#!/usr/bin/env python3
# AFEGIR PARÀMETRES DE GMX_IMAGE: PBC, CENTER, UR, FIT (NOMÉS APPEND SI L'USUARI ELS AFEGEIX)
"""Module containing the GMX TrjConvStr class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_analysis.gromacs.common import get_binary_path, check_input_path, check_traj_path, check_index_path, get_selection_index_file, get_selection, check_out_traj_path
[docs]class GMXTrjConvStr(BiobbObject):
"""
| biobb_analysis GMXTrjConvStr
| Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.
| GROMACS trjconv module can convert trajectory files in many ways. See the `GROMACS trjconv <http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html>`_ official documentation for further information.
Args:
input_structure_path (str): Path to the input structure file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr>`_. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876).
input_top_path (str): Path to the GROMACS input topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr>`_. Accepted formats: tpr (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), brk (edam:format_2033), ent (edam:format_1476).
input_index_path (str) (Optional): Path to the GROMACS index file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx>`_. Accepted formats: ndx (edam:format_2033).
output_str_path (str): Path to the output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_trjconv.str.pdb>`_. Accepted formats: pdb (edam:format_1476), xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), tng (edam:format_3876).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **selection** (*str*) - ("System") Group where the trjconv will be performed. If **input_index_path** provided, check the file for the accepted values. Values: System (all atoms in the system), Protein (all protein atoms), Protein-H (protein atoms excluding hydrogens), C-alpha (C-alpha atoms), Backbone (protein backbone atoms: N; C-alpha and C), MainChain (protein main chain atoms: N; C-alpha; C and O; including oxygens in C-terminus), MainChain+Cb (protein main chain atoms including C-beta), MainChain+H (protein main chain atoms including backbone amide hydrogens and hydrogens on the N-terminus), SideChain (protein side chain atoms: that is all atoms except N; C-alpha; C; O; backbone amide hydrogens and oxygens in C-terminus and hydrogens on the N-terminus), SideChain-H (protein side chain atoms excluding all hydrogens), Prot-Masses (protein atoms excluding dummy masses), non-Protein (all non-protein atoms), Water (water molecules), SOL (water molecules), non-Water (anything not covered by the Water group), Ion (any name matching an Ion entry in residuetypes.dat), NA (all NA atoms), CL (all CL atoms), Water_and_ions (combination of the Water and Ions groups), DNA (all DNA atoms), RNA (all RNA atoms), Protein_DNA (all Protein-DNA complex atoms), Protein_RNA (all Protein-RNA complex atoms), Protein_DNA_RNA (all Protein-DNA-RNA complex atoms), DNA_RNA (all DNA-RNA complex atoms).
* **pbc** (*str*) - ("mol") PBC treatment (see help text for full description). Values: none (No PBC treatment), mol (Puts the center of mass of molecules in the box), res (Puts the center of mass of residues in the box), atom (Puts all the atoms in the box), nojump (Checks if atoms jump across the box and then puts them back), cluster (Clusters all the atoms in the selected index such that they are all closest to the center of mass of the cluster which is iteratively updated), whole (Only makes broken molecules whole).
* **center** (*bool*) - (True) Center atoms in box.
* **ur** (*str*) - ("compact") Unit-cell representation. Values: rect (It's the ordinary brick shape), tric (It's the triclinic unit cell), compact (Puts all atoms at the closest distance from the center of the box).
* **fit** (*str*) - ("none") Fit molecule to ref structure in the structure file. Values: none, rot+trans, rotxy+transxy, translation, transxy, progressive.
* **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Container path definition.
* **container_image** (*str*) - ('gromacs/gromacs:2022.2') Container image definition.
* **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
* **container_working_dir** (*str*) - (None) Container working directory definition.
* **container_user_id** (*str*) - (None) Container user_id definition.
