Source code for OCDockerConsole

#!/usr/bin/env python3

# Description
###############################################################################
'''
This script is used for fast import of all funcionalities in the OCDocker suite
making easier to debug and possibly allowing a future OCDocker console to enable
the user to perform the steps step by step.
'''

# Imports
###############################################################################
import inspect
import os
import shutil

import textwrap as tw

from glob import glob
from pprint import pprint
from typing import Any

import OCDocker.Docking.Gnina as ocgnina
import OCDocker.Docking.PLANTS as ocplants
import OCDocker.Docking.Smina as ocsmina
import OCDocker.Docking.Vina as ocvina
import OCDocker.Error as ocerror
import OCDocker.Ligand as ocl
import OCDocker.Processing.Preprocessing.RmsdClustering as ocrmsdclust
import OCDocker.Receptor as ocr
import OCDocker.Rescoring.ODDT as ocoddt
import OCDocker.Toolbox.Conversion as occonversion
import OCDocker.Toolbox.MoleculeProcessing as ocmolproc
import OCDocker.Toolbox as octools

from OCDocker.Initialise import *

# License
###############################################################################
'''
OCDocker
Authors: Rossi, A.D.; Monachesi, M.C.E.; Spelta, G.I.; Torres, P.H.M.
Federal University of Rio de Janeiro
Carlos Chagas Filho Institute of Biophysics
Laboratory for Molecular Modeling and Dynamics

This program is proprietary software owned by the Federal University of Rio de Janeiro (UFRJ),
developed by Rossi, A.D.; Monachesi, M.C.E.; Spelta, G.I.; Torres, P.H.M., and protected under Brazilian Law No. 9,609/1998.
All rights reserved. Use, reproduction, modification, and distribution are restricted and subject
to formal authorization from UFRJ. See the LICENSE file for details.

Contact: Artur Duque Rossi - arturossi10@gmail.com
'''

# Classes
###############################################################################


# Functions
###############################################################################
## Private ##

## Public ##


[docs]
def clean_test_files(baseProtPath: str, baseLigPath: str, baseDecPath: str, baseCanPath: str) -> None:
    '''Rests the test_files folder to its original state

    Parameters
    ----------
    baseProtPath : str
        Path to the base protein folder
    baseLigPath : str
        Path to the base ligand folder
    baseDecPath : str
        Path to the base decoy folder
    baseCanPath : str
        Path to the base candidates folder
    '''

    # Remove all files in the baseProtPath except the receptor.pdb
    for f in glob(f"{baseProtPath}/*"):
        # If the file is a file and not the receptor.pdb
        if os.path.isfile(f) and not f.endswith(f"{baseProtPath}/receptor.pdb"):
            os.remove(f)

    # For each ligand folder
    for ligFolder in [baseLigPath, baseDecPath, baseCanPath]:
        # Remove all the files inside all ligand folders except for the ligand.smi or ligand.mol2
        for f in glob(f"{ligFolder}/*/*"):
            # If the file is a file and not the ligand.smi
            if os.path.isfile(f) and not f.endswith("ligand.smi"):
                os.remove(f)
            # If the file is a folder and not the boxes folder
            elif os.path.isdir(f) and not f.endswith("boxes"):
                shutil.rmtree(f)

    return None







# The environment variable OCDOCKER_CONFIG must be set to the OCDocker.cfg file before importing OCDocker
cfg_path = os.environ.get('OCDOCKER_CONFIG') or 'OCDocker.cfg'

output_level = ocerror.ReportLevel.NONE

message = tw.dedent(f"""{clrs["y"]}
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{clrs["c"]}
                              CONSOLE MODE{clrs["y"]}
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{clrs["n"]}
          Welcome to the OCDocker interactive console!

      This console allows you to interact with the OCDocker pipeline
      step by step.

      {clrs["g"]}TIP{clrs["n"]} It's an interesting way to learn OCDocker, useful
      for debugging, and great for quick API interaction and
      experimentation.

      To check the args variable use print_args() function.{clrs["y"]}
      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
{clrs["n"]}""")

print(message)

if __name__ == "__main__":
    # Set the variables based on args
    bootstrap(argument_parsing())
else:
    # CPU cores -2, and 1 if cpu has only one or two cores
    cpu_count = os.cpu_count() or 1
    cpu_cores = cpu_count - 2 if cpu_count > 2 else 1
    available_cores = cpu_cores - 1
    multiprocess = True
    update = False