Coverage for biobb_gromacs/gromacs/solvate.py: 86%
63 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 Editconf class and the command line interface."""
4import shutil
5from typing import Optional
6from pathlib import Path, PurePath
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
13class Solvate(BiobbObject):
14 """
15 | biobb_gromacs Solvate
16 | Wrapper of the `GROMACS solvate <http://manual.gromacs.org/current/onlinehelp/gmx-solvate.html>`_ module.
17 | The GROMACS solvate module, generates a box of solvent around the selected structure.
19 Args:
20 input_solute_gro_path (str): Path to the input GRO file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/solvate.gro>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476).
21 output_gro_path (str): Path to the output GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_solvate.gro>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476).
22 input_top_zip_path (str): Path the input TOP topology in zip format. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/solvate.zip>`_. Accepted formats: zip (edam:format_3987).
23 output_top_zip_path (str): Path the output topology in zip format. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_solvate.zip>`_. Accepted formats: zip (edam:format_3987).
24 input_solvent_gro_path (str) (Optional): (spc216.gro) Path to the GRO file containing the structure of the solvent. File type: input. Accepted formats: gro (edam:format_2033).
25 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
26 * **shell** (*float*) - (0.0) [0~100|0.1] Thickness in nanometers of optional water layer around solute.
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.solvate import Solvate
43 prop = { 'shell': 1.0 }
44 solvate(input_solute_gro_path='/path/to/myStructure.gro',
45 output_gro_path='/path/to/newStructure.gro',
46 input_top_zip_path='/path/to/myTopology.zip',
47 output_top_zip_path='/path/to/newTopology.zip',
48 properties=prop)
51 Info:
52 * wrapped_software:
53 * name: GROMACS Solvate
54 * version: 2025.2
55 * license: LGPL 2.1
56 * ontology:
57 * name: EDAM
58 * schema: http://edamontology.org/EDAM.owl
59 """
61 def __init__(self, input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str,
62 output_top_zip_path: str, input_solvent_gro_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> None:
63 properties = properties or {}
65 # Call parent class constructor
66 super().__init__(properties)
67 self.locals_var_dict = locals().copy()
69 # Input/Output files
70 self.io_dict = {
71 "in": {"input_solute_gro_path": input_solute_gro_path, "input_solvent_gro_path": input_solvent_gro_path},
72 "out": {"output_gro_path": output_gro_path, "output_top_zip_path": output_top_zip_path}
73 }
75 # Should not be copied inside container
76 self.input_top_zip_path = input_top_zip_path
78 # Properties specific for BB
79 self.shell = properties.get('shell')
80 if not self.io_dict["in"].get('input_solvent_gro_path'):
81 self.io_dict["in"]['input_solvent_gro_path'] = 'spc216.gro'
83 # Properties common in all GROMACS BB
84 self.gmx_lib = properties.get('gmx_lib', None)
85 self.binary_path = properties.get('binary_path', 'gmx')
86 self.gmx_nobackup = properties.get('gmx_nobackup', True)
87 self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
88 if self.gmx_nobackup:
89 self.binary_path += ' -nobackup'
90 if self.gmx_nocopyright:
91 self.binary_path += ' -nocopyright'
92 if not self.container_path:
93 self.gmx_version = get_gromacs_version(self.binary_path)
95 # Check the properties
96 self.check_properties(properties)
97 self.check_arguments()
99 @launchlogger
100 def launch(self) -> int:
101 """Execute the :class:`Solvate <gromacs.solvate.Solvate>` object."""
103 # Setup Biobb
104 if self.check_restart():
105 return 0
106 self.stage_files()
108 # Unzip topology to topology_out
109 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", ""))
110 top_dir = str(Path(top_file).parent)
112 if self.container_path:
113 shutil.copytree(top_dir, str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath(Path(top_dir).name)))
114 top_file = str(Path(Path(top_dir).name).joinpath(Path(top_file).name))
116 if self.container_path:
117 working_dir = self.container_volume_path if self.container_volume_path else "/data"
118 else:
119 working_dir = self.stage_io_dict.get('unique_dir', '')
121 self.cmd = ["cd", working_dir, ";",
122 self.binary_path, 'solvate',
123 '-cp', PurePath(self.stage_io_dict["in"]["input_solute_gro_path"]).name,
124 '-cs', PurePath(self.stage_io_dict["in"]["input_solvent_gro_path"]).name,
125 '-o', PurePath(self.stage_io_dict["out"]["output_gro_path"]).name,
126 '-p', top_file]
128 if self.shell:
129 self.cmd.append("-shell")
130 self.cmd.append(str(self.shell))
132 if self.gmx_lib:
133 self.env_vars_dict['GMXLIB'] = self.gmx_lib
135 # Run Biobb block
136 self.run_biobb()
138 # Copy files to host
139 self.copy_to_host()
141 if self.container_path:
142 top_file = str(Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(
143 Path(top_dir).name, Path(top_file).name))
145 # zip topology
146 fu.log('Compressing topology to: %s' % self.stage_io_dict["out"]["output_top_zip_path"], self.out_log,
147 self.global_log)
148 fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=top_file, out_log=self.out_log, remove_original_files=self.remove_tmp)
150 # Remove temporal files
151 self.remove_tmp_files()
153 self.check_arguments(output_files_created=True, raise_exception=False)
154 return self.return_code
157def solvate(input_solute_gro_path: str, output_gro_path: str, input_top_zip_path: str,
158 output_top_zip_path: str, input_solvent_gro_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
159 """Create :class:`Solvate <gromacs.solvate.Solvate>` class and
160 execute the :meth:`launch() <gromacs.solvate.Solvate.launch>` method."""
161 return Solvate(**dict(locals())).launch()
164solvate.__doc__ = Solvate.__doc__
165main = Solvate.get_main(solvate, "Wrapper for the GROMACS solvate module.")
168if __name__ == '__main__':
169 main()