[bugfix] escape some pyright warnings and fix ad4 option parsing in a…

…utogrid runner
dptech-corp · Apr 8, 2024 · 089cc4f · 089cc4f
1 parent 183dbd8
commit 089cc4f
Show file tree

Hide file tree

Showing 7 changed files with 11 additions and 123 deletions.
diff --git a/unidock_tools/src/unidock_tools/data/__init__.py b/unidock_tools/src/unidock_tools/data/__init__.py
diff --git a/unidock_tools/src/unidock_tools/data/docking/AD4.1_bound.dat b/unidock_tools/src/unidock_tools/data/docking/AD4.1_bound.dat
diff --git a/unidock_tools/src/unidock_tools/data/docking/__init__.py b/unidock_tools/src/unidock_tools/data/docking/__init__.py
diff --git a/...ls/src/unidock_tools/modules/protein_prep/receptor_standardization/receptor_pdb_reader.py b/...ls/src/unidock_tools/modules/protein_prep/receptor_standardization/receptor_pdb_reader.py
@@ -119,6 +119,10 @@ def __prepare_protein_pdb_file__(self):
         protein_cleaned_ag = protein_cleaned_universe.atoms
         residue_group = protein_cleaned_ag.residues
 
+        ########################################
+        ## to get rid of annoying test warnings
+        current_segid = 'A'
+        ########################################
         for current_residue_idx, current_residue in enumerate(residue_group):
             prepared_resid = current_residue.resid
             for segment_idx, segment_resid_list in enumerate(segment_resid_nested_list):

diff --git a/unidock_tools/src/unidock_tools/modules/protein_prep/receptor_topology/autogrid_runner.py b/unidock_tools/src/unidock_tools/modules/protein_prep/receptor_topology/autogrid_runner.py
@@ -73,6 +73,7 @@ def run(self):
                                                             num_grid_points=self.num_grid_points,
                                                             grid_spacing=self.grid_spacing,
                                                             covalent_residue_atom_info_list=covalent_residue_atom_info_list,
+                                                            generate_ad4_grids=self.generate_ad4_grids,
                                                             working_dir_name=current_working_dir_name)
 
             docking_grids_generator.generate_docking_grids()

diff --git a/...tools/src/unidock_tools/modules/protein_prep/receptor_topology/docking_grids_generator.py b/...tools/src/unidock_tools/modules/protein_prep/receptor_topology/docking_grids_generator.py
@@ -257,5 +257,7 @@ def generate_docking_grids(self):
             gpf_generator.write_grid_parameter_file()
 
             autogrid_binary_file_name = os.path.join(os.path.dirname(__file__), 'bin', 'autogrid4')
+            autogrid_chmod_command = f'chmod +x {autogrid_binary_file_name}'
             autogrid_command = f'cd {self.working_dir_name}; {autogrid_binary_file_name} -p {os.path.basename(protein_output_gpf_file_name)} -l {os.path.basename(protein_output_glg_file_name)}; cd -'
+            os.system(autogrid_chmod_command)
             os.system(autogrid_command)
diff --git a/...ck_tools/src/unidock_tools/modules/protein_prep/receptor_topology/protein_pdbqt_writer.py b/...ck_tools/src/unidock_tools/modules/protein_prep/receptor_topology/protein_pdbqt_writer.py
@@ -7,14 +7,12 @@
 from unidock_tools.modules.protein_prep.receptor_topology.smarts_definition import HB_DONOR, HB_ACCEPTOR
 from unidock_tools.modules.protein_prep.receptor_topology.amber_atom_types import AMBER_RESIDUE_PARAMETER_DICT
 
-
 class ProteinPDBQTWriter(object):
     def __init__(self,
                  protein_pdb_file_name,
                  working_dir_name='.'):
 
         self.residue_parameter_dict = AMBER_RESIDUE_PARAMETER_DICT
-
         self.protein_pdb_file_name = os.path.abspath(protein_pdb_file_name)
         self.protein_mol, self.protein_residue_mol_list = prepare_protein_residue_mol_list(self.protein_pdb_file_name)
 
@@ -112,6 +110,10 @@ def write_protein_pdbqt_file(self):
         self.pdbqt_atom_line_list = []
         self.pdbqt_atom_line_format = '{:4s}  {:5d} {:^4s} {:3s} {:1s}{:4d}    {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f}    {:6.3f} {:<2s}\n'
 
+        if self.protein_mol.GetNumAtoms() == 0:
+            raise ValueError('Empty protein mol!!')
+
+        atom_idx = 0
         for atom in self.protein_mol.GetAtoms():
             atom_idx = atom.GetIntProp('atom_idx')
             atom_info_tuple = ('ATOM',  # atom record name