Coverage for biobb_gromacs/gromacs/trjcat.py: 92%
53 statements
« prev ^ index » next coverage.py v7.14.1, created at 2026-05-28 06:50 +0000
1#!/usr/bin/env python3
3"""Module containing the Trjcat class and the command line interface."""
4from typing import Optional
5from pathlib import PurePath
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.tools import file_utils as fu
8from biobb_common.tools.file_utils import launchlogger
9from biobb_gromacs.gromacs.common import get_gromacs_version
12class Trjcat(BiobbObject):
13 """
14 | biobb_gromacs Trjcat
15 | Wrapper class for the `GROMACS trjcat <http://manual.gromacs.org/current/onlinehelp/gmx-trjcat.html>`_ module.
16 | The GROMACS solvate module generates a box around the selected structure.
18 Args:
19 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).
20 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).
21 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
22 * **concatenate** (*bool*) - (True) Only concatenate the files without removal of frames with identical timestamps.
23 * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
24 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
25 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
26 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
27 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
28 * **container_path** (*str*) - (None) Path to the binary executable of your container.
29 * **container_image** (*str*) - (None) Container Image identifier.
30 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
31 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
32 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
33 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
35 Examples:
36 This is a use example of how to use the building block from Python::
38 from biobb_gromacs.gromacs.trjcat import trjcat
39 prop = { 'concatenate': True }
40 trjcat(input_trj_zip_path='/path/to/trajectory_bundle.zip',
41 output_gro_path='/path/to/concatenated_trajectories.xtc',
42 properties=prop)
44 Info:
45 * wrapped_software:
46 * name: GROMACS trjcat
47 * version: 2025.2
48 * license: LGPL 2.1
49 * ontology:
50 * name: EDAM
51 * schema: http://edamontology.org/EDAM.owl
52 """
54 def __init__(self, input_trj_zip_path: str, output_trj_path: str, properties: Optional[dict] = None, **kwargs) -> None:
55 properties = properties or {}
57 # Call parent class constructor
58 super().__init__(properties)
59 self.locals_var_dict = locals().copy()
61 # Input/Output files
62 self.io_dict: dict = {
63 "in": {},
64 "out": {"output_trj_path": output_trj_path}
65 }
67 # Should not be copied inside container
68 self.input_trj_zip_path = input_trj_zip_path
70 # Properties specific for BB
71 self.concatenate: bool = properties.get('concatenate', True)
73 # Properties common in all GROMACS BB
74 self.gmx_lib = properties.get('gmx_lib', None)
75 self.binary_path = properties.get('binary_path', 'gmx')
76 self.gmx_nobackup = properties.get('gmx_nobackup', True)
77 self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
78 if self.gmx_nobackup:
79 self.binary_path += ' -nobackup'
80 if self.gmx_nocopyright:
81 self.binary_path += ' -nocopyright'
82 if not self.container_path:
83 self.gmx_version = get_gromacs_version(self.binary_path)
85 # Check the properties
86 self.check_properties(properties)
87 self.check_arguments()
89 @launchlogger
90 def launch(self) -> int:
91 """Execute the :class:`Trjcat <gromacs.trjcat.Trjcat>` object."""
93 # Setup Biobb
94 if self.check_restart():
95 return 0
96 self.stage_files()
98 # Unzip trajectory bundle directly into unique_dir so basenames work after cd
99 trj_list: list[str] = fu.unzip_list(self.input_trj_zip_path, self.stage_io_dict.get("unique_dir", ""), self.out_log)
100 trj_list = [PurePath(p).name for p in trj_list]
102 if self.container_path:
103 working_dir = self.container_volume_path if self.container_volume_path else "/data"
104 else:
105 working_dir = self.stage_io_dict.get('unique_dir', '')
107 # Create command line
108 self.cmd = ["cd", working_dir, ";",
109 self.binary_path, 'trjcat',
110 '-f', " ".join(trj_list),
111 '-o', PurePath(self.stage_io_dict["out"]["output_trj_path"]).name]
113 if self.concatenate:
114 self.cmd.append('-cat')
115 fu.log('Only concatenate the files without removal of frames with identical timestamps.', self.out_log, self.global_log)
117 if self.gmx_lib:
118 self.env_vars_dict['GMXLIB'] = self.gmx_lib
120 # Run Biobb block
121 self.run_biobb()
123 # Copy files to host
124 self.copy_to_host()
126 # Remove temporal files
127 self.remove_tmp_files()
129 self.check_arguments(output_files_created=True, raise_exception=False)
130 return self.return_code
133def trjcat(input_trj_zip_path: str, output_trj_path: str, properties: Optional[dict] = None, **kwargs) -> int:
134 """Create :class:`Trjcat <gromacs.trjcat.Trjcat>` class and
135 execute the :meth:`launch() <gromacs.trjcat.Trjcat.launch>` method."""
136 return Trjcat(**dict(locals())).launch()
139trjcat.__doc__ = Trjcat.__doc__
140main = Trjcat.get_main(trjcat, "Wrapper for the GROMACS trjcat module.")
143if __name__ == '__main__':
144 main()