Merge pull request #205 from jvalegre/jv_branch

1. Hotfix remove dbstep default
jvalegre · Jul 30, 2024 · 0ff76c0 · 0ff76c0
2 parents 1163fe1 + a84765d
commit 0ff76c0
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Showing 3 changed files with 4 additions and 13 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -45,12 +45,11 @@ jobs:
           # install OpenBabel
           conda install -y -c conda-forge openbabel=3.1.1
           # install dependencies
-          conda install -y -c conda-forge xtb
-          conda install -y -c conda-forge crest
+          conda install -y -c conda-forge xtb=6.6.1
+          conda install -y -c conda-forge crest=2.12
           pip install ase
           conda install pytorch torchvision torchaudio cpuonly -c pytorch
           pip install torchani==2.2.3
-          pip install dbstep
           # install the dependencies of AQME with pip
           pip install .
           # install and run pytest

diff --git a/aqme/qdescp.py b/aqme/qdescp.py
@@ -102,7 +102,6 @@
 from rdkit import Chem
 from rdkit.Chem import rdFMCS
 from pathlib import Path
-import dbstep.Dbstep as db
 from aqme.utils import (
     load_variables,
     read_xyz_charge_mult,
@@ -800,6 +799,7 @@ def collect_xtb_properties(self,name_initial,atom_props,update_atom_props,smarts
 
                         # calculate DBSTEP descriptors
                         if self.args.dbstep_calc:
+                            import dbstep.Dbstep as db
                             self.args.log.write(f"\no   Running DBSTEP and collecting properties")
 
                             # calculates buried volume to the type of atom selected

diff --git a/tests/test_qdescp.py b/tests/test_qdescp.py
@@ -87,7 +87,7 @@ def test_qdescp_xtb(file):
     ]
 
     if file == 'test_atom.csv':
-        cmd_qdescp = cmd_qdescp + ["--qdescp_atoms", "[P]", "--dbstep_calc"]
+        cmd_qdescp = cmd_qdescp + ["--qdescp_atoms", "[P]"]
 
     if file == "test_idx.csv":
         cmd_qdescp = cmd_qdescp + ["--qdescp_atoms", "[1]"]
@@ -171,23 +171,17 @@ def test_qdescp_xtb(file):
         assert round(Fermi_lvl_boltz_calc,2) == round(Fermi_lvl_boltz_csv,2)
         assert pd_boltz["NumRotatableBonds"][0] == 3
         assert pd_boltz["NumRotatableBonds"][1] == 4
-        assert 'DBSTEP_Vbur' not in pd_boltz
 
     elif file in ['test_atom.csv','test_group.csv','test_multigroup.csv','test_robert.csv']:
         pd_boltz = pd.read_csv(file_descriptors)
 
         # mol_1 is methane and it doesn't have any P/O atoms or CC/C=O groups so the boltz json file shouldn't appear
         assert os.path.exists(f'{folder_qdescp}/mol_1_rdkit_conf_1.json')
         assert not os.path.exists(f'{folder_boltz}/mol_1_rdkit_boltz.json')
-        assert 'DBSTEP_Vbur' not in pd_boltz
         assert len(pd_boltz["NumRotatableBonds"]) == 3
 
         # check variables and X_ prefixes in variable names
         if file in ['test_atom.csv','test_multigroup.csv','test_robert.csv']:
-            if file == 'test_atom.csv':
-                assert 'P_DBSTEP_Vbur' in pd_boltz
-            else:
-                assert 'P_DBSTEP_Vbur' not in pd_boltz
             assert 'P_FUKUI+' in pd_boltz
 
             if file == 'test_atom.csv':
@@ -197,8 +191,6 @@ def test_qdescp_xtb(file):
                 assert 'Name' not in pd_boltz
 
         elif file == 'test_group.csv':
-            assert 'C=O_C_DBSTEP_Vbur' not in pd_boltz
-            assert 'C=O_O_DBSTEP_Vbur' not in pd_boltz
             assert 'C=O_C_FUKUI+' in pd_boltz
             assert 'C=O_O_FUKUI+' in pd_boltz