica_file)\n",
    "\n",
    "cluster_minikmeans(tica_dir, receptor_tica_file, traj_dir, n_clusters=300, clusterer_dir=receptor_clusterer_file)\n",
    "\n",
    "\n",
    "reseed_from_clusterer(receptor_clusterer_file, \"receptor\", reseeded_dir, receptor_tica_file, receptor_traj_files)\n",
    "\n",
    "\n",
    "samples_dir = \"%s/receptor_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "reseed_dir = \"%s/receptor_clusterer_%dclusters_%dsamples_samples_kdtree_reseed\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/receptor_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "if not os.path.exists(reseed_dir): os.makedirs(reseed_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(receptor_clusterer_file, receptor_tica_file, receptor_traj_files, \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"NON\", reseed_dir = reseed_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_tica.h5\"... (<type 'list'>)\n",
      "Clustering by KMeans\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_tica.h5\"...\n",
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer300\"... (<class 'msmbuilder.cluster.MiniBatchKMeans'>)\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer300\"...\n",
      "300\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer300\"...\n",
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      "[116, 4, 12, 24, 26, 32, 42, 48, 49, 55, 57, 59, 67, 76, 77, 82]\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_tica.h5\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer300\"...\n",
      "[[-0.08388811  1.39839214 -0.81482664 ...,  3.94649578  2.09372411\n",
      "   1.88673002]\n",
      " [-0.14405402  1.6224191   0.30289927 ...,  1.85772277  2.15875505\n",
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      " [-0.29141272  1.32843617 -0.66256532 ...,  2.61257508  1.69831735\n",
      "   0.7217179 ]\n",
      " ..., \n",
      " [-0.38269447  1.23571895 -0.17701688 ...,  2.4978833   2.66486975\n",
      "   1.37511035]\n",
      " [-0.17443953  1.51026076  0.16504412 ...,  2.15967658  2.390254\n",
      "   0.95708188]\n",
      " [-0.37103353  1.17167345 -0.55964812 ...,  2.3092833   1.64998335\n",
      "   0.87842459]]\n",
      "Printed all tICA coords and all requested clusters\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_tica.h5\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer300\"...\n",
      "Looking at cluster 4\n",
      "Snapshot in: (5, 109)\n",
      "Looking at cluster 12\n",
      "Snapshot in: (5, 42)\n",
      "Looking at cluster 24\n",
      "Snapshot in: (3, 72)\n",
      "Looking at cluster 26\n",
      "Snapshot in: (1, 95)\n",
      "Looking at cluster 32\n",
      "Snapshot in: (1, 62)\n",
      "Looking at cluster 42\n",
      "Snapshot in: (6, 1)\n",
      "Looking at cluster 48\n",
      "Snapshot in: (8, 0)\n",
      "Looking at cluster 49\n",
      "Snapshot in: (0, 323)\n",
      "Looking at cluster 55\n",
      "Snapshot in: (2, 19)\n",
      "Looking at cluster 57\n",
      "Snapshot in: (5, 136)\n",
      "Looking at cluster 59\n",
      "Snapshot in: (5, 20)\n",
      "Looking at cluster 67\n",
      "Snapshot in: (6, 33)\n",
      "Looking at cluster 76\n",
      "Snapshot in: (5, 53)\n",
      "Looking at cluster 77\n",
      "Snapshot in: (7, 28)\n",
      "Looking at cluster 82\n",
      "Snapshot in: (2, 145)\n",
      "Looking at cluster 116\n",
      "Snapshot in: (0, 28)\n",
      "/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer_300clusters_1samples_samples_kdtree\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer300\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_tica.h5\"...\n",
      "loading \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer300\"...\n",
      "[[  1  88]\n",
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      " [  2   6]]\n",
      "300\n",
      "Saving \"/home/enf/md_simulations/B1AR/sparse-tICA_t50_n_components10all_residues_5f8u_hom_under_cutoff6A-CA_regularization_wolf_autoShrinkage0pt01/gp_clusterer_300clusters_1samples_samples_kdtree_indices.h5\"... (<type 'numpy.ndarray'>)\n"
     ]
    }
   ],
   "source": [
    "gp_tica = [tica_coords[i] for i in gp_trajs]\n",
    "\n",
    "gp_clusterer_file = \"%s/gp_clusterer%d\" %(tica_dir, n_clusters)\n",
    "\n",
    "gp_tica_file = \"%s/gp_tica.h5\" %tica_dir\n",
    "reseeded_dir = \"%s/gp_reseeded_samples_%dclusters\" %(tica_dir, n_clusters)\n",
    "if not os.path.exists(reseeded_dir):\n",
    "    os.makedirs(reseeded_dir)\n",
    "verbosedump(gp_tica, gp_tica_file)\n",
    "\n",
    "cluster_minikmeans(tica_dir, gp_tica_file, traj_dir, n_clusters=300, clusterer_dir=gp_clusterer_file)\n",
    "\n",
    "\n",
    "reseed_from_clusterer(gp_clusterer_file, \"gp\", reseeded_dir, gp_tica_file, gp_traj_files)\n",
    "\n",
    "\n",