* **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
Examples:
This is a use example of how to use the building block from Python::
from biobb_analysis.gromacs.gmx_trjconv_str import gmx_trjconv_str
prop = {
'selection': 'System'
}
gmx_trjconv_str(input_structure_path='/path/to/myStructure.trr',
input_top_path='/path/to/myTopology.tpr',
output_str_path='/path/to/newStructure.pdb',
input_index_path='/path/to/myIndex.ndx',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS trjconv
* version: >=2019.1
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_structure_path, input_top_path, output_str_path,
input_index_path=None, properties=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, "input_top_path": input_top_path, "input_index_path": input_index_path},
"out": {"output_str_path": output_str_path}
}
# Properties specific for BB
self.selection = properties.get('selection', "System")
self.pbc = properties.get('pbc', None)
self.center = properties.get('dista', None)
self.ur = properties.get('ur', None)
self.fit = properties.get('fit', None)
self.properties = properties
# Properties common in all GROMACS BB
self.binary_path = get_binary_path(properties, 'binary_path')
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.io_dict["in"]["input_structure_path"] = check_traj_path(self.io_dict["in"]["input_structure_path"], out_log, self.__class__.__name__)
self.io_dict["in"]["input_top_path"] = check_input_path(self.io_dict["in"]["input_top_path"], out_log, self.__class__.__name__)
self.io_dict["in"]["input_index_path"] = check_index_path(self.io_dict["in"]["input_index_path"], out_log, self.__class__.__name__)
self.io_dict["out"]["output_str_path"] = check_out_traj_path(self.io_dict["out"]["output_str_path"], out_log, self.__class__.__name__)
if not self.io_dict["in"]["input_index_path"]:
self.selection = get_selection(self.properties, out_log, self.__class__.__name__)
else:
self.selection = get_selection_index_file(self.properties, self.io_dict["in"]["input_index_path"], 'selection', out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`GMXTrjConvStr <gromacs.gmx_trjconv_str.GMXTrjConvStr>` gromacs.gmx_trjconv_str.GMXTrjConvStr object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
# standard input
self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.selection}')
self.stage_files()
self.cmd = [self.binary_path, 'trjconv',
'-f', self.stage_io_dict["in"]["input_structure_path"],
'-s', self.stage_io_dict["in"]["input_top_path"],
'-o', self.stage_io_dict["out"]["output_str_path"]]
if self.pbc:
self.cmd.append('-pbc')
self.cmd.append(self.pbc)
self.cmd.append('-center' if self.center else '-nocenter')
if self.ur:
self.cmd.append('-ur')
self.cmd.append(self.ur)
if self.fit:
self.cmd.append('-fit')
self.cmd.append(self.fit)
if self.stage_io_dict["in"].get("input_index_path"):
self.cmd.extend(['-n', self.stage_io_dict["in"]["input_index_path"]])
# Add stdin input file
self.cmd.append('<')
self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
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)
[docs]def gmx_trjconv_str(input_structure_path: str, input_top_path: str, output_str_path: str, input_index_path: str = None, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`GMXTrjConvStr <gromacs.gmx_trjconv_str.GMXTrjConvStr>` class and
execute the :meth:`launch() <gromacs.gmx_trjconv_str.GMXTrjConvStr.launch>` method."""
return GMXTrjConvStr(input_structure_path=input_structure_path,
input_top_path=input_top_path,
output_str_path=output_str_path,
input_index_path=input_index_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Converts between GROMACS compatible structure file formats and/or extracts a selection of atoms.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_structure_path', required=True, help='Path to the input structure file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.')
required_args.add_argument('--input_top_path', required=True, help='Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.')
parser.add_argument('--input_index_path', required=False, help="Path to the GROMACS index file. Accepted formats: ndx.")
required_args.add_argument('--output_str_path', required=True, help='Path to the output file. Accepted formats: xtc, trr, gro, g96, pdb, tng.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# Specific call of each building block
gmx_trjconv_str(input_structure_path=args.input_structure_path,
input_top_path=args.input_top_path,
output_str_path=args.output_str_path,
input_index_path=args.input_index_path,
properties=properties)
if __name__ == '__main__':
main()