#!/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 ImodImode(BiobbObject):
"""
| biobb_flexdyn imod_imode
| Wrapper of the imode tool
| Compute the normal modes of a macromolecule using the imode 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.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_dat_path (str): Output dat with normal modes. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/imod_imode_evecs.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **cg** (*int*) - (2) Coarse-Grained model. Values: 0 (CA), 1 (C5), 2 (Heavy atoms).
* **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_imode import imod_imode
prop = {
'cg' : 2
}
imod_imode( input_pdb_path='/path/to/structure.pdb',
output_dat_path='/path/to/output_evecs.dat',
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, output_dat_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},
'out': {'output_dat_path': output_dat_path}
}
# Properties specific for BB
self.properties = properties
self.binary_path = properties.get('binary_path', 'imode_gcc')
self.cg = properties.get('cg', 2)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self):
"""Launches the execution of the FlexDyn iMOD imode 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)
# Output temporary file
# out_file_prefix = Path(self.stage_io_dict.get("unique_dir")).joinpath("imods_evecs")
# out_file = Path(self.stage_io_dict.get("unique_dir")).joinpath("imods_evecs_ic.evec")
out_file_prefix = "imods_evecs" # Needed as imod is appending the _ic.evec extension
out_file = "imods_evecs_ic.evec"
# Command line
# imode_gcc 1ake_backbone.pdb -m 0 -o patata.evec
# self.cmd = [self.binary_path,
# str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())),
# "-o", str(out_file_prefix),
# "-m", str(self.cg)
# ]
self.cmd = ['cd', self.tmp_folder, ';',
self.binary_path,
PurePath(self.io_dict["in"]["input_pdb_path"]).name,
'-o', out_file_prefix,
'-m', str(self.cg)
]
# 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_dat_path"])
# Copy outputs from temporary folder to output path
shutil.copy2(PurePath(self.tmp_folder).joinpath(out_file), PurePath(self.io_dict["out"]["output_dat_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_imode(input_pdb_path: str, output_dat_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`ImodImode <flexdyn.imod_imode.ImodImode>`flexdyn.imod_imode.ImodImode class and
execute :meth:`launch() <flexdyn.imod_imode.ImodImode.launch>` method"""
return ImodImode(input_pdb_path=input_pdb_path,
output_dat_path=output_dat_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Compute the normal modes of a macromolecule using the imode 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('--output_dat_path', required=True, help='Output evecs dat file. Accepted formats: dat.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call
imod_imode(input_pdb_path=args.input_pdb_path,
output_dat_path=args.output_dat_path,
properties=properties)
if __name__ == '__main__':
main()