#!/usr/bin/env python3
"""Module containing the concoord_disco 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 ConcoordDisco(BiobbObject):
"""
| biobb_flexdyn ConcoordDisco
| Wrapper of the Disco tool from the Concoord package.
| Structure generation based on a set of geometric constraints extracted with the Concoord Dist tool.
Args:
input_pdb_path (str): Input structure file in PDB format. 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).
input_dat_path (str): Input dat with structure interpretation and bond definitions. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/data/flexdyn/dist.dat>`_. Accepted formats: dat (edam:format_1637), txt (edam:format_2330).
output_traj_path (str): Output trajectory file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/disco_trj.pdb>`_. Accepted formats: pdb (edam:format_1476), xtc (edam:format_3875), gro (edam:format_2033).
output_rmsd_path (str): Output rmsd file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/disco_rmsd.dat>`_. Accepted formats: dat (edam:format_1637).
output_bfactor_path (str): Output B-factor file. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexdyn/raw/master/biobb_flexdyn/test/reference/flexdyn/disco_bfactor.pdb>`_. Accepted formats: pdb (edam:format_1476).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **binary_path** (*str*) - ("disco") Concoord disco 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-)
* **num_structs** (*int*) - (500) Number of structures to be generated
* **num_iterations** (*int*) - (2500) Maximum number of iterations per structure
* **chirality_check** (*int*) - (2) Chirality check. Values: 0 (no chirality checks), 1 (only check afterwards), 2 (check on the fly)
* **bs** (*int*) - (0) Number of rounds of triangular bound smoothing (default 0), (if >= 6, tetragonal BS is activated)
* **nofit** (*bool*) - (False) Do not fit generated structures to reference
* **seed** (*int*) - (741265) Initial random seed
* **violation** (*float*) - (1.0) Maximal acceptable sum of violations (nm)
* **nofit** (*bool*) - (False) Do not fit generated structures to reference
* **convergence** (*int*) - (50) Consider convergence failed after this number of non-productive iterations
* **trials** (*int*) - (25) Maximum number of trials per run
* **damp** (*int*) - (1) Damping factor for distance corrections. Values: 1 (default), 2 (for cases with convergence problems)
* **dyn** (*int*) - (1) Number of rounds to dynamically set tolerances
* **bump** (*bool*) - (False) Do extra bump check
* **pairlist_freq** (*int*) - (10) Pairlist update frequency in steps (only valid together with bump)
* **cutoff** (*float*) - (0.5) Cut-off radius for pairlist (nm) (only valid together with bump)
* **ref** (*bool*) - (False) Use input coordinates instead of random starting coordinates
* **scale** (*int*) - (1) Pre-scale coordinates with this factor
* **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_disco import concoord_disco
prop = {
'vdw' : 4,
'num_structs' : 20
}
concoord_disco( input_pdb_path='/path/to/dist_input.pdb',
input_dat_path='/path/to/dist_input.dat',
output_traj_path='/path/to/disco_out_traj.pdb',
output_rmsd_path='/path/to/disco_out_rmsd.dat',
output_bfactor_path='/path/to/disco_out_bfactor.pdb',
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_pdb_path: str, input_dat_path: str, output_traj_path: str,
output_rmsd_path: str, output_bfactor_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,
'output_rmsd_path': output_rmsd_path,
'output_bfactor_path': output_bfactor_path}
}
# Properties specific for BB
self.properties = properties
self.binary_path = properties.get('binary_path', 'disco')
self.vdw = properties.get('vdw')
self.num_structs = properties.get('num_structs')
self.num_iterations = properties.get('num_iterations')
self.chirality_check = properties.get('chirality_check')
self.bs = properties.get('bs')
self.nofit = properties.get('nofit')
self.seed = properties.get('seed')
self.violation = properties.get('violation')
self.convergence = properties.get('convergence')
self.trials = properties.get('trials')
self.damp = properties.get('damp')
self.dyn = properties.get('dyn')
self.bump = properties.get('bump')
self.pairlist_freq = properties.get('pairlist_freq')
self.cutoff = properties.get('cutoff')
self.ref = properties.get('ref')
self.scale = properties.get('scale')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self):
"""Launches the execution of the FlexDyn ConcoordDisco module."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Copy auxiliary files (MARGINS, ATOMS, BONDS) according to the VdW property to the working dir
concoord_lib = os.getenv("CONCOORDLIB")
