Coverage for biobb_gromacs / gromacs / make_ndx.py: 91%
53 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 MakeNdx class and the command line interface."""
4from typing import Optional
5from pathlib import Path
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 MakeNdx(BiobbObject):
13 """
14 | biobb_gromacs MakeNdx
15 | Wrapper of the `GROMACS make_ndx <http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_ module.
16 | The GROMACS make_ndx module, generates an index file using the atoms of the selection.
18 Args:
19 input_structure_path (str): Path to the input GRO/PDB/TPR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/make_ndx.tpr>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476), tpr (edam:format_2333).
20 output_ndx_path (str): Path to the output index NDX file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_make_ndx.ndx>`_. Accepted formats: ndx (edam:format_2033).
21 input_ndx_path (str) (Optional): Path to the input index NDX file. File type: input. Accepted formats: ndx (edam:format_2033).
22 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
23 * **selection** (*str*) - ("a CA C N O") Heavy atoms. Atom selection string.
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*) - ("gromacs/gromacs:latest") 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.make_ndx import make_ndx
40 prop = { 'selection': 'a CA C N O' }
41 make_ndx(input_structure_path='/path/to/myStructure.gro',
42 output_ndx_path='/path/to/newIndex.ndx',
43 properties=prop)
45 Info:
46 * wrapped_software:
47 * name: GROMACS MakeNdx
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_structure_path: str, output_ndx_path: str, input_ndx_path: Optional[str] = None,
56 properties: Optional[dict] = None, **kwargs) -> None:
57 properties = properties or {}
59 # Call parent class constructor
60 super().__init__(properties)
61 self.locals_var_dict = locals().copy()
63 # Input/Output files
64 self.io_dict = {
65 "in": {"input_structure_path": input_structure_path, "input_ndx_path": input_ndx_path},
66 "out": {"output_ndx_path": output_ndx_path}
67 }
69 # Properties specific for BB
70 self.binary_path = properties.get('binary_path', 'gmx')
71 self.selection = properties.get('selection', "a CA C N O")
73 # Properties common in all GROMACS BB
74 self.gmx_lib = properties.get('gmx_lib', None)
75 self.gmx_nobackup = properties.get('gmx_nobackup', True)
76 self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
77 if self.gmx_nobackup:
78 self.binary_path += ' -nobackup'
79 if self.gmx_nocopyright:
80 self.binary_path += ' -nocopyright'
81 if not self.container_path:
82 self.gmx_version = get_gromacs_version(self.binary_path)
84 # Check the properties
85 self.check_properties(properties)
86 self.check_arguments()
88 @launchlogger
89 def launch(self) -> int:
90 """Execute the :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` object."""
92 # Setup Biobb
93 if self.check_restart():
94 return 0
96 self.selection = str(self.selection)
97 self.selection = self.selection.replace("\\n", "\n")
98 self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.selection}\nq\n')
99 self.stage_files()
101 # Create command line
102 self.cmd = [self.binary_path, 'make_ndx',
103 '-f', self.stage_io_dict["in"]["input_structure_path"],
104 '-o', self.stage_io_dict["out"]["output_ndx_path"]]
106 if self.stage_io_dict["in"].get("input_ndx_path")\
107 and Path(self.stage_io_dict["in"].get("input_ndx_path")).exists():
108 self.cmd.append('-n')
109 self.cmd.append(self.stage_io_dict["in"].get("input_ndx_path"))
111 # Add stdin input file
112 self.cmd.append('<')
113 self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
115 if self.gmx_lib:
116 self.env_vars_dict['GMXLIB'] = self.gmx_lib
118 # create_cmd_line and execute_command
119 self.run_biobb()
121 # Retrieve results
122 self.copy_to_host()
124 # Remove temporal files
125 self.tmp_files.append(self.io_dict['in'].get("stdin_file_path", ''))
126 self.remove_tmp_files()
128 self.check_arguments(output_files_created=True, raise_exception=False)
129 return self.return_code
132def make_ndx(input_structure_path: str, output_ndx_path: str,
133 input_ndx_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
134 """Create :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` class and
135 execute the :meth:`launch() <gromacs.make_ndx.MakeNdx.launch>` method."""
136 return MakeNdx(**dict(locals())).launch()
139make_ndx.__doc__ = MakeNdx.__doc__
140main = MakeNdx.get_main(make_ndx, "Wrapper for the GROMACS make_ndx module.")
143if __name__ == '__main__':
144 main()