Coverage for biobb_gromacs/gromacs/genion.py: 76%
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« prev ^ index » next coverage.py v7.9.1, created at 2025-06-25 09:23 +0000
1#!/usr/bin/env python3
3"""Module containing the Genion class and the command line interface."""
5import argparse
6import shutil
7from pathlib import Path
8from typing import Optional, Union
10from biobb_common.configuration import settings
11from biobb_common.generic.biobb_object import BiobbObject
12from biobb_common.tools import file_utils as fu
13from biobb_common.tools.file_utils import launchlogger
15from biobb_gromacs.gromacs.common import get_gromacs_version
18class Genion(BiobbObject):
19 """
20 | biobb_gromacs Genion
21 | Wrapper class for the `GROMACS genion <http://manual.gromacs.org/current/onlinehelp/gmx-genion.html>`_ module.
22 | The GROMACS genion module randomly replaces solvent molecules with monoatomic ions. The group of solvent molecules should be continuous and all molecules should have the same number of atoms.
24 Args:
25 input_tpr_path (str): Path to the input portable run input TPR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/genion.tpr>`_. Accepted formats: tpr (edam:format_2333).
26 output_gro_path (str): Path to the input structure GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genion.gro>`_. Accepted formats: gro (edam:format_2033).
27 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/genion.zip>`_. Accepted formats: zip (edam:format_3987).
28 output_top_zip_path (str): Path the output topology TOP and ITP files zipball. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_genion.zip>`_. Accepted formats: zip (edam:format_3987).
29 input_ndx_path (str) (Optional): Path to the input index NDX file. File type: input. Accepted formats: ndx (edam:format_2033).
30 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
31 * **replaced_group** (*str*) - ("SOL") Group of molecules that will be replaced by the solvent.
32 * **neutral** (*bool*) - (False) Neutralize the charge of the system.
33 * **concentration** (*float*) - (0.0) [0~10|0.01] Concentration of the ions in (mol/liter).
34 * **seed** (*int*) - (1993) Seed for random number generator.
35 * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
36 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
37 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
38 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
39 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
40 * **container_path** (*str*) - (None) Path to the binary executable of your container.
41 * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
42 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
43 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
44 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
45 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
47 Examples:
48 This is a use example of how to use the building block from Python::
50 from biobb_gromacs.gromacs.genion import genion
51 prop = { 'concentration': 0.05,
52 'replaced_group': 'SOL'}
53 genion(input_tpr_path='/path/to/myPortableBinaryRunInputFile.tpr',
54 output_gro_path='/path/to/newStructure.gro',
55 input_top_zip_path='/path/to/myTopology.zip',
56 output_top_zip_path='/path/to/newTopology.zip',
57 properties=prop)
59 Info:
60 * wrapped_software:
61 * name: GROMACS Genion
62 * version: 2024.5
63 * license: LGPL 2.1
64 * ontology:
65 * name: EDAM
66 * schema: http://edamontology.org/EDAM.owl
67 """
69 def __init__(
70 self,
71 input_tpr_path: Union[str, Path],
72 output_gro_path: Union[str, Path],
73 input_top_zip_path: Union[str, Path],
74 output_top_zip_path: Union[str, Path],
75 input_ndx_path: Optional[Union[str, Path]] = None,
76 properties: Optional[dict] = None,
77 **kwargs,
78 ) -> None:
79 properties = properties or {}
81 # Call parent class constructor
82 super().__init__(properties)
83 self.locals_var_dict = locals().copy()
85 # Input/Output files
86 self.io_dict = {
87 "in": {"input_tpr_path": input_tpr_path, "input_ndx_path": input_ndx_path},
88 "out": {
89 "output_gro_path": output_gro_path,
90 "output_top_zip_path": output_top_zip_path,
91 },
92 }
93 # Should not be copied inside container
94 self.input_top_zip_path = input_top_zip_path
96 # Properties specific for BB
97 self.output_top_path = properties.get(
98 "output_top_path", "gio.top"
99 ) # Not in documentation for clarity
100 self.replaced_group = properties.get("replaced_group", "SOL")
101 self.neutral = properties.get("neutral", False)
102 self.concentration = properties.get("concentration", 0.0)
103 self.seed = properties.get("seed", 1993)
105 # Properties common in all GROMACS BB
106 self.gmx_lib = properties.get("gmx_lib", None)
107 self.binary_path = properties.get("binary_path", "gmx")
108 self.gmx_nobackup = properties.get("gmx_nobackup", True)
109 self.gmx_nocopyright = properties.get("gmx_nocopyright", True)
110 if self.gmx_nobackup:
111 self.binary_path = f"{self.binary_path} -nobackup"
112 if self.gmx_nocopyright:
113 self.binary_path = f"{self.binary_path} -nocopyright"
114 if not self.container_path:
115 self.gmx_version = get_gromacs_version(str(self.binary_path))
117 # Check the properties
118 self.check_properties(properties)
119 self.check_arguments()
121 @launchlogger
122 def launch(self) -> int:
123 """Execute the :class:`Genion <gromacs.genion.Genion>` object."""
