Coverage for biobb_gromacs/gromacs/grompp.py: 88%
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« 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 Grompp class and the command line interface."""
4from typing import Optional
5from pathlib import Path, 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
10from biobb_gromacs.gromacs.common import create_mdp
11from biobb_gromacs.gromacs.common import mdp_preset
14class Grompp(BiobbObject):
15 """
16 | biobb_gromacs Grompp
17 | Wrapper of the `GROMACS grompp <http://manual.gromacs.org/current/onlinehelp/gmx-grompp.html>`_ module.
18 | The GROMACS preprocessor module needs to be fed with the input system and the dynamics parameters to create a portable binary run input file TPR. The simulation parameters can be specified by two methods: 1.The predefined mdp settings defined at simulation_type property or 2.A custom mdp file defined at the input_mdp_path argument. These two methods are mutually exclusive. In both cases can be further modified by adding parameters to the mdp section in the yaml configuration file. The simulation parameter names and default values can be consulted in the `official MDP specification <http://manual.gromacs.org/current/user-guide/mdp-options.html>`_.
20 Args:
21 input_gro_path (str): Path to the input GROMACS structure GRO file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/grompp.gro>`_. Accepted formats: gro (edam:format_2033).
22 input_top_zip_path (str): Path to the input GROMACS topology TOP and ITP files in zip format. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/grompp.zip>`_. Accepted formats: zip (edam:format_3987).
23 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).
24 input_cpt_path (str) (Optional): Path to the input GROMACS checkpoint file CPT. File type: input. Accepted formats: cpt (edam:format_2333).
25 input_ndx_path (str) (Optional): Path to the input GROMACS index files NDX. File type: input. Accepted formats: ndx (edam:format_2033).
26 input_mdp_path (str) (Optional): Path to the input GROMACS `MDP file <http://manual.gromacs.org/current/user-guide/mdp-options.html>`_. File type: input. Accepted formats: mdp (edam:format_2330).
27 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
28 * **mdp** (*dict*) - ({}) MDP options specification.
29 * **simulation_type** (*str*) - (None) Default options for the mdp file. Each one creates a different mdp file. Values: `minimization <https://biobb-gromacs.readthedocs.io/en/latest/_static/mdp/minimization.mdp>`_ (Energy minimization using steepest descent algorithm is used), `nvt <https://biobb-gromacs.readthedocs.io/en/latest/_static/mdp/nvt.mdp>`_ (substance N Volume V and Temperature T are conserved), `npt <https://biobb-gromacs.readthedocs.io/en/latest/_static/mdp/npt.mdp>`_ (substance N pressure P and Temperature T are conserved), `free <https://biobb-gromacs.readthedocs.io/en/latest/_static/mdp/free.mdp>`_ (No design constraints applied; Free MD), `ions <https://biobb-gromacs.readthedocs.io/en/latest/_static/mdp/minimization.mdp>`_ (Synonym of minimization), index (Creates an empty mdp file).
30 * **maxwarn** (*int*) - (0) [0~1000|1] Maximum number of allowed warnings. If simulation_type is index default is 10.
31 * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
32 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
33 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
34 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
35 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
36 * **container_path** (*str*) - (None) Path to the binary executable of your container.
37 * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
38 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
39 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
40 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
41 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
43 Examples:
44 This is a use example of how to use the building block from Python::
46 from biobb_gromacs.gromacs.grompp import grompp
48 prop = { 'simulation_type': 'minimization',
49 'mdp':
50 { 'emtol':'500',
51 'nsteps':'5000'}}
52 grompp(input_gro_path='/path/to/myStructure.gro',
53 input_top_zip_path='/path/to/myTopology.zip',
54 output_tpr_path='/path/to/newCompiledBin.tpr',
55 properties=prop)
57 Info:
58 * wrapped_software:
59 * name: GROMACS Grompp
60 * version: 2025.2
61 * license: LGPL 2.1
62 * ontology:
63 * name: EDAM
64 * schema: http://edamontology.org/EDAM.owl
