Merge pull request #21 from davidkastner/bug-fix

Fixed a number of bugs

pyef/analysis.py

@@ -10,6 +10,7 @@
 import pandas as pd
 import scipy.linalg as la
 from collections import deque
+from importlib import resources
 from distutils.dir_util import copy_tree
 
 class Electrostatics:
@@ -99,7 +100,7 @@ def fix_ECPmolden(self):
 
             with open('final_optim.molden', 'w') as file:
                 file.write(content)
-            print("      > Molden file is fixed")
+            print("      > Molden file is fixed\n")
         os.chdir(owd)
 
     def prepData(self):
@@ -713,24 +714,29 @@ def getESPData(self, charge_types, ESPdata_filename):
                         [sorted_distances, sorted_esps, cum_esps] = Electrostatics.esp_bydistance(atom_idx, full_file_path)
                         ESP_fcoord = self.esp_first_coord(atom_idx, full_file_path, path_to_xyz)
                         ESP_scoord = self.esp_second_coord(atom_idx, full_file_path, path_to_xyz)
+
                     except Exception as e:
                         print('The Exception is: ' + str(e))
                         print(traceback.format_exc())
                         print('Error when trying to access electrostatic information: Attemtping to re-compute partial charges of type: ' + str(key))
+
                         # Re-run multiwfn computation of partial charge 
                         proc = subprocess.Popen(command_A, stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
                         calc_command = self.dict_of_calcs[key]
                         commands = ['7', calc_command, '1', 'y', '0', 'q'] # for atomic charge type corresponding to dict key
+
                         if key == 'CHELPG':
                             commands = ['7', calc_command, '1','\n', 'y', '0', 'q']
                         output = proc.communicate("\n".join(commands).encode())
                         new_name = 'final_optim_' +key+'.txt'
                         os.rename('final_optim.chg', new_name)
+
                         if self.inGaCageBool:                        
                             # With newly analyzed partial charges, re-compute ESP data
                             [ESP_all, ESP_just_ligand, ESP_just_cage, atom_type] = Electrostatics.ESP_all_calcs(full_file_path, atom_idx, self.inGaCageBool)
                         else:
                             [ESP_all, atom_type] = Electrostatics.ESP_all_calcs(full_file_path, atom_idx, self.inGaCageBool)
+
                         [total_charge,partial_charge_atom] = Electrostatics.charge_atom(full_file_path, atom_idx)
                         [sorted_distances, sorted_esps, cum_esps] = Electrostatics.esp_bydistance(atom_idx, full_file_path)
                         ESP_fcoord = self.esp_first_coord(atom_idx, full_file_path, path_to_xyz)
@@ -770,6 +776,7 @@ def getESPData(self, charge_types, ESPdata_filename):
 
     # input_bond_indices is a list of a list of tuples
     def getEFieldData(self, Efield_data_filename, input_bond_indices=[]):
+
         metal_idxs = self.lst_of_tmcm_idx
         folder_to_molden = self.folder_to_file_path
         list_of_file = self.lst_of_folders
@@ -784,30 +791,39 @@ def getEFieldData(self, Efield_data_filename, input_bond_indices=[]):
             bool_manual_mode = True
 
         for f in list_of_file:
+            load_multiwfn = "module load multiwfn/noGUI"
             atom_idx = metal_idxs[counter] 
             os.chdir(owd)
             os.chdir(f + folder_to_molden)
-            subprocess.call("module load multiwfn/noGUI", shell=True)
-            # First For this to work, the .molden file should be named: f.molden
+            subprocess.call(load_multiwfn, shell=True)
 
