Coverage for biobb_gromacs / gromacs / trjcat.py: 89%
56 statements
« prev ^ index » next coverage.py v7.13.4, created at 2026-03-05 08:26 +0000
1#!/usr/bin/env python3
3"""Module containing the Trjcat class and the command line interface."""
4import shutil
5from typing import Optional
6from pathlib import Path
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.tools import file_utils as fu
9from biobb_common.tools.file_utils import launchlogger
10from biobb_gromacs.gromacs.common import get_gromacs_version
13class Trjcat(BiobbObject):
14 """
15 | biobb_gromacs Trjcat
16 | Wrapper class for the `GROMACS trjcat <http://manual.gromacs.org/current/onlinehelp/gmx-trjcat.html>`_ module.
17 | The GROMACS solvate module generates a box around the selected structure.
19 Args:
20 input_trj_zip_path (str): Path the input GROMACS trajectories (xtc, trr, cpt, gro, pdb, tng) to concatenate in zip format. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/trjcat.zip>`_. Accepted formats: zip (edam:format_3987).
21 output_trj_path (str): Path to the output trajectory file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_trjcat.trr>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033), xtc (edam:format_3875), trr (edam:format_3910), tng (edam:format_3876).
22 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
23 * **concatenate** (*bool*) - (True) Only concatenate the files without removal of frames with identical timestamps.
24 * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
25 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
26 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
27 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
28 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
29 * **container_path** (*str*) - (None) Path to the binary executable of your container.
30 * **container_image** (*str*) - (None) Container Image identifier.
31 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
32 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
33 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
34 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
36 Examples:
37 This is a use example of how to use the building block from Python::
39 from biobb_gromacs.gromacs.trjcat import trjcat
40 prop = { 'concatenate': True }
41 trjcat(input_trj_zip_path='/path/to/trajectory_bundle.zip',
42 output_gro_path='/path/to/concatenated_trajectories.xtc',
43 properties=prop)
45 Info:
46 * wrapped_software:
47 * name: GROMACS trjcat
48 * version: 2025.2
49 * license: LGPL 2.1
50 * ontology:
51 * name: EDAM
52 * schema: http://edamontology.org/EDAM.owl
53 """
55 def __init__(self, input_trj_zip_path: str, output_trj_path: str, properties: Optional[dict] = None, **kwargs) -> None:
56 properties = properties or {}
58 # Call parent class constructor
59 super().__init__(properties)
60 self.locals_var_dict = locals().copy()
62 # Input/Output files
63 self.io_dict: dict = {
64 "in": {},
65 "out": {"output_trj_path": output_trj_path}
66 }
68 # Should not be copied inside container
69 self.input_trj_zip_path = input_trj_zip_path
71 # Properties specific for BB
72 self.concatenate: bool = properties.get('concatenate', True)
74 # Properties common in all GROMACS BB
75 self.gmx_lib = properties.get('gmx_lib', None)
76 self.binary_path = properties.get('binary_path', 'gmx')
77 self.gmx_nobackup = properties.get('gmx_nobackup', True)
78 self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
79 if self.gmx_nobackup:
80 self.binary_path += ' -nobackup'
81 if self.gmx_nocopyright:
82 self.binary_path += ' -nocopyright'
83 if not self.container_path:
84 self.gmx_version = get_gromacs_version(self.binary_path)
86 # Check the properties
87 self.check_properties(properties)
88 self.check_arguments()
90 @launchlogger
91 def launch(self) -> int:
92 """Execute the :class:`Trjcat <gromacs.trjcat.Trjcat>` object."""
94 # Setup Biobb
95 if self.check_restart():
96 return 0
97 self.stage_files()
99 # Unzip trajectory bundle
100 trj_dir: str = fu.create_unique_dir()
101 trj_list: list[str] = fu.unzip_list(self.input_trj_zip_path, trj_dir, self.out_log)
103 # Copy trajectories to container
104 if self.container_path:
105 for index, trajectory_file_path in enumerate(trj_list):
106 shutil.copy2(trajectory_file_path, self.stage_io_dict.get("unique_dir", ""))
107 trj_list[index] = str(Path(self.container_volume_path).joinpath(Path(trajectory_file_path).name))
109 # Create command line
110 self.cmd = [self.binary_path, 'trjcat',
111 '-f', " ".join(trj_list),
112 '-o', self.stage_io_dict["out"]["output_trj_path"]]
114 if self.concatenate:
115 self.cmd.append('-cat')
116 fu.log('Only concatenate the files without removal of frames with identical timestamps.', self.out_log, self.global_log)
118 if self.gmx_lib:
119 self.env_vars_dict['GMXLIB'] = self.gmx_lib
121 # Run Biobb block
122 self.run_biobb()
124 # Copy files to host
125 self.copy_to_host()
127 # Remove temporal files
128 self.tmp_files.append(trj_dir)
129 self.remove_tmp_files()
131 self.check_arguments(output_files_created=True, raise_exception=False)
132 return self.return_code
135def trjcat(input_trj_zip_path: str, output_trj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
136 """Create :class:`Trjcat <gromacs.trjcat.Trjcat>` class and
137 execute the :meth:`launch() <gromacs.trjcat.Trjcat.launch>` method."""
138 return Trjcat(**dict(locals())).launch()
141trjcat.__doc__ = Trjcat.__doc__
142main = Trjcat.get_main(trjcat, "Wrapper for the GROMACS trjcat module.")
145if __name__ == '__main__':
146 main()