#!/usr/bin/env python3
"""Module containing the concoord_dist class and the command line interface."""
import argparse
import os
import shutil
from pathlib import Path
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 ConcoordDist(BiobbObject):
"""
| biobb_flexdyn ConcoordDist
| Wrapper of the Dist tool from the Concoord package.
| Structure interpretation and bond definitions from a PDB/GRO file.
Args:
input_structure_path (str): Input structure 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), gro (edam:format_2033).
output_pdb_path (str): Output pdb file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/dist.pdb>`_. Accepted formats: pdb (edam:format_1476).
output_gro_path (str): Output gro file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/dist.gro>`_. Accepted formats: gro (edam:format_2033).
output_dat_path (str): Output dat with structure interpretation and bond definitions. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/dist.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **binary_path** (*str*) - ("dist") Concoord dist binary path to be used.
* **vdw** (*int*) - (1) Select a set of Van der Waals parameters. Values: 1 (OPLS-UA -united atoms- parameters), 2 (OPLS-AA -all atoms- parameters), 3 (PROLSQ repel parameters), 4 (Yamber2 parameters), 5 (Li et al. parameters), 6 (OPLS-X parameters -recommended for NMR structure determination-).
* **bond_angle** (*int*) - (1) Select a set of bond/angle parameters. Values: 1 (Concoord default parameters), 2 (Engh-Huber parameters).
* **retain_hydrogens** (*bool*) - (False) Retain hydrogen atoms
* **nb_interactions** (*bool*) - (False) Try to find alternatives for non-bonded interactions (by default the native contacts will be preserved)
* **cutoff** (*float*) - (4.0) cut-off radius (Angstroms) for non-bonded interacting pairs (the cut-off distances are additional to the sum of VDW radii)
* **min_distances** (*int*) - (50) Minimum number of distances to be defined for each atom
* **damp** (*float*) - (1.0) Multiply each distance margin by this value
* **fixed_atoms** (*bool*) - (False) Interpret zero occupancy as atoms to keep fixed
* **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.concoord_dist import concoord_dist
prop = {
'vdw' : 4,
'bond_angle' : 1
}
concoord_dist( input_structure_path='/path/to/structure.pdb',
output_pdb_path='/path/to/output.pdb',
output_gro_path='/path/to/output.gro',
output_dat_path='/path/to/output.dat',
properties=prop)
Info:
* wrapped_software:
* name: Concoord
* version: >=2.1.2
* license: other
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_structure_path: str, output_pdb_path: str,
output_gro_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_structure_path': input_structure_path},
'out': {'output_pdb_path': output_pdb_path,
'output_gro_path': output_gro_path,
'output_dat_path': output_dat_path}
}
# Properties specific for BB
self.properties = properties
self.binary_path = properties.get('binary_path', 'dist')
self.retain_hydrogens = properties.get('retain_hydrogens', False)
self.nb_interactions = properties.get('nb_interactions', False)
self.cutoff = properties.get('cutoff', 4.0)
self.min_distances = properties.get('min_distances', 50)
self.damp = properties.get('damp', 1.0)
self.fixed_atoms = properties.get('fixed_atoms', False)
self.vdw = properties.get('vdw', 1)
self.bond_angle = properties.get('bond_angle', 1)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self):
"""Launches the execution of the FlexDyn ConcoordDist module."""