-            command_A = '/opt/Multiwfn_3.7_bin_Linux_noGUI/Multiwfn '+ 'final_optim.molden'
-            results_dir = os.getcwd() + '/'
+            # First For this to work, the .molden file should be named: f.molden
             results_dict = {}
             results_dict['Name'] = f
-            Command_Polarization = '/opt/Multiwfn_3.7_bin_Linux_noGUI/Multiwfn '+ 'final_optim.molden >' +  'final_optim_polarization.txt'
+            multiwfn_path = "/opt/Multiwfn_3.7_bin_Linux_noGUI/Multiwfn"
+            molden_filename = "final_optim.molden"
+            final_structure_file = "final_optim.xyz"
+            polarization_file = "final_optim_polarization.txt"
+
+            # Dynamically get path to package settings.ini file
+            with resources.path('pyef.resources', 'settings.ini') as ini_path:
+                path_to_ini_file = str(ini_path)
+                Command_Polarization = f"{multiwfn_path} {molden_filename} -set {path_to_ini_file} > {polarization_file}"
 
             # Check if the atomic polarizations have been computed
-            path_to_pol = os.getcwd() + '/' + 'final_optim_polarization.txt'
-            xyz_file_path =  os.getcwd() + '/' 'final_optim.xyz'
-            print('Attempting this path to the polarization file')
+            path_to_pol = os.path.join(os.getcwd(), polarization_file)
+            xyz_file_path = os.path.join(os.getcwd(), final_structure_file)
+            print(f"Attempting polarization file path: {path_to_pol}")
+
             if os.path.exists(path_to_pol):
-                print('   > Polarization file: ' + f + "!!")
+                print(f"   > Polarization file: {f}!!")
             else:
                 print('Starting to run polarization calculation!')
                 # Now Run the calculation for atomic dipole and quadrupole moment
+                print(f"   > Submitting Multiwfn job using: {Command_Polarization}")
                 proc = subprocess.Popen(Command_Polarization, stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True)
-                polarization_commands = ['15', '-1', '3', '2', '0', 'q'] # for atomic dipole and quadrupole moment of Hirshfeld-I type
-                output = proc.communicate("\n".join(polarization_commands).encode())
+                polarization_commands = ['15', '-1', '3', '2', '0', 'q'] # For atomic dipole and quadrupole moment of Hirshfeld-I type
+                proc.communicate("\n".join(polarization_commands).encode())
 
             try:
                 # If bond_indices is longer then one, default to manually entry mode
@@ -817,20 +833,23 @@ def getEFieldData(self, Efield_data_filename, input_bond_indices=[]):
                 # Otherwise, automatically sense atoms bonded to metal and output E-fields of those
                 else:
                     [proj_Efields, bondedAs, bonded_idx, bond_lens] = self.E_proj_first_coord(atom_idx,xyz_file_path, path_to_pol)
+
                 results_dict['Max Eproj'] = max(abs(np.array(proj_Efields)))
                 results_dict['Projected_Efields V/Angstrom'] = proj_Efields
                 results_dict['Bonded Atoms'] = bondedAs
                 results_dict['Bonded Indices'] = bonded_idx
                 results_dict['Bond Lengths']= bond_lens
+
             except Exception as e:
                 print(repr(e))
 
             counter = counter + 1
 
             # Probably want to add other bonds to this list!
             allspeciesdict.append(results_dict)
+
         os.chdir(owd)
         df = pd.DataFrame(allspeciesdict)
-        df.to_csv(Efield_data_filename +'.csv')
+        df.to_csv(f"{Efield_data_filename}.csv")
 
 

pyef/cli.py

@@ -1,5 +1,6 @@
 """Command-line interface (CLI) entry point"""
 
+import os
 import pyef
 import click
 
@@ -22,9 +23,10 @@ def welcome():
     print("Default programmed actions for the pyEF package.")
     print("GitHub: https://github.com/davidkastner/pyef")
     print("Documentation: https://pyef.readthedocs.io")
-    print("• Command for electric field analysis: pyef ef --run")
-    print("• Command for electrostatic analysis: pyef esp --run")
-    print("• Example annotated job file: github.com/davidkastner/pyEF/tree/main/demo/jobs.in\n")
+    print("• Command for electric field analysis: pyef ef -i path/to/jobs.in")
+    print("• Command for electrostatic analysis: pyef esp -i path/to/jobs.in")
+    print("• Example annotated job file: github.com/davidkastner/pyEF/tree/main/demo/jobs.in")
+    print("• Update the settings.ini file in pyef.resources, especially the `nthreads` variable\n")
 
