More files related to the energy calculations added to the repo.

Author: kumaranu

README.txt

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+-------------------------------------- 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.
+__________________________________________________________________________________________________________
+

energy_protein/protein.py

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+import os, glob, sys
+from rdkit import Chem
+from multiprocessing import Pool
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import numpy as np
+
+enzymeFile = '../3sxr_dasatinib_removed.pdb'
+m = Chem.rdmolfiles.MolFromPDBFile(enzymeFile)
+m = Chem.AddHs(m, addCoords=True)
+res = AllChem.MMFFOptimizeMoleculeConfs(m, maxIters=0, numThreads=0)
+np.savetxt('energies.txt', [res[0][1]])
+
+

energy_protein/run.slurm

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+#!/bin/bash
+#####  Constructed by HPC everywhere #####
+#SBATCH --mail-user=kumaranu@iu.edu
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=48
+#SBATCH --time=0-3:59:00
+#SBATCH --mem=58gb
+#SBATCH --partition=general
+#SBATCH --mail-type=FAIL,BEGIN,END
+#SBATCH --job-name=my_job
+
+######  Module commands #####
+module unload python
+module load anaconda/python3.8/2020.07
+
+conda activate docking-rdock
+
+######  Job commands go below this line #####
+python protein.py
+

energy_protein/slurm-2397773.out

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+anaconda version 2020.07 loaded.

run_template.slurm

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+#!/bin/bash
+#####  Constructed by HPC everywhere #####
+#SBATCH --mail-user=kumaranu@iu.edu
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=48
+#SBATCH --time=0-3:59:00
+#SBATCH --mem=58gb
+#SBATCH --partition=general
+#SBATCH --mail-type=FAIL,BEGIN,END
+#SBATCH --job-name=XX
+
+######  Module commands #####
+module unload python
+module load anaconda/python3.8/2020.07
+
+conda activate docking-rdock
+
+######  Job commands go below this line #####
+python combine.py XX
+
+