65 """
67 def __init__(self, input_gro_path: str, input_top_zip_path: str, output_tpr_path: str,
68 input_cpt_path: Optional[str] = None, input_ndx_path: Optional[str] = None, input_mdp_path: Optional[str] = None,
69 properties: Optional[dict] = None, **kwargs) -> None:
70 properties = properties or {}
72 # Call parent class constructor
73 super().__init__(properties)
74 self.locals_var_dict = locals().copy()
76 # Input/Output files
77 self.io_dict = {
78 "in": {"input_gro_path": input_gro_path, "input_cpt_path": input_cpt_path,
79 "input_ndx_path": input_ndx_path, "input_mdp_path": input_mdp_path},
80 "out": {"output_tpr_path": output_tpr_path}
81 }
82 # Should not be copied inside container
83 self.input_top_zip_path = input_top_zip_path
85 # Properties specific for BB
86 self.output_mdp_path = properties.get('output_mdp_path', 'grompp.mdp')
87 self.output_top_path = properties.get('output_top_path', 'grompp.top')
88 self.simulation_type = properties.get('simulation_type')
89 self.maxwarn = str(properties.get('maxwarn', 0))
90 if self.simulation_type and self.simulation_type != 'index':
91 self.maxwarn = str(properties.get('maxwarn', 10))
92 self.mdp = {k: str(v) for k, v in properties.get('mdp', dict()).items()}
94 # Properties common in all GROMACS BB
95 self.gmx_lib = properties.get('gmx_lib', None)
96 self.binary_path = properties.get('binary_path', 'gmx')
97 self.gmx_nobackup = properties.get('gmx_nobackup', True)
98 self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
99 if self.gmx_nobackup:
100 self.binary_path += ' -nobackup'
101 if self.gmx_nocopyright:
102 self.binary_path += ' -nocopyright'
103 if not self.container_path:
104 self.gmx_version = get_gromacs_version(self.binary_path)
106 # Check the properties
107 self.check_properties(properties)
108 self.check_arguments()
110 @launchlogger
111 def launch(self) -> int:
112 """Execute the :class:`Grompp <gromacs.grompp.Grompp>` object."""
114 # Setup Biobb
115 if self.check_restart():
116 return 0
117 self.stage_files()
119 # Unzip topology to topology_out
120 top_file = fu.unzip_top(zip_file=self.input_top_zip_path, out_log=self.out_log, unique_dir=self.stage_io_dict.get("unique_dir", ""))
122 # Create MDP file
123 self.output_mdp_path = create_mdp(output_mdp_path=str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(self.output_mdp_path)),
124 input_mdp_path=self.io_dict["in"]["input_mdp_path"],
125 preset_dict=mdp_preset(str(self.simulation_type)),
126 mdp_properties_dict=self.mdp)
128 if self.container_path:
129 working_dir = self.container_volume_path if self.container_volume_path else "/data"
130 else:
131 working_dir = self.stage_io_dict.get('unique_dir', '')
133 self.cmd = ["cd", working_dir, ";",
134 self.binary_path, 'grompp',
135 '-f', PurePath(self.output_mdp_path).name,
136 '-c', PurePath(self.stage_io_dict["in"]["input_gro_path"]).name,
137 '-r', PurePath(self.stage_io_dict["in"]["input_gro_path"]).name,
138 '-p', PurePath(top_file).name,
139 '-o', PurePath(self.stage_io_dict["out"]["output_tpr_path"]).name,
140 '-po', PurePath(self.create_tmp_file('mdout.mdp')).name,
141 '-maxwarn', self.maxwarn]
143 if self.stage_io_dict["in"].get("input_cpt_path") and Path(self.stage_io_dict["in"]["input_cpt_path"]).exists():
144 self.cmd.append('-t')
145 self.cmd.append(PurePath(self.stage_io_dict["in"]["input_cpt_path"]).name)
146 if self.stage_io_dict["in"].get("input_ndx_path") and Path(self.stage_io_dict["in"]["input_ndx_path"]).exists():
147 self.cmd.append('-n')
148 self.cmd.append(PurePath(self.stage_io_dict["in"]["input_ndx_path"]).name)
150 if self.gmx_lib:
151 self.env_vars_dict['GMXLIB'] = self.gmx_lib
153 # Run Biobb block
154 self.run_biobb()
156 # Copy files to host
157 self.copy_to_host()
159 # Remove temporal files
160 self.remove_tmp_files()
162 self.check_arguments(output_files_created=True, raise_exception=False)
163 return self.return_code
166def grompp(input_gro_path: str, input_top_zip_path: str, output_tpr_path: str,
167 input_cpt_path: Optional[str] = None, input_ndx_path: Optional[str] = None, input_mdp_path: Optional[str] = None,
168 properties: Optional[dict] = None, **kwargs) -> int:
169 """Create :class:`Grompp <gromacs.grompp.Grompp>` class and
170 execute the :meth:`launch() <gromacs.grompp.Grompp.launch>` method."""
171 return Grompp(**dict(locals())).launch()
174grompp.__doc__ = Grompp.__doc__
175main = Grompp.get_main(grompp, "Wrapper for the GROMACS grompp module.")
178if __name__ == '__main__':
179 main()