From ee7d37701503bbaf37c612d372763f5c676d8129 Mon Sep 17 00:00:00 2001
From: Wei-Tse Hsu <wehs7661@colorado.edu>
Date: Sun, 20 Aug 2023 17:34:25 -0600
Subject: [PATCH] Tweaked analyze_traj.py and clustering.py

---
 ensemble_md/analysis/analyze_traj.py |  4 +-
 ensemble_md/analysis/clustering.py   | 72 ++++++++++++++--------------
 2 files changed, 39 insertions(+), 37 deletions(-)

diff --git a/ensemble_md/analysis/analyze_traj.py b/ensemble_md/analysis/analyze_traj.py
index f92331fd..385febf6 100644
--- a/ensemble_md/analysis/analyze_traj.py
+++ b/ensemble_md/analysis/analyze_traj.py
@@ -247,7 +247,9 @@ def stitch_trajs(gmx_executable, files, rep_trajs):
         arguments = [gmx_executable, 'trjcat', '-f']
         arguments.extend(files_sorted[i])
         arguments.extend(['-o', f'traj_{i}.xtc'])
-        utils.run_gmx_cmd(arguments)
+        returncode, stdout, stderr = utils.run_gmx_cmd(arguments)
+        if returncode != 0:
+            print(f'Error with return code: {returncode}):\n{stderr}')
 
 
 def traj2transmtx(traj, N, normalize=True):
diff --git a/ensemble_md/analysis/clustering.py b/ensemble_md/analysis/clustering.py
index 98d456ed..4a2cda2f 100644
--- a/ensemble_md/analysis/clustering.py
+++ b/ensemble_md/analysis/clustering.py
@@ -126,6 +126,42 @@ def cluster_traj(gmx_executable, inputs, grps, method='linkage', cutoff=0.1, suf
         print(f'Inter-medoid RMSD between the two biggest clusters: {rmsd:.3f} nm')
 
 
+def get_cluster_info(cluster_log):
+    """
+    Gets the metadata of the LOG file generated by the GROMACS :code:`gmx cluster` command.
+
+    Parameters
+    ----------
+    cluster_log : str
+        The LOG file generated by the GROMACS :code:`gmx cluster` command.
+
+    Returns
+    -------
+    rmsd_range: list
+        The range of RMSD values
+    rmsd_avg: float
+        The average RMSD value.
+    n_clusters : int
+        The number of clusters.
+    """
+    f = open(cluster_log, 'r')
+    lines = f.readlines()
+    f.close()
+
+    rmsd_range = []
+    for line in lines:
+        if 'The RMSD ranges from' in line:
+            rmsd_range.append(float(line.split('from')[-1].split('to')[0]))
+            rmsd_range.append(float(line.split('from')[-1].split('to')[-1].split('nm')[0]))
+        if 'Average RMSD' in line:
+            rmsd_avg = float(line.split('is')[-1])
+        if 'Found' in line:
+            n_clusters = int(line.split()[1])
+            break
+
+    return rmsd_range, rmsd_avg, n_clusters
+
+
 def get_cluster_members(cluster_log):
     """
     Gets the members of each cluster from the LOG file generated by the GROMACS :code:`gmx cluster` command.
@@ -208,39 +244,3 @@ def count_transitions(clusters):
             t_transitions.append(member[0])
 
     return n_transitions, t_transitions
-
-
-def get_cluster_info(cluster_log):
-    """
-    Gets the metadata of the LOG file generated by the GROMACS :code:`gmx cluster` command.
-
-    Parameters
-    ----------
-    cluster_log : str
-        The LOG file generated by the GROMACS :code:`gmx cluster` command.
-
-    Returns
-    -------
-    rmsd_range: list
-        The range of RMSD values
-    rmsd_avg: float
-        The average RMSD value.
-    n_clusters : int
-        The number of clusters.
-    """
-    f = open(cluster_log, 'r')
-    lines = f.readlines()
-    f.close()
-
-    rmsd_range = []
-    for line in lines:
-        if 'The RMSD ranges from' in line:
-            rmsd_range.append(float(line.split('from')[-1].split('to')[0]))
-            rmsd_range.append(float(line.split('from')[-1].split('to')[-1].split('nm')[0]))
-        if 'Average RMSD' in line:
-            rmsd_avg = float(line.split('is')[-1])
-        if 'Found' in line:
-            n_clusters = int(line.split()[1])
-            break
-
-    return rmsd_range, rmsd_avg, n_clusters