Coverage for biobb_gromacs / gromacs / grompp.py: 79%
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« 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 Grompp class and the command line interface."""
4from typing import Optional
5import shutil
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
11from biobb_gromacs.gromacs.common import create_mdp
12from biobb_gromacs.gromacs.common import mdp_preset
15class Grompp(BiobbObject):
16 """
17 | biobb_gromacs Grompp
18 | Wrapper of the `GROMACS grompp <http://manual.gromacs.org/current/onlinehelp/gmx-grompp.html>`_ module.
19 | 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>`_.
21 Args:
22 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).
23 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).
24 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).
25 input_cpt_path (str) (Optional): Path to the input GROMACS checkpoint file CPT. File type: input. Accepted formats: cpt (edam:format_2333).
26 input_ndx_path (str) (Optional): Path to the input GROMACS index files NDX. File type: input. Accepted formats: ndx (edam:format_2033).
27 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).
28 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
29 * **mdp** (*dict*) - ({}) MDP options specification.
30 * **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).
31 * **maxwarn** (*int*) - (0) [0~1000|1] Maximum number of allowed warnings. If simulation_type is index default is 10.
32 * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
33 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
34 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
35 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
36 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
37 * **container_path** (*str*) - (None) Path to the binary executable of your container.
38 * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
39 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
40 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
41 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
42 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
44 Examples:
45 This is a use example of how to use the building block from Python::
47 from biobb_gromacs.gromacs.grompp import grompp
49 prop = { 'simulation_type': 'minimization',
50 'mdp':
51 { 'emtol':'500',
52 'nsteps':'5000'}}
53 grompp(input_gro_path='/path/to/myStructure.gro',
54 input_top_zip_path='/path/to/myTopology.zip',
55 output_tpr_path='/path/to/newCompiledBin.tpr',
56 properties=prop)
58 Info:
59 * wrapped_software:
60 * name: GROMACS Grompp
61 * version: 2025.2
62 * license: LGPL 2.1
63 * ontology:
64 * name: EDAM
65 * schema: http://edamontology.org/EDAM.owl
66 """
68 def __init__(self, input_gro_path: str, input_top_zip_path: str, output_tpr_path: str,
69 input_cpt_path: Optional[str] = None, input_ndx_path: Optional[str] = None, input_mdp_path: Optional[str] = None,
70 properties: Optional[dict] = None, **kwargs) -> None:
71 properties = properties or {}
73 # Call parent class constructor
74 super().__init__(properties)
75 self.locals_var_dict = locals().copy()
77 # Input/Output files
78 self.io_dict = {
79 "in": {"input_gro_path": input_gro_path, "input_cpt_path": input_cpt_path,
80 "input_ndx_path": input_ndx_path, "input_mdp_path": input_mdp_path},
81 "out": {"output_tpr_path": output_tpr_path}
82 }
83 # Should not be copied inside container
84 self.input_top_zip_path = input_top_zip_path
86 # Properties specific for BB
87 self.output_mdp_path = properties.get('output_mdp_path', 'grompp.mdp')
88 self.output_top_path = properties.get('output_top_path', 'grompp.top')
89 self.simulation_type = properties.get('simulation_type')
90 self.maxwarn = str(properties.get('maxwarn', 0))
91 if self.simulation_type and self.simulation_type != 'index':
92 self.maxwarn = str(properties.get('maxwarn', 10))
93 self.mdp = {k: str(v) for k, v in properties.get('mdp', dict()).items()}
95 # Properties common in all GROMACS BB
96 self.gmx_lib = properties.get('gmx_lib', None)
97 self.binary_path = properties.get('binary_path', 'gmx')
98 self.gmx_nobackup = properties.get('gmx_nobackup', True)
99 self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
100 if self.gmx_nobackup:
101 self.binary_path += ' -nobackup'
102 if self.gmx_nocopyright:
103 self.binary_path += ' -nocopyright'
104 if not self.container_path:
105 self.gmx_version = get_gromacs_version(self.binary_path)
107 # Check the properties
108 self.check_properties(properties)
109 self.check_arguments()
111 @launchlogger
112 def launch(self) -> int:
113 """Execute the :class:`Grompp <gromacs.grompp.Grompp>` object."""
115 # Setup Biobb
116 if self.check_restart():
117 return 0
118 self.stage_files()
120 # Unzip topology to topology_out
121 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", ""))
123 # Create MDP file
124 self.output_mdp_path = create_mdp(output_mdp_path=str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(self.output_mdp_path)),
125 input_mdp_path=self.io_dict["in"]["input_mdp_path"],
126 preset_dict=mdp_preset(str(self.simulation_type)),
127 mdp_properties_dict=self.mdp)
129 # Copy extra files to container: MDP file and topology folder
130 if self.container_path:
131 self.output_mdp_path = str(Path(self.container_volume_path).joinpath(Path(self.output_mdp_path).name))
132 top_file = str(Path(self.container_volume_path).joinpath(Path(top_file).name))
134 self.cmd = [self.binary_path, 'grompp',
135 '-f', self.output_mdp_path,
136 '-c', self.stage_io_dict["in"]["input_gro_path"],
137 '-r', self.stage_io_dict["in"]["input_gro_path"],
138 '-p', top_file,
139 '-o', self.stage_io_dict["out"]["output_tpr_path"],
140 '-po', self.create_tmp_file('mdout.mdp'),
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 if self.container_path:
146 shutil.copy2(self.stage_io_dict["in"]["input_cpt_path"], self.stage_io_dict.get("unique_dir", ""))
147 self.cmd.append(str(Path(self.container_volume_path).joinpath(Path(self.stage_io_dict["in"]["input_cpt_path"]).name)))
148 else:
149 self.cmd.append(self.stage_io_dict["in"]["input_cpt_path"])
150 if self.stage_io_dict["in"].get("input_ndx_path") and Path(self.stage_io_dict["in"]["input_ndx_path"]).exists():
151 self.cmd.append('-n')
152 if self.container_path:
153 shutil.copy2(self.stage_io_dict["in"]["input_ndx_path"], self.stage_io_dict.get("unique_dir", ""))
154 self.cmd.append(str(Path(self.container_volume_path).joinpath(Path(self.stage_io_dict["in"]["input_ndx_path"]).name)))
155 else:
156 self.cmd.append(self.stage_io_dict["in"]["input_ndx_path"])
158 if self.gmx_lib:
159 self.env_vars_dict['GMXLIB'] = self.gmx_lib
161 # Run Biobb block
162 self.run_biobb()
164 # Copy files to host
165 self.copy_to_host()
167 # Remove temporal files
168 self.remove_tmp_files()
170 self.check_arguments(output_files_created=True, raise_exception=False)
171 return self.return_code
174def grompp(input_gro_path: str, input_top_zip_path: str, output_tpr_path: str,
175 input_cpt_path: Optional[str] = None, input_ndx_path: Optional[str] = None, input_mdp_path: Optional[str] = None,
176 properties: Optional[dict] = None, **kwargs) -> int:
177 """Create :class:`Grompp <gromacs.grompp.Grompp>` class and
178 execute the :meth:`launch() <gromacs.grompp.Grompp.launch>` method."""
179 return Grompp(**dict(locals())).launch()
182grompp.__doc__ = Grompp.__doc__
183main = Grompp.get_main(grompp, "Wrapper for the GROMACS grompp module.")
186if __name__ == '__main__':
187 main()