Coverage for biobb_chemistry/acpype/acpype_params_gmx.py: 78%
73 statements
« prev ^ index » next coverage.py v7.6.12, created at 2025-03-12 09:28 +0000
1#!/usr/bin/env python3
3"""Module containing the AcpypeParamsGMX class and the command line interface."""
4import argparse
5from typing import Optional
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.configuration import settings
8from biobb_common.tools.file_utils import launchlogger
9from biobb_chemistry.acpype.common import get_binary_path, check_input_path, check_output_path, get_basename, get_charge, create_unique_name, get_default_value, process_output_gmx
12class AcpypeParamsGMX(BiobbObject):
13 """
14 | biobb_chemistry AcpypeParamsGMX
15 | This class is a wrapper of `Acpype <https://github.com/alanwilter/acpype>`_ tool for generation of topologies for GROMACS.
16 | Generation of topologies for GROMACS. Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA. `Visit the official page <https://github.com/alanwilter/acpype>`_.
18 Args:
19 input_path (str): Path to the input file. File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/acpype/acpype.params.mol2>`_. Accepted formats: pdb (edam:format_1476), mdl (edam:format_3815), mol2 (edam:format_3816).
20 output_path_gro (str): Path to the GRO output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro>`_. Accepted formats: gro (edam:format_2033).
21 output_path_itp (str): Path to the ITP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.itp>`_. Accepted formats: itp (edam:format_3883).
22 output_path_top (str): Path to the TOP output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top>`_. Accepted formats: top (edam:format_3880).
23 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
24 * **basename** (*str*) - ("BBB") A basename for the project (folder and output files).
25 * **charge** (*int*) - (0) [-20~20|1] Net molecular charge, for gas default is 0. If None the charge is guessed by acpype.
26 * **binary_path** (*str*) - ("acpype") Path to the acpype executable binary.
27 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
28 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
29 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
30 * **container_path** (*str*) - (None) Container path definition.
31 * **container_image** (*str*) - ('acpype/acpype:2022.7.21') Container image definition.
32 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
33 * **container_working_dir** (*str*) - (None) Container working directory definition.
34 * **container_user_id** (*str*) - (None) Container user_id definition.
35 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
37 Examples:
38 This is a use example of how to use the building block from Python::
40 from biobb_chemistry.acpype.acpype_params_gmx import acpype_params_gmx
41 prop = {
42 'basename': 'BBB',
43 'charge': 0
44 }
45 acpype_params_gmx(input_path='/path/to/myStructure.mol2',
46 output_path_gro='/path/to/newGRO.gro',
47 output_path_itp='/path/to/newITP.itp',
48 output_path_top='/path/to/newTOP.top',
49 properties=prop)
51 Info:
52 * wrapped_software:
53 * name: Acpype
54 * version: 2019.10.05.12.26
55 * license: GNU
56 * ontology:
57 * name: EDAM
58 * schema: http://edamontology.org/EDAM.owl
60 """
62 def __init__(self, input_path, output_path_gro, output_path_itp, output_path_top,
63 properties=None, **kwargs) -> None:
64 properties = properties or {}
66 # Call parent class constructor
67 super().__init__(properties)
68 self.locals_var_dict = locals().copy()
70 # Input/Output files
71 self.io_dict = {
72 "in": {"input_path": input_path},
73 "out": {"output_path_gro": output_path_gro, "output_path_itp": output_path_itp, "output_path_top": output_path_top}
74 }
76 # Properties specific for BB
77 self.basename = properties.get('basename', 'BBB')
78 self.charge = properties.get('charge', '')
79 self.binary_path = get_binary_path(properties, 'binary_path')
80 self.properties = properties
82 # Check the properties
83 self.check_properties(properties)
84 self.check_arguments()
86 def check_data_params(self, out_log, err_log):
87 """ Checks all the input/output paths and parameters """
88 self.io_dict["in"]["input_path"] = check_input_path(self.io_dict["in"]["input_path"], out_log, self.__class__.__name__)
89 self.io_dict["out"]["output_path_gro"] = check_output_path(self.io_dict["out"]["output_path_gro"], 'gro', out_log, self.__class__.__name__)
90 self.io_dict["out"]["output_path_itp"] = check_output_path(self.io_dict["out"]["output_path_itp"], 'itp', out_log, self.__class__.__name__)
91 self.io_dict["out"]["output_path_top"] = check_output_path(self.io_dict["out"]["output_path_top"], 'top', out_log, self.__class__.__name__)
92 self.output_files = {
93 'gro': self.io_dict["out"]["output_path_gro"],
94 'itp': self.io_dict["out"]["output_path_itp"],
95 'top': self.io_dict["out"]["output_path_top"],
96 }
98 def create_cmd(self, container_io_dict, out_log, err_log):
99 """Creates the command line instruction using the properties file settings"""
100 instructions_list = []
102 # generating output path
103 if self.container_path:
104 out_pth = self.container_volume_path + '/' + get_basename(self.basename, out_log) + '.' + self.unique_name
105 else:
106 out_pth = get_basename(self.basename, out_log) + '.' + self.unique_name
108 # executable path
109 instructions_list.append(self.binary_path)
111 # generating input
112 ipath = '-i ' + container_io_dict["in"]["input_path"]
113 instructions_list.append(ipath)
115 # generating output
116 basename = '-b ' + out_pth
117 instructions_list.append(basename)
119 # adding charge if not None
120 charge = get_charge(self.charge, out_log)
121 if charge:
122 charge = '-n ' + charge
123 instructions_list.append(charge)
125 return instructions_list
127 @launchlogger
128 def launch(self) -> int:
129 """Execute the :class:`AcpypeParamsGMX <acpype.acpype_params_gmx.AcpypeParamsGMX>` acpype.acpype_params_gmx.AcpypeParamsGMX object."""
