Coverage for biobb_gromacs/gromacs/convert_tpr.py: 80%
69 statements
« prev ^ index » next coverage.py v7.15.2, created at 2026-07-27 16:28 +0000
1#!/usr/bin/env python3
3"""Module containing the Convert_tpr class and the command line interface."""
4from pathlib import Path, PurePath
5from typing import Optional
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 ConvertTpr(BiobbObject):
13 """
14 | biobb_gromacs ConvertTpr
15 | Wrapper of the `GROMACS convert-tpr <https://manual.gromacs.org/current/onlinehelp/gmx-convert-tpr.html>`_ module.
16 | The GROMACS convert-tpr module can edit run input files (.tpr): modify the run length (extend/until/nsteps) or trim the tpr file to a subset of atoms defined in an index file (input_ndx_path). Note that GROMACS does not allow both operations in a single call, so when an index file is provided the extend/until/nsteps properties are ignored.
18 Args:
19 input_tpr_path (str): Path to the input portable binary run file TPR. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr>`_. Accepted formats: tpr (edam:format_2333).
20 output_tpr_path (str): Path to the output portable binary run file TPR. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_grompp.tpr>`_. Accepted formats: tpr (edam:format_2333).
21 input_ndx_path (str) (Optional): Path to the input index NDX file, used to trim the tpr file to a subset of atoms. File type: input. Accepted formats: ndx (edam:format_2033).
22 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
23 * **extend** (*int*) - (0) Extend the runtime by this amount (ps).
24 * **until** (*int*) - (0) Extend the runtime until this ending time (ps).
25 * **nsteps** (*int*) - (0) Change the number of steps remaining to be made.
26 * **output_group** (*str*) - ("System") Index group to write to the output tpr file when trimming to a subset of atoms. Only used when input_ndx_path is provided.
27 * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
28 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
29 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
30 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
31 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
32 * **container_path** (*str*) - (None) Path to the binary executable of your container.
33 * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
34 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
35 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
36 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
37 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
39 Examples:
40 This is a use example of how to use the building block from Python::
42 from biobb_gromacs.gromacs.convert_tpr import convert_tpr
44 prop = { 'extend': 100000}
45 convert_tpr(input_tpr_path='/path/to/myStructure.tpr',
46 output_tpr_path='/path/to/newCompiledBin.tpr',
47 properties=prop)
49 # Trim the tpr file to a subset of atoms defined in an index file
50 prop = { 'output_group': 'Protein'}
51 convert_tpr(input_tpr_path='/path/to/myStructure.tpr',
52 output_tpr_path='/path/to/trimmedBin.tpr',
53 input_ndx_path='/path/to/myIndex.ndx',
54 properties=prop)
56 Info:
57 * wrapped_software:
58 * name: GROMACS Convert-tpr
59 * version: 2025.2
60 * license: LGPL 2.1
61 * ontology:
62 * name: EDAM
63 * schema: http://edamontology.org/EDAM.owl
64 """
66 def __init__(self, input_tpr_path: str, output_tpr_path: str,
67 input_ndx_path: Optional[str] = None,
68 properties: Optional[dict] = None, **kwargs) -> None:
69 properties = properties or {}
71 # Call parent class constructor
72 super().__init__(properties)
73 self.locals_var_dict = locals().copy()
75 # Input/Output files
76 self.io_dict = {
77 "in": {"input_tpr_path": input_tpr_path, "input_ndx_path": input_ndx_path},
78 "out": {"output_tpr_path": output_tpr_path}
79 }
81 # Properties specific for BB
82 self.extend = properties.get('extend')
83 self.until = properties.get('until')
84 self.nsteps = properties.get('nsteps')
85 self.output_group = properties.get('output_group', 'System')
87 # Properties common in all GROMACS BB
88 self.gmx_lib = properties.get('gmx_lib', None)
89 self.binary_path = properties.get('binary_path', 'gmx')
90 self.gmx_nobackup = properties.get('gmx_nobackup', True)
91 self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
92 if self.gmx_nobackup:
93 self.binary_path += ' -nobackup'
94 if self.gmx_nocopyright:
95 self.binary_path += ' -nocopyright'
96 if not self.container_path:
97 self.gmx_version = get_gromacs_version(self.binary_path)
99 # Check the properties
100 self.check_properties(properties)
101 self.check_arguments()
103 @launchlogger
104 def launch(self) -> int:
105 """Execute the :class:`ConvertTpr <gromacs.convert_tpr.ConvertTpr>` object."""
