Source code for gromacs.gmx_rgyr

#!/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.file_utils import launchlogger
from biobb_analysis.gromacs.common import *


[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). * **gmx_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:latest') 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) # 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.gmx_path = get_binary_path(properties, 'gmx_path') # Check the properties self.check_properties(properties)
[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 self.stage_files() self.cmd = ['echo', '\"'+self.selection+'\"', '|', self.gmx_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"]["input_index_path"]: self.cmd.extend(['-n', self.stage_io_dict["in"]["input_index_path"]]) # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() # if container execution, remove temporary folder if self.container_path: self.tmp_files.append(self.stage_io_dict.get("unique_dir")) self.remove_tmp_files() 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()