Source code for flexdyn.imod_imc

#!/usr/bin/env python3

"""Module containing the imode class and the command line interface."""
import argparse
import shutil
from pathlib import PurePath
from biobb_common.tools import file_utils as fu
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools.file_utils import launchlogger


[docs]class ImodImc(BiobbObject): """ | biobb_flexdyn imod_imc | Wrapper of the imc tool | Compute a Monte-Carlo IC-NMA based conformational ensemble using the imc tool from the iMODS package. Args: input_pdb_path (str): Input PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/structure_cleaned.pdb>`_. Accepted formats: pdb (edam:format_1476). input_dat_path (str): Input dat with normal modes. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/imod_imode_evecs.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330). output_traj_path (str): Output multi-model PDB file with the generated ensemble. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/imod_imc_output.pdb>`_. Accepted formats: pdb (edam:format_1476). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **num_structs** (*int*) - (500) Number of structures to be generated * **num_modes** (*int*) - (5) Number of eigenvectors to be employed * **amplitude** (*int*) - (1) Amplitude linear factor to scale motion * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. Examples: This is a use example of how to use the building block from Python:: from biobb_flexdyn.flexdyn.imod_imc import imod_imc prop = { 'num_structs' : 500 } imod_imc( input_pdb_path='/path/to/structure.pdb', input_dat_path='/path/to/input_evecs.dat', output_traj_path='/path/to/output_ensemble.pdb', properties=prop) Info: * wrapped_software: * name: iMODS * version: >=1.0.4 * license: other * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_pdb_path: str, input_dat_path: str, output_traj_path: str, properties: dict = None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) self.locals_var_dict = locals().copy() # Input/Output files self.io_dict = { 'in': {'input_pdb_path': input_pdb_path, 'input_dat_path': input_dat_path}, 'out': {'output_traj_path': output_traj_path} } # Properties specific for BB self.properties = properties self.binary_path = properties.get('binary_path', 'imc') self.num_structs = properties.get('num_structs', 500) self.num_modes = properties.get('num_modes', 5) self.amplitude = properties.get('amplitude', 1.0) # Check the properties self.check_properties(properties) self.check_arguments()
[docs] @launchlogger def launch(self): """Launches the execution of the FlexDyn iMOD imc module.""" # Setup Biobb if self.check_restart(): return 0 # self.stage_files() # Manually creating a Sandbox to avoid issues with input parameters buffer overflow: # Long strings defining a file path makes Fortran or C compiled programs crash if the string # declared is shorter than the input parameter path (string) length. # Generating a temporary folder and working inside this folder (sandbox) fixes this problem. # The problem was found in Galaxy executions, launching Singularity containers (May 2023). # Creating temporary folder self.tmp_folder = fu.create_unique_dir() fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) shutil.copy2(self.io_dict["in"]["input_pdb_path"], self.tmp_folder) shutil.copy2(self.io_dict["in"]["input_dat_path"], self.tmp_folder) # Output temporary file # out_file_prefix = Path(self.stage_io_dict.get("unique_dir")).joinpath("imod_ensemble") # out_file = Path(self.stage_io_dict.get("unique_dir")).joinpath("imod_ensemble.pdb") out_file_prefix = "imod_ensemble" # Needed as imod is appending the .pdb extension out_file = "imod_ensemble.pdb" # Command line # imc 1ake_backbone.pdb 1ake_backbone_evecs.dat -o 1ake_backbone.ensemble.pdb -c 500 # self.cmd = [self.binary_path, # str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())), # str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path.cwd())), # "-o", str(out_file_prefix) # ] self.cmd = ['cd', self.tmp_folder, ';', self.binary_path, PurePath(self.io_dict["in"]["input_pdb_path"]).name, PurePath(self.io_dict["in"]["input_dat_path"]).name, '-o', out_file_prefix ] # Properties if self.num_structs: self.cmd.append('-c') self.cmd.append(str(self.num_structs)) if self.num_modes: self.cmd.append('-n') self.cmd.append(str(self.num_modes)) if self.amplitude: self.cmd.append('-a') self.cmd.append(str(self.amplitude)) # Run Biobb block self.run_biobb() # Copying generated output file to the final (user-given) file name # shutil.copy2(out_file, self.stage_io_dict["out"]["output_traj_path"]) # Copy outputs from temporary folder to output path shutil.copy2(PurePath(self.tmp_folder).joinpath(out_file), PurePath(self.io_dict["out"]["output_traj_path"])) # Copy files to host # self.copy_to_host() # remove temporary folder(s) self.tmp_files.extend([ # self.stage_io_dict.get("unique_dir") self.tmp_folder ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def imod_imc(input_pdb_path: str, input_dat_path: str, output_traj_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`ImodImc <flexdyn.imod_imc.ImodImc>`flexdyn.imod_imc.ImodImc class and execute :meth:`launch() <flexdyn.imod_imc.ImodImc.launch>` method""" return ImodImc(input_pdb_path=input_pdb_path, input_dat_path=input_dat_path, output_traj_path=output_traj_path, properties=properties).launch()
[docs]def main(): parser = argparse.ArgumentParser(description='Compute a Monte-Carlo IC-NMA based conformational ensemble using the imc tool from the iMODS package.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_pdb_path', required=True, help='Input structure file. Accepted formats: pdb') required_args.add_argument('--input_dat_path', required=True, help='Input evecs file. Accepted formats: dat') required_args.add_argument('--output_traj_path', required=True, help='Output traj file. Accepted formats: pdb.') args = parser.parse_args() args.config = args.config or "{}" properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call imod_imc(input_pdb_path=args.input_pdb_path, input_dat_path=args.input_dat_path, output_traj_path=args.output_traj_path, properties=properties)
if __name__ == '__main__': main()