Moved files to the src/MolecularDockingKit folder and corrected the i…

…nformation in the README file.

README.md

@@ -1,3 +1,49 @@
 # MolecularDockingKit
 
 A simple python tool to perform molecular docking computations.
+
+-------------------------------------- Outline of the program ---------------------------------------------
+Main script to run:
+  make.bash
+
+Supplementary scripts:
+  1) main.py
+  2) getSmilesFromFile.py
+  3) xyzFromSmiles.py
+  4) getScores.tcsh
+  5) call_combine.tcsh
+  6) combine.py
+  7) run.slurm inside a directory named energy_protein
+  8) getEnergy.py
+  9) run_template.slurm
+
+Files and directories needed from the user:
+  1) A file named "drugs.txt" which contains the initial data from the website given in the problem.
+  2) A file named "3sxr_dasatinib_removed.pdb" containing the protein without dasatinib. I could have
+     removed this user input but kept it this way.
+  3) A directory named "energy_protein" that contains a slurm script run.py which would submit the job
+     for protein.py such as run.slurm
+  4) A template file named 'prm-template.prm' for the prm input file to be used for docking calculations.
+
+-------------------------------------- Summary of the program ---------------------------------------------
+All of the scripts contain comments to clarify their purpose in the program. A brief summary is provided below:
+1) The bash script main.bash calls main.py.
+   - main.py extracts the smiles formats for the drugs from the file called drugs.txt.
+   - A directory structure is created for the docking calculations which looks like:
+     |---- rDock_inputs/
+     |     |----MoleculeName/
+   - xyz coordinates are generated from the smiles using the script xyzFromSmiles
+   - .prm input files are generated from the prm-template.prm and are stored as moleculeName_rdock.prm as:
+     |---- rDock_inputs/
+     |     |----MoleculeName/
+     |     |    |----moleculeName_rdock.prm 
+2) A 10 runs-per-ligand rDock job is submitted for each drug molecule.
+3) getScores.tcsh is called to extract the scores from the docking output files.
+4) The scores and the molecule names are put in a file and molecule are sorted according to their docking scores. 
+5) A shell script call_combine is called which submits slurm jobs for binding energy calculations.
+6) Energy calculations are submitted for the protein without ligand.
+7) A python script getEnergy.py is called to extract energies and return binding energies in kcal/mol.
+8) Molecules are sorted according to their binding energies to get their ranking.
+__________________________________________________________________________________________________________
+
+

combine.py → src/MolecularDockingKit/combine.py

@@ -44,7 +44,7 @@
 
     #Saving the energies for the (ligand + protein) and the ligand only geometry in a file
     np.savetxt('energies.txt', [res[0][1], res1[0][1]])
-    os.chdir('../')
-os.chdir('../')
+    os.chdir('../../../')
+os.chdir('../../../')
 
 

getEnergy.py → src/MolecularDockingKit/getEnergy.py

@@ -11,10 +11,10 @@
 #######################################################################
 
 
-os.chdir('moleculeLists')
+os.chdir('../../moleculeLists')
 molList = open('fileList.txt', 'r').readlines()
 molList = [mol.strip() for mol in molList]
-os.chdir('../')
+os.chdir('../../../')
 
 e1 = np.loadtxt('energy_protein/energies.txt')
 
@@ -24,9 +24,9 @@
     try:
         eCombined = np.loadtxt('energies.txt')
         print("%s, %3f, %3f, %3f, %3f, %3f" % (mol, eCombined[0], eCombined[1], e1, (eCombined[0] - eCombined[1] - e1), (eCombined[0] - eCombined[1] - e1)*627.503))
-        os.chdir('../') 
+        os.chdir('../../../')
     except:
-        os.chdir('../') 
+        os.chdir('../../../')
         continue
         print(mol, 'skipped due to some error')
-os.chdir('../')
+os.chdir('../../../')

getSmilesFromFile.py → src/MolecularDockingKit/getSmilesFromFile.py

@@ -19,9 +19,9 @@ def getSmilesFromFile(fileName):
 
     #Writing the names of molecules in a file inside a separate directory
     #for future calculations
-    if not os.path.exists('moleculeLists'):
-        os.mkdir('moleculeLists')
-    os.chdir('moleculeLists')
+    if not os.path.exists('../../moleculeLists'):
+        os.mkdir('../../moleculeLists')
+    os.chdir('../../moleculeLists')
     with open("fileList.txt", 'w') as file:
         file.write('\n'.join(molNames))
 

main.py → src/MolecularDockingKit/main.py

@@ -1,8 +1,5 @@
-import getSmilesFromFile
-from rdkit import Chem
-from rdkit.Chem import AllChem
+from src.MolecularDockingKit import getSmilesFromFile, xyzFromSmiles
 import os
-import xyzFromSmiles
 
 ############################################################
 #                                                          #
@@ -20,7 +17,7 @@
 os.chdir('rDock_inputs')
 
 #Loading a prm file template to be edited later for each molecule
-f = open('prm-template.prm', 'r').read()
+f = open('../../prm-template.prm', 'r').read()
 
 for i in range(len(molNames)):
     #Creating a separate directory for each drug's calculation
@@ -38,6 +35,6 @@
     file1.write(f1)
     file1.close() 
 
-    os.chdir('../')
-os.chdir('../')
+    os.chdir('../../../')
+os.chdir('../../../')