131 # check input/output paths and parameters
132 self.check_data_params(self.out_log, self.err_log)
134 # Setup Biobb
135 if self.check_restart():
136 return 0
137 self.stage_files()
139 # create unique name for temporary folder (created by acpype)
140 self.unique_name = create_unique_name(6)
142 # create command line instruction
143 self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log)
145 # Run Biobb block
146 self.run_biobb()
148 # Copy files to host
149 self.copy_to_host()
151 # move files to output_path and removes temporary folder
152 if self.container_path:
153 process_output_gmx(self.unique_name,
154 # self.stage_io_dict['unique_dir'],
155 self.remove_tmp,
156 self.basename,
157 get_default_value(self.__class__.__name__),
158 self.output_files, self.out_log)
159 else:
160 self.tmp_files.extend([self.basename + "." + self.unique_name + ".acpype"])
161 process_output_gmx(self.unique_name,
162 self.basename + "." + self.unique_name + ".acpype",
163 self.remove_tmp,
164 self.basename,
165 get_default_value(self.__class__.__name__),
166 self.output_files, self.out_log)
168 self.remove_tmp_files()
169 self.check_arguments(output_files_created=True, raise_exception=False)
171 return self.return_code
174def acpype_params_gmx(input_path: str, output_path_gro: str, output_path_itp: str, output_path_top: str, properties: Optional[dict] = None, **kwargs) -> int:
175 """Execute the :class:`AcpypeParamsGMX <acpype.acpype_params_gmx.AcpypeParamsGMX>` class and
176 execute the :meth:`launch() <acpype.acpype_params_gmx.AcpypeParamsGMX.launch>` method."""
178 return AcpypeParamsGMX(input_path=input_path,
179 output_path_gro=output_path_gro,
180 output_path_itp=output_path_itp,
181 output_path_top=output_path_top,
182 properties=properties, **kwargs).launch()
184 acpype_params_gmx.__doc__ = AcpypeParamsGMX.__doc__
187def main():
188 """Command line execution of this building block. Please check the command line documentation."""
189 parser = argparse.ArgumentParser(description="Small molecule parameterization for GROMACS MD package.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
190 parser.add_argument('--config', required=False, help='Configuration file')
192 # Specific args of each building block
193 required_args = parser.add_argument_group('required arguments')
194 required_args.add_argument('--input_path', required=True, help='Path to the input file. Accepted formats: pdb, mdl, mol2.')
195 required_args.add_argument('--output_path_gro', required=True, help='Path to the GRO output file. Accepted formats: gro.')
196 required_args.add_argument('--output_path_itp', required=True, help='Path to the ITP output file. Accepted formats: itp.')
197 required_args.add_argument('--output_path_top', required=True, help='Path to the TOP output file. Accepted formats: top.')
199 args = parser.parse_args()
200 args.config = args.config or "{}"
201 properties = settings.ConfReader(config=args.config).get_prop_dic()
203 # Specific call of each building block
204 acpype_params_gmx(input_path=args.input_path,
205 output_path_gro=args.output_path_gro,
206 output_path_itp=args.output_path_itp,
207 output_path_top=args.output_path_top,
208 properties=properties)
211if __name__ == '__main__':
212 main()