 # Welcome even if no flags
 welcome()
@@ -35,41 +37,35 @@ def cli():
     pass
 
 @cli.command()
-@click.option("--run", is_flag=True, help="Analyze electric fields.")
-def ef(run):
+@click.option("-i", "--input", "job_path", required=True, type=str, help="Path to pyEF job file.")
+def ef(job_path):
     """Analyzes electric fields"""
-    click.echo("Calculate the projected electric field.")
-    if run:
-        click.echo("Importing dependencies...")
-        from pyef.run import main
-        from pyef.manage import parse_job_batch_file
+    click.echo("Importing dependencies...")
+    from pyef.run import main
+    from pyef.manage import parse_job_batch_file
 
-        geom_flag = False   # Perform a geometry check
-        esp_flag = False    # Perform analysis of electrostatics
+    geom_flag = False   # Perform a geometry check
+    esp_flag = False    # Perform analysis of electrostatics
 
-        job_path = input("   > Path to pyEF job file: ")
-        jobs, metal_indices, bond_indices = parse_job_batch_file(job_path)
-
-        pyef.run.main(jobs, metal_indices, bond_indices, geom_flag, esp_flag)
+    # Now using the job_path provided by the -i option
+    jobs, metal_indices, bond_indices = parse_job_batch_file(job_path)
+    job_name = os.path.splitext(job_path)[0]
+    pyef.run.main(job_name, jobs, metal_indices, bond_indices, geom_flag, esp_flag)
 
 # THE ESP SECTION IS UNDERCONSTRUCTION AND MAY NOT WORK        
 @cli.command()
-@click.option("--run", is_flag=True, help="Perform an action")
-def esp(run):
+@click.option("-i", "--input", "job_path", required=True, type=str, help="Path to pyEF job file.")
+def esp(job_path):
     """Analyzes electrostatic potential"""
     click.echo("Performing electrostatic analysis.")
-    if run:
-        click.echo("Importing dependencies...")
-        from pyef.run import main
+    from pyef.run import main
+    from pyef.manage import parse_job_batch_file
 
-        geom_flag = False   # Perform a geometry check
-        esp_flag = True     # Perform analysis of electrostatics
+    geom_flag = False   # Perform a geometry check
+    esp_flag = True     # Perform analysis of electrostatics
 
-        job_paths = input("   > Paths to jobs separated by commas: ")
-        jobs = [job.strip() for job in job_paths.split(",")]
-        metal_indices = input("   > Indices of your metals, separated by commas: ")
-        metal_indices = [int(metal.strip()) for metal in metal_indices.split(",")]
-        pyef.run.main(jobs, geom_flag, esp_flag, metal_indices)
+    jobs, metal_indices, bond_indices = parse_job_batch_file(job_path)
+    pyef.run.main(jobs, geom_flag, esp_flag, metal_indices)
 
 
 if __name__ == '__main__':

pyef/manage.py

@@ -26,15 +26,16 @@ def parse_job_batch_file(file_path):
 
     with open(file_path, 'r') as file:
         for line in file:
-            # Skip empty lines and lines starting with '#'
+            # Skip empty lines and comments '#'
             if line.strip() == '' or line.strip().startswith('#'):
                 continue
 
-            columns = line.strip().split(',')
+            columns = [col.strip() for col in line.strip().split(',')]
             # Extracting and appending data to respective lists
             jobs.append(columns[0])
             metal_index = int(columns[1])
+            bonded_atom_index = int(columns[2])
             metal_indices.append(metal_index)
-            column_pairs.append((metal_index, columns[2]))
+            column_pairs.append([(metal_index, bonded_atom_index)])
 
     return jobs, metal_indices, column_pairs