    "samples_dir = \"%s/gp_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "reseed_dir = \"%s/gp_clusterer_%dclusters_%dsamples_samples_kdtree_reseed\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/gp_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "if not os.path.exists(reseed_dir): os.makedirs(reseed_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(gp_clusterer_file, gp_tica_file, gp_traj_files, \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"NON\", reseed_dir = reseed_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "43"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(dview)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "\n",
    "n_samples = 1\n",
    "n_clusters = 300\n",
    "\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "featurized_trajectories = [traj_files[i] for i in feature_indices]\n",
    "apo_traj_files = [t for t in featurized_trajectories if \"apo\" in t]\n",
    "reduced_clusterer = verboseload(clusterer300_clusters)\n",
    "apo_reduced_clusterer_file = \"%s/apo_reduced_clusterer.h5\" %tica_dir\n",
    "\n",
    "apo_reduced_tica_file = \"%s/apo_reduced_tica.h5\" %tica_dir\n",
    "apo_reduced_tica = [x[:,range(1,5)] for x in apo_tica]\n",
    "apo_reseeded_dir = \"%s/apo_reseeded_samples\" %tica_dir\n",
    "if not os.path.exists(apo_reseeded_dir):\n",
    "    os.makedirs(apo_reseeded_dir)\n",
    "verbosedump(apo_reduced_tica, apo_reduced_tica_file)\n",
    "\n",
    "apo_reduced_clusters = [reduced_clusterer.labels_[i] for i in apo_trajs]\n",
    "apo_reduced_clusterer = copy.deepcopy(reduced_clusterer)\n",
    "apo_reduced_clusterer.labels_ = apo_reduced_clusters\n",
    "verbosedump(apo_reduced_clusterer, apo_reduced_clusterer_file)\n",
    "#reseed_from_clusterer(apo_reduced_clusterer_file, \"apo\", apo_reseeded_dir, apo_reduced_tica_file, apo_traj_files)\n",
    "\n",
    "\n",
    "samples_dir = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree\" %(tica_dir, n_clusters, n_samples)\n",
    "reseed_dir = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree_reseed\" %(tica_dir, n_clusters, n_samples)\n",
    "samples_indices_file = \"%s/apo_clusterer_%dclusters_%dsamples_samples_kdtree_indices.h5\" %(tica_dir, n_clusters, n_samples)\n",
    "if not os.path.exists(samples_dir): os.makedirs(samples_dir)\n",
    "if not os.path.exists(reseed_dir): os.makedirs(reseed_dir)\n",
    "print(samples_dir)\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)    \n",
    "sample_from_clusterer(apo_reduced_clusterer_file, apo_reduced_tica_file, [traj_files[i] for i in apo_trajs], \n",
    "                      n_samples, samples_dir, samples_indices_file,\n",
    "                      worker_pool=dview, parallel=False, lig_name=\"LIG\", reseed_dir = reseed_dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "import custom_clusterer\n",
    "reload(custom_clusterer)\n",
    "from custom_clusterer import *\n",
    "traj_files = get_trajectory_files(traj_dir, traj_ext)\n",
    "featurized_trajectories = [traj_files[i] for i in feature_indices]\n",
    "oxy_traj_files = [t for t in featurized_trajectories if \"oxy\" in t]\n",
    "reduced_clusterer = verboseload(clusterer300_clusters)\n",
    "oxy_reduced_clusterer_file = \"%s/oxy_reduced_clusterer.h5\" %tica_dir\n",
    "\n",
    "oxy_reduced_tica_file = \"%s/oxy_reduced_tica.h5\" %tica_dir\n",
    "oxy_reduced_tica = [x[:,range(1,10)] for x in oxy_tica]\n",
    "verbosedump(oxy_reduced_tica, oxy_reduced_tica_file)\n",
    "\n",
    "oxy_reduced_clusters = [reduced_clusterer.labels_[i] for i in oxy_trajs]\n",
    "oxy_reduced_clusterer = copy.deepcopy(reduced_clusterer)\n",
    "oxy_reduced_clusterer.labels_ = oxy_reduced_clusters\n",
    "verbosedump(oxy_reduced_clusterer, oxy_reduced_clusterer_file)\n",
    "reseed_from_clusterer(oxy_reduced_clusterer_file, \"oxy\", tica_dir, oxy_reduced_tica_file, oxy_traj_files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "closest_indices = find_closest_indices_to_cluster_center(tics_1_3_file, clusterer16_clusters)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "closest_indices"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from scipy.stats import gamma \n",
    "x = np.linspace(0.,16.0, 100)\n",
    "y = gamma.pdf(x, 5.0, loc=8.0, scale=1)\n",
    "plt.plot(x,y)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from scipy.stats import gamma \n",
    "x = np.linspace(0.,16.0, 100)\n",
    "y = gamma.pdf(x, 3.0, loc=8.0, scale=0.4)\n",
    "plt.plot(x,y)\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "reseed_from_clusterer(oxy_clusterer_file, \"oxy\", tica_dir, oxy_tica_file, [trajs[i] for i in oxy_trajs])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "min_pop = [3, 4, 6, 8, 9, 26, 29, 30, 31, 32, 33, 39, 41, 43, 52, 55]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "plot_all_tics_and_clusters(tica_dir, oxy_tica_file, oxy_clusterer_file, lag_time, tic_range=range(0,5), main = \"Oxy_Reseeds\", label = \"cluster_id\", active_cluster_ids = min_pop, intermediate_cluster_ids = [], inactive_cluster_ids = [], concatenate=True, axes=tica_axes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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