Coverage for biobb_analysis/gromacs/gmx_trjconv_str.py: 85%
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« prev ^ index » next coverage.py v7.10.6, created at 2025-09-08 10:47 +0000
1#!/usr/bin/env python3
3# AFEGIR PARÀMETRES DE GMX_IMAGE: PBC, CENTER, UR, FIT (NOMÉS APPEND SI L'USUARI ELS AFEGEIX)
5"""Module containing the GMX TrjConvStr class and the command line interface."""
7from typing import Optional
8from biobb_common.generic.biobb_object import BiobbObject
9from biobb_common.tools import file_utils as fu
10from biobb_common.tools.file_utils import launchlogger
11from 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
14class GMXTrjConvStr(BiobbObject):
15 """
16 | biobb_analysis GMXTrjConvStr
17 | Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.
18 | 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.
20 Args:
21 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).
22 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).
23 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).
24 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).
25 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
26 * **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).
27 * **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).
28 * **center** (*bool*) - (True) Center atoms in box.
29 * **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).
30 * **fit** (*str*) - ("none") Fit molecule to ref structure in the structure file. Values: none, rot+trans, rotxy+transxy, translation, transxy, progressive.
31 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
32 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
33 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
34 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
35 * **container_path** (*str*) - (None) Container path definition.
36 * **container_image** (*str*) - ('gromacs/gromacs:2022.2') Container image definition.
37 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
38 * **container_working_dir** (*str*) - (None) Container working directory definition.
39 * **container_user_id** (*str*) - (None) Container user_id definition.
40 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
42 Examples:
43 This is a use example of how to use the building block from Python::
45 from biobb_analysis.gromacs.gmx_trjconv_str import gmx_trjconv_str
46 prop = {
47 'selection': 'System'
48 }
49 gmx_trjconv_str(input_structure_path='/path/to/myStructure.trr',
50 input_top_path='/path/to/myTopology.tpr',
51 output_str_path='/path/to/newStructure.pdb',
52 input_index_path='/path/to/myIndex.ndx',
53 properties=prop)
55 Info:
56 * wrapped_software:
57 * name: GROMACS trjconv
58 * version: >=2024.5
59 * license: LGPL 2.1
60 * ontology:
61 * name: EDAM
62 * schema: http://edamontology.org/EDAM.owl
64 """
66 def __init__(self, input_structure_path, input_top_path, output_str_path,
67 input_index_path=None, properties=None, **kwargs) -> None:
68 properties = properties or {}
70 # Call parent class constructor
71 super().__init__(properties)
72 self.locals_var_dict = locals().copy()
74 # Input/Output files
75 self.io_dict = {
76 "in": {"input_structure_path": input_structure_path, "input_top_path": input_top_path, "input_index_path": input_index_path},
77 "out": {"output_str_path": output_str_path}
78 }
80 # Properties specific for BB
81 self.selection = properties.get('selection', "System")
82 self.pbc = properties.get('pbc', None)
83 self.center = properties.get('dista', None)
84 self.ur = properties.get('ur', None)
85 self.fit = properties.get('fit', None)
86 self.properties = properties
88 # Properties common in all GROMACS BB
89 self.binary_path = get_binary_path(properties, 'binary_path')
91 # Check the properties
92 self.check_init(properties)
94 def check_data_params(self, out_log, err_log):
95 """ Checks all the input/output paths and parameters """
96 self.io_dict["in"]["input_structure_path"] = check_traj_path(self.io_dict["in"]["input_structure_path"], out_log, self.__class__.__name__)
97 self.io_dict["in"]["input_top_path"] = check_input_path(self.io_dict["in"]["input_top_path"], out_log, self.__class__.__name__)
98 self.io_dict["in"]["input_index_path"] = check_index_path(self.io_dict["in"]["input_index_path"], out_log, self.__class__.__name__)
99 self.io_dict["out"]["output_str_path"] = check_out_traj_path(self.io_dict["out"]["output_str_path"], out_log, self.__class__.__name__)
100 if not self.io_dict["in"]["input_index_path"]:
101 self.selection = get_selection(self.properties, out_log, self.__class__.__name__)
102 else:
103 self.selection = get_selection_index_file(self.properties, self.io_dict["in"]["input_index_path"], 'selection', out_log, self.__class__.__name__)
105 @launchlogger
106 def launch(self) -> int:
107 """Execute the :class:`GMXTrjConvStr <gromacs.gmx_trjconv_str.GMXTrjConvStr>` object."""
109 # check input/output paths and parameters
110 self.check_data_params(self.out_log, self.err_log)
112 # Setup Biobb
113 if self.check_restart():
114 return 0
116 # standard input
117 self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.selection}')
118 self.stage_files()
120 self.cmd = [self.binary_path, 'trjconv',
121 '-f', self.stage_io_dict["in"]["input_structure_path"],
122 '-s', self.stage_io_dict["in"]["input_top_path"],
123 '-o', self.stage_io_dict["out"]["output_str_path"]]
125 if self.pbc:
126 self.cmd.append('-pbc')
127 self.cmd.append(self.pbc)
128 self.cmd.append('-center' if self.center else '-nocenter')
129 if self.ur:
130 self.cmd.append('-ur')
131 self.cmd.append(self.ur)
132 if self.fit:
133 self.cmd.append('-fit')
134 self.cmd.append(self.fit)
136 if self.stage_io_dict["in"].get("input_index_path"):
137 self.cmd.extend(['-n', self.stage_io_dict["in"]["input_index_path"]])
139 # Add stdin input file
140 self.cmd.append('<')
141 self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
143 # Run Biobb block
144 self.run_biobb()
145 # Copy files to host
146 self.copy_to_host()
147 self.tmp_files.append(self.io_dict['in'].get("stdin_file_path", ""))
148 self.remove_tmp_files()
149 self.check_arguments(output_files_created=True, raise_exception=False)
150 return self.return_code
153def gmx_trjconv_str(input_structure_path: str,
154 input_top_path: str,
155 output_str_path: str,
156 input_index_path: Optional[str] = None,
157 properties: Optional[dict] = None,
158 **kwargs) -> int:
159 """Execute the :class:`GMXTrjConvStr <gromacs.gmx_trjconv_str.GMXTrjConvStr>` class and
160 execute the :meth:`launch() <gromacs.gmx_trjconv_str.GMXTrjConvStr.launch>` method."""
161 return GMXTrjConvStr(**dict(locals())).launch()
164gmx_trjconv_str.__doc__ = GMXTrjConvStr.__doc__
165main = GMXTrjConvStr.get_main(gmx_trjconv_str, "Converts between GROMACS compatible structure file formats and/or extracts a selection of atoms.")
167if __name__ == '__main__':
168 main()