#!/usr/bin/env python3
"""Module containing the imode class and the command line interface."""
from typing import Optional
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.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.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
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: Optional[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
tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % tmp_folder, self.out_log)
shutil.copy2(self.io_dict["in"]["input_pdb_path"], tmp_folder)
shutil.copy2(self.io_dict["in"]["input_dat_path"], 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', 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(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.append(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: Optional[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(**dict(locals())).launch()
imod_imc.__doc__ = ImodImc.__doc__
main = ImodImc.get_main(imod_imc, "Compute a Monte-Carlo IC-NMA based conformational ensemble using the imc tool from the iMODS package.")
if __name__ == '__main__':
main()