Coverage for biobb_gromacs/gromacs/editconf.py: 76%
68 statements
« 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 Editconf class and the command line interface."""
5import argparse
6from typing import Optional
8from biobb_common.configuration import settings
9from biobb_common.generic.biobb_object import BiobbObject
10from biobb_common.tools import file_utils as fu
11from biobb_common.tools.file_utils import launchlogger
13from biobb_gromacs.gromacs.common import get_gromacs_version
16class Editconf(BiobbObject):
17 """
18 | biobb_gromacs Editconf
19 | Wrapper class for the `GROMACS editconf <http://manual.gromacs.org/current/onlinehelp/gmx-editconf.html>`_ module.
20 | The GROMACS solvate module generates a box around the selected structure.
22 Args:
23 input_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/editconf.gro>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476).
24 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_editconf.gro>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
25 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
26 * **distance_to_molecule** (*float*) - (1.0) [0~100|0.1] Distance of the box from the outermost atom in nm. ie 1.0nm = 10 Angstroms.
27 * **box_vector_lenghts** (*str*) - (None) Array of floats defining the box vector lenghts ie "0.5 0.5 0.5". If this option is used the distance_to_molecule property will be ignored.
28 * **box_type** (*str*) - ("cubic") Geometrical shape of the solvent box. Values: cubic (rectangular box with all sides equal), triclinic (triclinic box), dodecahedron (rhombic dodecahedron), octahedron (truncated octahedron).
29 * **center_molecule** (*bool*) - (True) Center molecule in the box.
30 * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
31 * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
32 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
33 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
34 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
35 * **container_path** (*str*) - (None) Path to the binary executable of your container.
36 * **container_image** (*str*) - (None) Container Image identifier.
37 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
38 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
39 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
40 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
42 Examples:
43 This is a use example of how to use the building block from Python::
45 from biobb_gromacs.gromacs.editconf import editconf
46 prop = { 'distance_to_molecule': 1.0,
47 'box_type': 'cubic'}
48 editconf(input_gro_path='/path/to/structure.gro',
49 output_gro_path='/path/to/newStructure.gro',
50 properties=prop)
52 Info:
53 * wrapped_software:
54 * name: GROMACS Solvate
55 * version: 2024.5
56 * license: LGPL 2.1
57 * ontology:
58 * name: EDAM
59 * schema: http://edamontology.org/EDAM.owl
60 """
62 def __init__(
63 self,
64 input_gro_path: str,
65 output_gro_path: str,
66 properties: Optional[dict] = None,
67 **kwargs,
68 ) -> 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_gro_path": input_gro_path},
78 "out": {"output_gro_path": output_gro_path},
79 }
81 # Properties specific for BB
82 self.distance_to_molecule = properties.get("distance_to_molecule", 1.0)
83 self.box_vector_lenghts = properties.get("box_vector_lenghts")
84 self.box_type = properties.get("box_type", "cubic")
85 self.center_molecule = properties.get("center_molecule", True)
87 # Properties common in all GROMACS BB
88 self.gmx_lib = properties.get("gmx_lib", None)
89 self.binary_path: str = 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:`Editconf <gromacs.editconf.Editconf>` object."""
107 # Setup Biobb
108 if self.check_restart():
109 return 0
110 self.stage_files()
112 # Create command line
113 self.cmd = [
114 self.binary_path,
115 "editconf",
116 "-f",
117 self.stage_io_dict["in"]["input_gro_path"],
118 "-o",
119 self.stage_io_dict["out"]["output_gro_path"],
120 "-bt",
121 self.box_type,
122 ]
124 if self.box_vector_lenghts:
125 if not isinstance(self.box_vector_lenghts, str):
126 self.box_vector_lenghts = " ".join(map(str, self.box_vector_lenghts))
127 self.cmd.append("-box")
128 self.cmd.append(self.box_vector_lenghts)
129 else:
130 self.cmd.append("-d")
131 self.cmd.append(str(self.distance_to_molecule))
132 fu.log(
133 "Distance of the box to molecule: %6.2f" % self.distance_to_molecule,
134 self.out_log,
135 self.global_log,
136 )
138 if self.center_molecule:
139 self.cmd.append("-c")
140 fu.log("Centering molecule in the box.", self.out_log, self.global_log)
142 fu.log("Box type: %s" % self.box_type, self.out_log, self.global_log)
144 if self.gmx_lib:
145 self.env_vars_dict = self.gmx_lib
147 # Run Biobb block
148 self.run_biobb()
150 # Copy files to host
151 self.copy_to_host()
153 # Remove temporal files
154 # self.tmp_files.append(str(self.stage_io_dict.get("unique_dir", "")))
155 self.remove_tmp_files()
157 # self.check_arguments(output_files_created=True, raise_exception=False)
158 return self.return_code
161def editconf(
162 input_gro_path: str,
163 output_gro_path: str,
164 properties: Optional[dict] = None,
165 **kwargs,
166) -> int:
167 """Create :class:`Editconf <gromacs.editconf.Editconf>` class and
168 execute the :meth:`launch() <gromacs.editconf.Editconf.launch>` method."""
170 return Editconf(
171 input_gro_path=input_gro_path,
172 output_gro_path=output_gro_path,
173 properties=properties,
174 **kwargs,
175 ).launch()
178editconf.__doc__ = Editconf.__doc__
181def main():
182 parser = argparse.ArgumentParser(
183 description="Wrapper of the GROMACS gmx editconf module.",
184 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
185 )
186 parser.add_argument(
187 "-c",
188 "--config",
189 required=False,
190 help="This file can be a YAML file, JSON file or JSON string",
191 )
193 # Specific args of each building block
194 required_args = parser.add_argument_group("required arguments")
195 required_args.add_argument("--input_gro_path", required=True)
196 required_args.add_argument("--output_gro_path", required=True)
198 args = parser.parse_args()
199 config = args.config if args.config else None
200 properties = settings.ConfReader(config=config).get_prop_dic()
202 # Specific call of each building block
203 editconf(
204 input_gro_path=args.input_gro_path,
205 output_gro_path=args.output_gro_path,
206 properties=properties,
207 )
210if __name__ == "__main__":
211 main()