Coverage for biobb_structure_utils/utils/str_check_add_hydrogens.py: 78%
63 statements
« prev ^ index » next coverage.py v7.5.3, created at 2024-06-14 19:03 +0000
« prev ^ index » next coverage.py v7.5.3, created at 2024-06-14 19:03 +0000
1#!/usr/bin/env python3
3"""Module containing the StrCheckAddHydrogens class and the command line interface."""
4import argparse
5from biobb_common.configuration import settings
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.tools.file_utils import launchlogger
8from biobb_structure_utils.utils.common import check_input_path, check_output_path_pdbqt, check_output_end
11class StrCheckAddHydrogens(BiobbObject):
12 """
13 | biobb_structure_utils StrCheckAddHydrogens
14 | This class is a wrapper of the Structure Checking tool to add hydrogens to a 3D structure.
15 | Wrapper for the `Structure Checking <https://github.com/bioexcel/biobb_structure_checking>`_ tool to add hydrogens to a 3D structure.
17 Args:
18 input_structure_path (str): Input structure file path. File type: input. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/data/utils/str_no_H.pdb>`_. Accepted formats: pdb (edam:format_1476).
19 output_structure_path (str): Output structure file path. File type: output. `Sample file <https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_str_H.pdbqt>`_. Accepted formats: pdb (edam:format_1476), pdbqt (edam:format_1476).
20 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
21 * **charges** (*bool*) - (False) Whether or not to add charges to the output file. If True the output is in PDBQT format.
22 * **mode** (*string*) - (auto) Selection mode. Values: auto, list, ph
23 * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH. Only in case mode ph selected.
24 * **list** (*string*) - ("") List of residues to modify separated by commas (i.e HISA234HID,HISB33HIE). Only in case mode list selected.
25 * **keep_canonical_resnames** (*bool*) - (False) Whether or not keep canonical residue names
26 * **binary_path** (*string*) - ("check_structure") path to the check_structure application
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.
31 Examples:
32 This is a use example of how to use the building block from Python::
34 from biobb_structure_utils.utils.str_check_add_hydrogens import str_check_add_hydrogens
35 prop = {
36 'charges': False,
37 'mode': 'auto'
38 }
39 str_check_add_hydrogens(input_structure_path='/path/to/myInputStr.pdb',
40 output_structure_path='/path/to/newStructure.pdb',
41 properties=prop)
43 Info:
44 * wrapped_software:
45 * name: Structure Checking from MDWeb
46 * version: >=3.0.3
47 * license: Apache-2.0
48 * ontology:
49 * name: EDAM
50 * schema: http://edamontology.org/EDAM.owl
52 """
54 def __init__(self, input_structure_path, output_structure_path, properties=None, **kwargs) -> None:
55 properties = properties or {}
57 # Call parent class constructor
58 super().__init__(properties)
59 self.locals_var_dict = locals().copy()
61 # Input/Output files
62 self.io_dict = {
63 "in": {"input_structure_path": input_structure_path},
64 "out": {"output_structure_path": output_structure_path}
65 }
67 # Properties specific for BB
68 self.binary_path = properties.get('binary_path', 'check_structure')
69 self.charges = properties.get('charges', False)
70 self.mode = properties.get('mode', 'auto')
71 self.ph = properties.get('ph', 7.4)
72 self.list = properties.get('list', '')
73 self.keep_canonical_resnames = properties.get('keep_canonical_resnames', False)
74 self.properties = properties
76 # Check the properties
77 self.check_properties(properties)
78 self.check_arguments()
80 @launchlogger
81 def launch(self) -> int:
82 """Execute the :class:`StrCheckAddHydrogens <utils.str_check_add_hydrogens.StrCheckAddHydrogens>` utils.str_check_add_hydrogens.StrCheckAddHydrogens object."""
84 self.io_dict['in']['input_structure_path'] = check_input_path(self.io_dict['in']['input_structure_path'],
85 self.out_log, self.__class__.__name__)
86 self.io_dict['out']['output_structure_path'] = check_output_path_pdbqt(self.io_dict['out']['output_structure_path'],
87 self.out_log, self.__class__.__name__)
89 # Setup Biobb
90 if self.check_restart():
91 return 0
92 self.stage_files()
94 self.cmd = [self.binary_path,
95 '-i', self.stage_io_dict['in']['input_structure_path'],
96 '-o', self.stage_io_dict['out']['output_structure_path'],
97 '--non_interactive',
98 '--force_save']
100 if self.keep_canonical_resnames:
101 self.cmd.append('--keep_canonical_resnames')
103 self.cmd.extend(['command_list', '--list', "'add_hydrogen"])
105 if self.charges:
106 self.cmd.append('--add_charges')
107 self.cmd.append('ADT')
109 if self.mode:
110 self.cmd.extend(['--add_mode', self.mode])
111 if self.mode == 'ph':
112 self.cmd.extend(['--pH', self.ph])
113 if self.mode == 'list':
114 self.cmd.extend(['--list', self.list])
115 else:
116 self.cmd.extend(['--add_mode', 'None'])
118 self.cmd.append("'")
119 # Run Biobb block
120 self.run_biobb()
122 # Copy files to host
123 self.copy_to_host()
125 check_output_end(self.io_dict["out"]["output_structure_path"], self.out_log)
127 # Remove temporal files
128 self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
129 self.remove_tmp_files()
131 self.check_arguments(output_files_created=True, raise_exception=False)
133 return self.return_code
136def str_check_add_hydrogens(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
137 """Execute the :class:`StrCheckAddHydrogens <utils.str_check_add_hydrogens.StrCheckAddHydrogens>` class and
138 execute the :meth:`launch() <utils.str_check_add_hydrogens.StrCheckAddHydrogens.launch>` method."""
140 return StrCheckAddHydrogens(input_structure_path=input_structure_path,
141 output_structure_path=output_structure_path,
142 properties=properties, **kwargs).launch()
145def main():
146 """Command line execution of this building block. Please check the command line documentation."""
147 parser = argparse.ArgumentParser(description="Class to add hydrogens to a 3D structure.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
148 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
150 # Specific args of each building block
151 required_args = parser.add_argument_group('required arguments')
152 required_args.add_argument('-i', '--input_structure_path', required=True, help="Input structure file path. Accepted formats: pdb.")
153 required_args.add_argument('-o', '--output_structure_path', required=True, help="Output structure file path. Accepted formats: pdb, pdbqt.")
155 args = parser.parse_args()
156 config = args.config if args.config else None
157 properties = settings.ConfReader(config=config).get_prop_dic()
159 # Specific call of each building block
160 str_check_add_hydrogens(input_structure_path=args.input_structure_path,
161 output_structure_path=args.output_structure_path,
162 properties=properties)
165if __name__ == '__main__':
166 main()