125 # Setup Biobb
126 if self.check_restart():
127 return 0
129 self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(
130 f"{self.replaced_group}"
131 )
132 self.stage_files()
134 # Unzip topology to topology_out
135 top_file = fu.unzip_top(zip_file=self.input_top_zip_path, out_log=self.out_log)
136 top_dir = str(Path(top_file).parent)
138 if self.container_path:
139 shutil.copytree(
140 top_dir,
141 Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(
142 Path(top_dir).name
143 ),
144 )
145 top_file = str(
146 Path(self.container_volume_path).joinpath(
147 Path(top_dir).name, Path(top_file).name
148 )
149 )
151 self.cmd = [
152 str(self.binary_path),
153 "genion",
154 "-s",
155 self.stage_io_dict["in"]["input_tpr_path"],
156 "-o",
157 self.stage_io_dict["out"]["output_gro_path"],
158 "-p",
159 top_file,
160 ]
162 if (
163 self.stage_io_dict["in"].get("input_ndx_path") and Path(self.stage_io_dict["in"].get("input_ndx_path")).exists()
164 ):
165 self.cmd.append("-n")
166 self.cmd.append(self.stage_io_dict["in"].get("input_ndx_path"))
168 if self.neutral:
169 self.cmd.append("-neutral")
171 if self.concentration:
172 self.cmd.append("-conc")
173 self.cmd.append(str(self.concentration))
174 fu.log(
175 "To reach up %g mol/litre concentration" % self.concentration,
176 self.out_log,
177 self.global_log,
178 )
180 if self.seed is not None:
181 self.cmd.append("-seed")
182 self.cmd.append(str(self.seed))
184 # Add stdin input file
185 self.cmd.append("<")
186 self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
188 if self.gmx_lib:
189 self.env_vars_dict["GMXLIB"] = self.gmx_lib
191 # Run Biobb block
192 self.run_biobb()
194 # Copy files to host
195 self.copy_to_host()
197 if self.container_path:
198 top_file = str(
199 Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(
200 Path(top_dir).name, Path(top_file).name
201 )
202 )
204 # zip topology
205 fu.log(
206 "Compressing topology to: %s"
207 % self.stage_io_dict["out"]["output_top_zip_path"],
208 self.out_log,
209 self.global_log,
210 )
211 fu.zip_top(
212 zip_file=self.io_dict["out"]["output_top_zip_path"],
213 top_file=top_file,
214 out_log=self.out_log,
215 remove_original_files=self.remove_tmp
216 )
218 # Remove temporal files
219 self.tmp_files.extend(
220 [
221 # str(self.stage_io_dict.get("unique_dir", "")),
222 top_dir,
223 str(self.io_dict["in"].get("stdin_file_path")),
224 ]
225 )
226 self.remove_tmp_files()
228 self.check_arguments(output_files_created=True, raise_exception=True)
229 return self.return_code
232def genion(
233 input_tpr_path: Union[str, Path],
234 output_gro_path: Union[str, Path],
235 input_top_zip_path: Union[str, Path],
236 output_top_zip_path: Union[str, Path],
237 input_ndx_path: Optional[Union[str, Path]] = None,
238 properties: Optional[dict] = None,
239 **kwargs,
240) -> int:
241 """Create :class:`Genion <gromacs.genion.Genion>` class and
242 execute the :meth:`launch() <gromacs.genion.Genion.launch>` method."""
243 return Genion(
244 input_tpr_path=input_tpr_path,
245 output_gro_path=output_gro_path,
246 input_top_zip_path=input_top_zip_path,
247 output_top_zip_path=output_top_zip_path,
248 input_ndx_path=input_ndx_path,
249 properties=properties,
250 **kwargs,
251 ).launch()
254genion.__doc__ = Genion.__doc__
257def main():
258 """Command line execution of this building block. Please check the command line documentation."""
259 parser = argparse.ArgumentParser(
260 description="Wrapper for the GROMACS genion module.",
261 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
262 )
263 parser.add_argument(
264 "-c",
265 "--config",
266 required=False,
267 help="This file can be a YAML file, JSON file or JSON string",
268 )
270 # Specific args of each building block
271 required_args = parser.add_argument_group("required arguments")
272 required_args.add_argument("--input_tpr_path", required=True)
273 required_args.add_argument("--output_gro_path", required=True)
274 required_args.add_argument("--input_top_zip_path", required=True)
275 required_args.add_argument("--output_top_zip_path", required=True)
276 parser.add_argument("--input_ndx_path", required=False)
278 args = parser.parse_args()
279 config = args.config if args.config else None
280 properties = settings.ConfReader(config=config).get_prop_dic()
282 # Specific call of each building block
283 genion(
284 input_tpr_path=args.input_tpr_path,
285 output_gro_path=args.output_gro_path,
286 input_top_zip_path=args.input_top_zip_path,
287 output_top_zip_path=args.output_top_zip_path,
288 input_ndx_path=args.input_ndx_path,
289 properties=properties,
290 )
293if __name__ == "__main__":
294 main()