107 # Setup Biobb
108 if self.check_restart():
109 return 0
111 # When trimming to a subset (an index file is provided), GROMACS
112 # convert-tpr prompts for the output group; answer it via stdin.
113 if self.io_dict["in"].get("input_ndx_path"):
114 self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(f"{self.output_group}")
116 self.stage_files()
118 if self.container_path:
119 working_dir = self.container_volume_path if self.container_volume_path else "/data"
120 else:
121 working_dir = self.stage_io_dict.get('unique_dir', '')
123 self.cmd = ["cd", working_dir, ";", self.binary_path, 'convert-tpr',
124 '-s', PurePath(self.stage_io_dict["in"]["input_tpr_path"]).name,
125 '-o', PurePath(self.stage_io_dict["out"]["output_tpr_path"]).name
126 ]
128 trimming = bool(self.stage_io_dict["in"].get("input_ndx_path")) and \
129 Path(self.stage_io_dict["in"].get("input_ndx_path")).exists()
131 if trimming:
132 # Trim the tpr to the selected index group. GROMACS does not allow
133 # combining index-group extraction with runtime modification
134 # (-extend/-until/-nsteps) in a single convert-tpr call.
135 self.cmd.append('-n')
136 self.cmd.append(PurePath(self.stage_io_dict["in"].get("input_ndx_path")).name)
137 if self.extend or self.until or self.nsteps:
138 fu.log("Warning: extend, until and nsteps are ignored when trimming the tpr "
139 "file to an index group; GROMACS convert-tpr cannot do both in a single call.",
140 self.out_log, self.global_log)
141 else:
142 if self.extend:
143 self.cmd.extend(['-extend', str(self.extend)])
144 if self.until:
145 self.cmd.extend(['-until', str(self.until)])
146 if self.nsteps:
147 self.cmd.extend(['-nsteps', str(self.nsteps)])
149 # Add stdin input file to answer the output group prompt when trimming
150 if self.io_dict["in"].get("stdin_file_path"):
151 self.cmd.append('<')
152 self.cmd.append(PurePath(self.stage_io_dict["in"]["stdin_file_path"]).name)
154 if self.gmx_lib:
155 self.env_vars_dict['GMXLIB'] = self.gmx_lib
157 # Run Biobb block
158 self.run_biobb()
160 # Copy files to host
161 self.copy_to_host()
163 if self.io_dict["in"].get("stdin_file_path"):
164 self.tmp_files.append(str(self.io_dict["in"].get("stdin_file_path")))
165 self.remove_tmp_files()
167 self.check_arguments(output_files_created=True, raise_exception=False)
168 return self.return_code
171def convert_tpr(input_tpr_path: str, output_tpr_path: str, input_ndx_path: Optional[str] = None,
172 properties: Optional[dict] = None, **kwargs) -> int:
173 """Create :class:`ConvertTpr <gromacs.convert_tpr.ConvertTpr>` class and
174 execute the :meth:`launch() <gromacs.convert_tpr.ConvertTpr.launch>` method."""
175 return ConvertTpr(**dict(locals())).launch()
178convert_tpr.__doc__ = ConvertTpr.__doc__
179main = ConvertTpr.get_main(
180 convert_tpr, "Wrapper of the GROMACS convert-tpr module.")
183if __name__ == '__main__':
184 main()