# Set input params
self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.vdw}\n{self.bond_angle}\n')
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Copy auxiliary file (HBONDS) to the working dir
concoord_lib = os.getenv("CONCOORDLIB")
hbonds_file = concoord_lib + "/HBONDS.DAT"
shutil.copy2(hbonds_file, self.stage_io_dict.get("unique_dir"))
# Command line
# (concoord) OROZCO67:biobb_flexdyn hospital$ dist -p biobb_flexdyn/test/data/flexdyn/structure.pdb
# -op dist.pdb -og dist.gro -od dist.dat
# Select a set of Van der Waals parameters:
# 1: OPLS-UA (united atoms) parameters
# 2: OPLS-AA (all atoms) parameters
# 3: PROLSQ repel parameters
# 4: Yamber2 parameters
# 5: Li et al. parameters
# 6: OPLS-X parameters (recommended for NMR structure determination)
# 2
# Selected parameter set 2
# copying /opt/anaconda3/envs/concoord/share/concoord/lib/ATOMS_oplsaa.DAT to ATOMS.DAT in current working directory
# copying /opt/anaconda3/envs/concoord/share/concoord/lib/MARGINS_oplsaa.DAT to MARGINS.DAT in current working directory
# Select a set of bond/angle parameters:
# 1: Concoord default parameters
# 2: Engh-Huber parameters
# 1
# Selected parameter set 1
# copying /opt/anaconda3/envs/concoord/share/concoord/lib/BONDS.DAT.noeh to BONDS.DAT in current working directory
self.cmd = ["cd ", self.stage_io_dict.get('unique_dir'), ";", self.binary_path,
# "-op", self.stage_io_dict["out"]["output_pdb_path"],
# "-og", self.stage_io_dict["out"]["output_gro_path"],
# "-od", self.stage_io_dict["out"]["output_dat_path"]
"-op", str(Path(self.stage_io_dict["out"]["output_pdb_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
"-og", str(Path(self.stage_io_dict["out"]["output_gro_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
"-od", str(Path(self.stage_io_dict["out"]["output_dat_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir'))))
]
# If input structure in pdb format:
file_extension = Path(self.stage_io_dict["in"]["input_structure_path"]).suffix
if file_extension == ".pdb":
self.cmd.append('-p')
# self.cmd.append(self.stage_io_dict["in"]["input_structure_path"])
self.cmd.append(str(Path(self.stage_io_dict["in"]["input_structure_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
elif file_extension == ".gro":
self.cmd.append('-g')
# self.cmd.append(self.stage_io_dict["in"]["input_structure_path"])
self.cmd.append(str(Path(self.stage_io_dict["in"]["input_structure_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
else:
fu.log("ERROR: input_structure_path ({}) must be a PDB or a GRO formatted file ({})".format(self.io_dict["in"]["input_structure_path"], file_extension), self.out_log, self.global_log)
if self.retain_hydrogens:
self.cmd.append('-r')
if self.nb_interactions:
self.cmd.append('-nb')
if self.fixed_atoms:
self.cmd.append('-q')
if self.cutoff:
self.cmd.append('-c')
self.cmd.append(str(self.cutoff))
if self.min_distances:
self.cmd.append('-m')
self.cmd.append(str(self.min_distances))
if self.damp:
self.cmd.append('-damp')
self.cmd.append(str(self.damp))
# Add stdin input file
self.cmd.append('<')
# self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
self.cmd.append(str(Path(self.stage_io_dict["in"]["stdin_file_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
self.io_dict['in'].get("stdin_file_path")
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def concoord_dist(input_structure_path: str,
output_pdb_path: str, output_gro_path: str, output_dat_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`ConcoordDist <flexdyn.concoord_dist.ConcoordDist>`flexdyn.concoord_dist.ConcoordDist class and
execute :meth:`launch() <flexdyn.concoord_dist.ConcoordDist.launch>` method"""
return ConcoordDist(input_structure_path=input_structure_path,
output_pdb_path=output_pdb_path,
output_gro_path=output_gro_path,
output_dat_path=output_dat_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Structure interpretation and bond definitions from a PDB/GRO file.', 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_structure_path', required=True, help='Input structure file. Accepted formats: pdb, gro.')
required_args.add_argument('--output_pdb_path', required=True, help='Output pdb file. Accepted formats: pdb.')
required_args.add_argument('--output_gro_path', required=True, help='Output gro file. Accepted formats: gro.')
required_args.add_argument('--output_dat_path', required=True, help='Output dat file with structure interpretation and bond definitions. Accepted formats: dat, txt.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call
concoord_dist(input_structure_path=args.input_structure_path,
output_pdb_path=args.output_pdb_path,
output_gro_path=args.output_gro_path,
output_dat_path=args.output_dat_path,
properties=properties)
if __name__ == '__main__':
main()