Coverage for biobb_analysis/gromacs/gmx_rgyr.py: 77%
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1#!/usr/bin/env python3
3"""Module containing the GMX Rgyr class and the command line interface."""
4import argparse
5from typing import Optional
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.configuration import settings
8from biobb_common.tools import file_utils as fu
9from biobb_common.tools.file_utils import launchlogger
10from 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
13class GMXRgyr(BiobbObject):
14 """
15 | biobb_analysis GMXRgyr
16 | 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.
17 | `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.
19 Args:
20 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).
21 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).
22 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).
23 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).
24 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
25 * **xvg** (*str*) - ("none") XVG plot formatting. Values: xmgrace, xmgr, none.
26 * **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).
27 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
28 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
29 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
30 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
31 * **container_path** (*str*) - (None) Container path definition.
32 * **container_image** (*str*) - ('gromacs/gromacs:2022.2') Container image definition.
33 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
34 * **container_working_dir** (*str*) - (None) Container working directory definition.
35 * **container_user_id** (*str*) - (None) Container user_id definition.
36 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
38 Examples:
39 This is a use example of how to use the building block from Python::
41 from biobb_analysis.gromacs.gmx_rgyr import gmx_rgyr
42 prop = {
43 'xvg': 'xmgr',
44 'selection': 'Water_and_ions'
45 }
46 gmx_rgyr(input_structure_path='/path/to/myStructure.tpr',
47 input_traj_path='/path/to/myTrajectory.trr',
48 output_xvg_path='/path/to/newXVG.xvg',
49 input_index_path='/path/to/myIndex.ndx',
50 properties=prop)
52 Info:
53 * wrapped_software:
54 * name: GROMACS gyrate
55 * version: >=2019.1
56 * license: LGPL 2.1
57 * ontology:
58 * name: EDAM
59 * schema: http://edamontology.org/EDAM.owl
61 """
63 def __init__(self, input_structure_path, input_traj_path, output_xvg_path,
64 input_index_path=None, properties=None, **kwargs) -> None:
65 properties = properties or {}
67 # Call parent class constructor
68 super().__init__(properties)
69 self.locals_var_dict = locals().copy()
71 # Input/Output files
72 self.io_dict = {
73 "in": {"input_structure_path": input_structure_path, "input_traj_path": input_traj_path, "input_index_path": input_index_path},
74 "out": {"output_xvg_path": output_xvg_path}
75 }
77 # Properties specific for BB
78 self.xvg = properties.get('xvg', "none")
79 self.selection = properties.get('selection', "System")
80 self.properties = properties
82 # Properties common in all GROMACS BB
83 self.binary_path = get_binary_path(properties, 'binary_path')
85 # Check the properties
86 self.check_properties(properties)
87 self.check_arguments()
89 def check_data_params(self, out_log, err_log):
90 """ Checks all the input/output paths and parameters """
91 self.io_dict["in"]["input_structure_path"] = check_input_path(self.io_dict["in"]["input_structure_path"], out_log, self.__class__.__name__)
92 self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
93 self.io_dict["in"]["input_index_path"] = check_index_path(self.io_dict["in"]["input_index_path"], out_log, self.__class__.__name__)
94 self.io_dict["out"]["output_xvg_path"] = check_out_xvg_path(self.io_dict["out"]["output_xvg_path"], out_log, self.__class__.__name__)
95 self.xvg = get_xvg(self.properties, out_log, self.__class__.__name__)
96 if not self.io_dict["in"]["input_index_path"]:
97 self.selection = get_selection(self.properties, out_log, self.__class__.__name__)
98 else:
99 self.selection = get_selection_index_file(self.properties, self.io_dict["in"]["input_index_path"], 'selection', out_log, self.__class__.__name__)
101 @launchlogger
102 def launch(self) -> int:
103 """Execute the :class:`GMXRgyr <gromacs.gmx_rgyr.GMXRgyr>` gromacs.gmx_rgyr.GMXRgyr object."""
105 # check input/output paths and parameters
106 self.check_data_params(self.out_log, self.err_log)
108 # Setup Biobb
109 if self.check_restart():
110 return 0
112 # standard input
113 self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.selection}')
114 self.stage_files()
116 self.cmd = [self.binary_path, 'gyrate',
117 '-s', self.stage_io_dict["in"]["input_structure_path"],
118 '-f', self.stage_io_dict["in"]["input_traj_path"],
119 '-o', self.stage_io_dict["out"]["output_xvg_path"],
120 '-xvg', self.xvg]
122 if self.stage_io_dict["in"].get("input_index_path"):
123 self.cmd.extend(['-n', self.stage_io_dict["in"]["input_index_path"]])
125 # Add stdin input file
126 self.cmd.append('<')
127 self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
129 # Run Biobb block
130 self.run_biobb()
132 # Copy files to host
133 self.copy_to_host()
135 self.tmp_files.extend([
136 self.stage_io_dict.get("unique_dir", ""),
137 self.io_dict['in'].get("stdin_file_path", "")
138 ])
139 self.remove_tmp_files()
141 self.check_arguments(output_files_created=True, raise_exception=False)
143 return self.return_code
146def gmx_rgyr(input_structure_path: str, input_traj_path: str, output_xvg_path: str, input_index_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
147 """Execute the :class:`GMXRgyr <gromacs.gmx_rgyr.GMXRgyr>` class and
148 execute the :meth:`launch() <gromacs.gmx_rgyr.GMXRgyr.launch>` method."""
150 return GMXRgyr(input_structure_path=input_structure_path,
151 input_traj_path=input_traj_path,
152 output_xvg_path=output_xvg_path,
153 input_index_path=input_index_path,
154 properties=properties, **kwargs).launch()
157def main():
158 """Command line execution of this building block. Please check the command line documentation."""
159 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))
160 parser.add_argument('--config', required=False, help='Configuration file')
162 # Specific args of each building block
163 required_args = parser.add_argument_group('required arguments')
164 required_args.add_argument('--input_structure_path', required=True, help='Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.')
165 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.')
166 parser.add_argument('--input_index_path', required=False, help="Path to the GROMACS index file. Accepted formats: ndx.")
167 required_args.add_argument('--output_xvg_path', required=True, help='Path to the XVG output file. Accepted formats: xvg.')
169 args = parser.parse_args()
170 args.config = args.config or "{}"
171 properties = settings.ConfReader(config=args.config).get_prop_dic()
173 # Specific call of each building block
174 gmx_rgyr(input_structure_path=args.input_structure_path,
175 input_traj_path=args.input_traj_path,
176 output_xvg_path=args.output_xvg_path,
177 input_index_path=args.input_index_path,
178 properties=properties)
181if __name__ == '__main__':
182 main()