Docking Module

This is a simple module for performing docking tasks. The goal is to provide a common system for naming files, folders and make parallelizing docking tasks on sherlock easy. This can work as an independent module for many different projects.

TODO: rewrite job submission to use job arrays TODO: write tests for protein and ligand prep steps TODO: bundle prep steps into in a single job

Install

git clone https://github.com/lxpowers33/docking.git
cd docking
python3 setup.py install

Testing

Setup Schrodinger Python3

ml load chemistry
ml load schrodinger

In the top level of this module directory, run unit testing

$SCHRODINGER/run python3 -m unittest docking/test/unit_test/*.py

Run functional testing (only on Sherlock)

$SCHRODINGER/run python3 -m unittest docking/test/functional_test/*.py

After functional tests run, you can see example docking output in testrun1 and testrun2 folders.

API and Example Usage

Provide only list of file names and paths, using methods in Docking_Set class. Example usage to perform docking and calculate rmsds: Docking example:

#this would be a file called dock_all.py
#run with $SCHRODINGER/run python3 dock_all.py

#import this docking module
import sys
sys.path.insert(0, '<path>/docking')
from docking.docking_class import Docking_Set, Docking

docking_config = [{'folder':'absolute/path/lig1_to_struc1',
                   'name':'lig1_to_struc1',
                   'grid_file':'absolute/path/gridname_struc1.zip',
                   'prepped_ligand_file': 'absolute/path/ligname1.mae',
                   'glide_settings': {'num_poses': 20}},
                  {'folder': 'absolute/path/test_docking2',
                   'name': 'lig2_to_struc1',
                   'grid_file': 'absolute/path/gridname_struc1.zip',
                   'prepped_ligand_file': 'absolute/path/ligname2.mae',
                   'glide_settings': {'num_poses': 20}}
                  ]
run_config = {'run_folder':'absolute/path/run',
             'group_size':5,
             'partition':'rondror',
             'dry_run':False}
             
dock_set = Docking_Set()
dock_set.run_docking_set(docking_config, run_config)
#wait until docking is done to perform rmsd calculations
for i in range(1,15):
    done_list, log_list = dock_set.check_docking_set_done(docking_config)
    if (all(done_list)):
        print("Docking Completed")
        dock_set.run_rmsd_set(docking_config, run_config)
print("Docking did not complete in 15 minutes - possible error")

There is also a module for prepping proteins and ligands to use as docking inputs.
See tests and comments for further details.

sys.path.insert(0, '<path>/docking')

from docking.prep_class import Prep_Protein_Set

run_config = {'run_folder': 'prep_run',
    'partition': 'rondror',
    'group_size': 1,
    'dry_run':False }

for s in ['CLC2_5TQQ_model', 'CLC2_5TR1_model', 'state_C_o', 'state_C_oi', 'state_O', 'state_U']:
    target_folder = base + '/' + s
    raw_protein_file = working +'/structures/'+s+'.pdb'
    raw_ligand_file = working +'/structures/MCFA_5TR1.pdb'
    prep_set_info.append(
            {'raw_protein_file': raw_protein_file,
      'raw_ligand_file': raw_ligand_file,
      'save_folder': target_folder,
      'name': s})

step = sys.argv[1]
Prepper = Prep_Protein_Set()
if step == '1':
        Prepper.run_prep_wizard_set(prep_set_info, run_config)
if step == '3':
        Prepper.run_split_prepped_set(prep_set_info)
if step == '4':
        Prepper.run_build_grids(prep_set_info, run_config)
if step == 'r':
        Prepper.report(prep_set_info)