# MARGINS_li.DAT, MARGINS_oplsaa.DAT, MARGINS_oplsua.DAT, MARGINS_oplsx.DAT, MARGINS_repel.DAT, MARGINS_yamber2.DAT
# 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-).
vdw_values = ["vdw_values", "oplsua", "oplsaa", "repel", "yamber2", "li", "oplsx"]
vdw_index = int(self.vdw)
margins_file = concoord_lib + "/MARGINS_" + vdw_values[vdw_index] + ".DAT"
atoms_file = concoord_lib + "/ATOMS_" + vdw_values[vdw_index] + ".DAT"
bonds_file = concoord_lib + "/BONDS.DAT"
shutil.copy2(margins_file, self.stage_io_dict.get("unique_dir"))
shutil.copy2(margins_file, self.stage_io_dict.get("unique_dir")+"/MARGINS.DAT")
shutil.copy2(atoms_file, self.stage_io_dict.get("unique_dir"))
shutil.copy2(bonds_file, self.stage_io_dict.get("unique_dir"))
# Command line
# (concoord) OROZCO67:biobb_flexdyn hospital$ disco -d biobb_flexdyn/test/reference/flexdyn/dist.dat
# -p biobb_flexdyn/test/reference/flexdyn/dist.pdb -op patata.pdb
self.cmd = ["cd ", self.stage_io_dict.get('unique_dir'), ";", self.binary_path,
# "-p", str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path.cwd())),
# "-d", str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path.cwd())),
# "-or", str(Path(self.stage_io_dict["out"]["output_rmsd_path"]).relative_to(Path.cwd())),
# "-of", str(Path(self.stage_io_dict["out"]["output_bfactor_path"]).relative_to(Path.cwd()))
"-p", str(Path(self.stage_io_dict["in"]["input_pdb_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
"-d", str(Path(self.stage_io_dict["in"]["input_dat_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
"-or", str(Path(self.stage_io_dict["out"]["output_rmsd_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))),
"-of", str(Path(self.stage_io_dict["out"]["output_bfactor_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir'))))
]
# Output structure formats:
file_extension = Path(self.stage_io_dict["out"]["output_traj_path"]).suffix
if file_extension == ".pdb":
self.cmd.append('-on') # NMR-PDB format (multi-model)
# self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path.cwd())))
self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
elif file_extension == ".gro":
self.cmd.append('-ot')
# self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path.cwd())))
self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
elif file_extension == ".xtc":
self.cmd.append('-ox')
# self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path.cwd())))
self.cmd.append(str(Path(self.stage_io_dict["out"]["output_traj_path"]).relative_to(Path(self.stage_io_dict.get('unique_dir')))))
else:
fu.log("ERROR: output_traj_path ({}) must be a PDB, GRO or XTC formatted file ({})".format(self.io_dict["out"]["output_traj_path"], file_extension), self.out_log, self.global_log)
# Properties
if self.num_structs:
self.cmd.append('-n')
self.cmd.append(str(self.num_structs))
if self.num_iterations:
self.cmd.append('-i')
self.cmd.append(str(self.num_iterations))
if self.chirality_check:
self.cmd.append('-c')
self.cmd.append(str(self.chirality_check))
if self.bs:
self.cmd.append('-bs')
self.cmd.append(str(self.bs))
if self.cutoff:
self.cmd.append('-rc')
self.cmd.append(str(self.cutoff))
if self.seed:
self.cmd.append('-s')
self.cmd.append(str(self.seed))
if self.damp:
self.cmd.append('-damp')
self.cmd.append(str(self.damp))
if self.violation:
self.cmd.append('-viol')
self.cmd.append(str(self.violation))
if self.convergence:
self.cmd.append('-con')
self.cmd.append(str(self.convergence))
if self.trials:
self.cmd.append('-t')
self.cmd.append(str(self.trials))
if self.dyn:
self.cmd.append('-dyn')
self.cmd.append(str(self.dyn))
if self.pairlist_freq:
self.cmd.append('-l')
self.cmd.append(str(self.pairlist_freq))
if self.scale:
self.cmd.append('-is')
self.cmd.append(str(self.scale))
if self.nofit:
self.cmd.append('-f')
if self.bump:
self.cmd.append('-bump')
if self.ref:
self.cmd.append('-ref')
# 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.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def concoord_disco(input_pdb_path: str, input_dat_path: str,
output_traj_path: str, output_rmsd_path: str, output_bfactor_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`ConcoordDisco <flexdyn.concoord_disco.ConcoordDisco>`flexdyn.concoord_disco.ConcoordDisco class and
execute :meth:`launch() <flexdyn.concoord_disco.ConcoordDisco.launch>` method"""
return ConcoordDisco(input_pdb_path=input_pdb_path,
input_dat_path=input_dat_path,
output_traj_path=output_traj_path,
output_rmsd_path=output_rmsd_path,
output_bfactor_path=output_bfactor_path,
properties=properties).launch()
[docs]def main():
parser = argparse.ArgumentParser(description='Structure generation based on a set of geometric constraints extracted with the Concoord Dist tool.', 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 in PDB format. Accepted formats: pdb')
required_args.add_argument('--input_dat_path', required=True, help='Input dat with structure interpretation and bond definitions. Accepted formats: dat, txt')
required_args.add_argument('--output_traj_path', required=True, help='Output trajectory file. Accepted formats: pdb, gro, xtc.')
required_args.add_argument('--output_rmsd_path', required=True, help='Output RMSd file. Accepted formats: dat.')
required_args.add_argument('--output_bfactor_path', required=True, help='Output B-factor file. Accepted formats: pdb.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call
concoord_disco(input_pdb_path=args.input_pdb_path,
input_dat_path=args.input_dat_path,
output_traj_path=args.output_traj_path,
output_rmsd_path=args.output_rmsd_path,
output_bfactor_path=args.output_bfactor_path,
properties=properties)
if __name__ == '__main__':
main()