Added score_only option.

src/metal_dock/docking.py

@@ -64,11 +64,12 @@ def run(self):
         os.chdir(dock_dir_path)
         self._run_autogrid(autogrid_logfile, gpf_path)
         self._run_autodock(autodock_logfile, dpf_path)
-        self._write_conformations(dlg_path, dock_dir_path)
-        # self._adding_and_optimizing_hydrogens()
-        self._clean_dummy_atoms()
-        self._write_pdbqt_to_xyz()
-        self._write_pose_to_pdb()
+        if not self.par.score_only:
+            self._write_conformations(dlg_path, dock_dir_path)
+            # self._adding_and_optimizing_hydrogens()
+            self._clean_dummy_atoms()
+            self._write_pdbqt_to_xyz()
+            self._write_pose_to_pdb()
 
     def _write_pdbqt_to_xyz(self):
         """
@@ -121,18 +122,22 @@ def analyze_results(self):
         self.logger.info('Ligand Efficiency = (binding energy) / (number of heavy atoms in metal complex)')
         self.logger.info('Interacting Residues = residues within 4 Angstrom of the metal complex\n')
 
-        for i in range(self.par.num_poses):
-            self.logger.info(f"Pose {i+1}:")
-            self.logger.info("-------------")
-            pose_path = self.par.output_dir / 'results' / f'pose_{i+1}' / f'{self.par.name_ligand}_{i+1}.xyz'
-            pdb_path = self.par.output_dir / 'results' / f'clean_{self.par.name_protein}.pdb'
-            pose_residues = self._extract_interacting_residues(pose_path, pdb_path)
-            self.logger.info(f'Binding Energy: {binding_energies[i]:7.4f} kcal/mol')
-            self.logger.info(f'Ligand Efficiency: {binding_efficiencies[i]:7.4f} kcal/mol')
-            self.logger.info(f'Interacting Residues:')
-            for residue in pose_residues:
-                self.logger.info(f'Residue: {residue[0]}, ID: {residue[1]:>3}')
+        if self.par.score_only:
+            self.logger.info(f'Binding Energy: {binding_energies[0]:7.4f} kcal/mol')
             self.logger.info('\n')
+        else:
+            for i in range(self.par.num_poses):
+                self.logger.info(f"Pose {i+1}:")
+                self.logger.info("-------------")
+                pose_path = self.par.output_dir / 'results' / f'pose_{i+1}' / f'{self.par.name_ligand}_{i+1}.xyz'
+                pdb_path = self.par.output_dir / 'results' / f'clean_{self.par.name_protein}.pdb'
+                pose_residues = self._extract_interacting_residues(pose_path, pdb_path)
+                self.logger.info(f'Binding Energy: {binding_energies[i]:7.4f} kcal/mol')
+                self.logger.info(f'Ligand Efficiency: {binding_efficiencies[i]:7.4f} kcal/mol')
+                self.logger.info(f'Interacting Residues:')
+                for residue in pose_residues:
+                    self.logger.info(f'Residue: {residue[0]}, ID: {residue[1]:>3}')
+                self.logger.info('\n')
 
         if self.par.rmsd:
             rmsd_path = self.par.output_dir / 'file_prep' / f'{self.par.name_ligand}_c.xyz'
@@ -435,6 +440,9 @@ def _create_dpf_file(self, dpf_path, gpf_path, parameter_path):
 
             dpf_file.write('# Activate SA\n')
             dpf_file.write('simanneal '+str(self.par.num_poses)+'                         # run this many SA docking\n')
+
+        elif self.par.score_only == True:
+            dpf_file.write('epdb                                # used to calculate the energy of a particular ligand conformation')
 
         dpf_file.write('analysis                             # perforem a ranked cluster analysis\n')
 

src/metal_dock/main.py

@@ -19,6 +19,7 @@ def docking(par: DockParser):
         par (DockParser): The parser object.
     """
     input_dir = Path.cwd()
+    par.input_dir = input_dir
     par.output_dir = input_dir / 'output'
     #=== OUTPUT DIRECTORY ===#
     par.output_dir.mkdir(exist_ok=True)

src/metal_dock/metal_complex.py

@@ -38,7 +38,10 @@ def create_mol_graph(self,
             run_type (str): The type of run.
         """
         mg = MolGraph()
-        mg.read_xyz(self.par.output_dir / 'QM' / run_type / 'output.xyz')
+        if self.par.score_only:
+            mg.read_xyz(self.par.input_dir / f'{self.par.name_ligand}.xyz')
+        else:
+            mg.read_xyz(self.par.output_dir / 'QM' / run_type / 'output.xyz')
         self.graph = to_networkx_graph(mg)
 
     def add_charges_to_graph(self):

src/metal_dock/parser_metal_dock.py

@@ -55,7 +55,8 @@
     'temp_reduction_factor': 0.90,
     'number_of_runs': 50,
     'max_cycles': 50,
-    'mc_steps': 250
+    'mc_steps': 250,
+    'score_only': False
 }
 
              #         e_NA, e_OA, e_SA,  e_HD,
@@ -154,8 +155,12 @@ def _validate_docking_algorithm(self):
         if self.sa_dock:
             self.dock_algorithm = [self.temp_reduction_factor, self.number_of_runs, self.max_cycles]
 
-        if not self.ga_dock and not self.sa_dock:
-            self.logger.info('At least ga_dock or sa_dock must be set to True for MetalDock to run properly')
+        if self.score_only and (self.ga_dock or self.sa_dock):
+            self.logger.info('ga_dock and/or sa_dock must be set to False when performing score_only')
+            sys.exit()
+
+        if not self.ga_dock and not self.sa_dock and not self.score_only:
+            self.logger.info('At least ga_dock or sa_dock or score_only must be set to True for MetalDock to run properly')
             sys.exit()
 
 
@@ -285,6 +290,8 @@ def _initialize_parameters(self):
         self.number_of_runs = self.get_config_value('DOCKING', 'number_of_runs', STANDARD_DEFAULTS['number_of_runs'], int)
         self.max_cycles = self.get_config_value('DOCKING', 'max_cycles', STANDARD_DEFAULTS['max_cycles'], int)
 
+        self.score_only = self.get_config_value('DOCKING', 'score_only', STANDARD_DEFAULTS['score_only'], bool)
+
         self._validate_docking_algorithm()
 
         # heavy atoms