#!/usr/bin/env python3
"""Module containing the GMX Rgyr 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, check_out_xvg_path, get_xvg, get_selection
[docs]class GMXRgyr(BiobbObject):
"""
| biobb_analysis GMXRgyr
| Wrapper of the GROMACS gyrate module for computing the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.
| `GROMACS gyrate <http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-gyrate.html>`_ computes the radius of gyration of a molecule and the radii of gyration about the x-, y- and z-axes, as a function of time. The atoms are explicitly mass weighted.
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/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_traj_path (str): Path to the GROMACS trajectory 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_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_xvg_path (str): Path to the XVG output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_rgyr.xvg>`_. Accepted formats: xvg (edam:format_2030).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **xvg** (*str*) - ("none") XVG plot formatting. Values: xmgrace, xmgr, none.
* **selection** (*str*) - ("System") Group where the rgyr 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).
* **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_rgyr import gmx_rgyr
prop = {
'xvg': 'xmgr',
'selection': 'Water_and_ions'
}
gmx_rgyr(input_structure_path='/path/to/myStructure.tpr',
input_traj_path='/path/to/myTrajectory.trr',
output_xvg_path='/path/to/newXVG.xvg',
input_index_path='/path/to/myIndex.ndx',
properties=prop)
Info:
* wrapped_software:
* name: GROMACS gyrate
* version: >=2019.1
* license: LGPL 2.1
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_structure_path, input_traj_path, output_xvg_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_traj_path": input_traj_path, "input_index_path": input_index_path},
"out": {"output_xvg_path": output_xvg_path}
}
# Properties specific for BB
self.xvg = properties.get('xvg', "none")
self.selection = properties.get('selection', "System")
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_input_path(self.io_dict["in"]["input_structure_path"], out_log, self.__class__.__name__)
self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_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_xvg_path"] = check_out_xvg_path(self.io_dict["out"]["output_xvg_path"], out_log, self.__class__.__name__)
self.xvg = get_xvg(self.properties, 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:`GMXRgyr <gromacs.gmx_rgyr.GMXRgyr>` gromacs.gmx_rgyr.GMXRgyr 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, 'gyrate',
'-s', self.stage_io_dict["in"]["input_structure_path"],
'-f', self.stage_io_dict["in"]["input_traj_path"],
'-o', self.stage_io_dict["out"]["output_xvg_path"],
'-xvg', self.xvg]
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)
return self.return_code
[docs]def gmx_rgyr(input_structure_path: str, input_traj_path: str, output_xvg_path: str, input_index_path: str = None, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`GMXRgyr <gromacs.gmx_rgyr.GMXRgyr>` class and
execute the :meth:`launch() <gromacs.gmx_rgyr.GMXRgyr.launch>` method."""
return GMXRgyr(input_structure_path=input_structure_path,
input_traj_path=input_traj_path,
output_xvg_path=output_xvg_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="Computes the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.", 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: tpr, gro, g96, pdb, brk, ent.')
required_args.add_argument('--input_traj_path', required=True, help='Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.')
parser.add_argument('--input_index_path', required=False, help="Path to the GROMACS index file. Accepted formats: ndx.")
required_args.add_argument('--output_xvg_path', required=True, help='Path to the XVG output file. Accepted formats: xvg.')
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_rgyr(input_structure_path=args.input_structure_path,
input_traj_path=args.input_traj_path,
output_xvg_path=args.output_xvg_path,
input_index_path=args.input_index_path,
properties=properties)
if __name__ == '__main__':
main()