Coverage for biobb_structure_utils/utils/remove_ligand.py: 80%
54 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 RemoveLigand class and the command line interface."""
4import argparse
5from pathlib import Path
6from biobb_common.configuration import settings
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_structure_utils.gro_lib.gro import Gro
13class RemoveLigand(BiobbObject):
14 """
15 | biobb_structure_utils RemoveLigand
16 | Class to remove the selected ligand atoms from a 3D structure.
17 | Remove the selected ligand atoms from a 3D structure.
19 Args:
20 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/WT_aq4_md_1.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
21 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/WT_apo_md_1.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).
22 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
23 * **ligand** (*str*) - ("AQ4") Residue code of the ligand to be removed.
24 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
25 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
26 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
28 Examples:
29 This is a use example of how to use the building block from Python::
31 from biobb_structure_utils.utils.remove_ligand import remove_ligand
32 prop = {
33 'ligand': 'AQ4'
34 }
35 remove_ligand(input_structure_path='/path/to/myStructure.pdb',
36 output_structure_path='/path/to/newStructure.pdb',
37 properties=prop)
39 Info:
40 * wrapped_software:
41 * name: In house
42 * license: Apache-2.0
43 * ontology:
44 * name: EDAM
45 * schema: http://edamontology.org/EDAM.owl
47 """
49 def __init__(self, input_structure_path, output_structure_path, properties=None, **kwargs) -> None:
50 properties = properties or {}
52 # Call parent class constructor
53 super().__init__(properties)
54 self.locals_var_dict = locals().copy()
56 # Input/Output files
57 self.io_dict = {
58 "in": {"input_structure_path": input_structure_path},
59 "out": {"output_structure_path": output_structure_path}
60 }
62 # Properties specific for BB
63 self.ligand = properties.get('ligand', 'AQ4')
65 # Check the properties
66 self.check_properties(properties)
67 self.check_arguments()
69 @launchlogger
70 def launch(self) -> int:
71 """Execute the :class:`RemoveLigand <utils.remove_ligand.RemoveLigand>` utils.remove_ligand.RemoveLigand object."""
73 # Setup Biobb
74 if self.check_restart():
75 return 0
76 self.stage_files()
78 # Business code
79 extension = Path(self.stage_io_dict['in']['input_structure_path']).suffix.lower()
80 if extension.lower() == '.gro':
81 fu.log('GRO format detected, removing all atoms from residues named %s' % self.ligand, self.out_log)
82 gro_st = Gro()
83 gro_st.read_gro_file(self.stage_io_dict['in']['input_structure_path'])
84 gro_st.remove_residues([self.ligand])
85 gro_st.write_gro_file(self.stage_io_dict['out']['output_structure_path'])
87 else:
88 fu.log('PDB format detected, removing all atoms from residues named %s' % self.ligand, self.out_log)
89 # Direct aproach solution implemented to avoid the issues
90 # presented in commit message (c92aab9604a6a31d13f4170ff47b231df0a588ef)
91 # with the Biopython library
92 with open(self.stage_io_dict['in']['input_structure_path'], "r") as input_pdb, open(self.stage_io_dict['out']['output_structure_path'], "w") as output_pdb:
93 for line in input_pdb:
94 if len(line) > 19 and self.ligand.lower() in line[17:20].lower():
95 continue
96 output_pdb.write(line)
98 self.return_code = 0
99 ##########
101 # Copy files to host
102 self.copy_to_host()
104 # Remove temporal files
105 self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
106 self.remove_tmp_files()
108 self.check_arguments(output_files_created=True, raise_exception=False)
110 return self.return_code
113def remove_ligand(input_structure_path: str, output_structure_path: str, properties: dict = None, **kwargs) -> int:
114 """Execute the :class:`RemoveLigand <utils.remove_ligand.RemoveLigand>` class and
115 execute the :meth:`launch() <utils.remove_ligand.RemoveLigand.launch>` method."""
117 return RemoveLigand(input_structure_path=input_structure_path,
118 output_structure_path=output_structure_path,
119 properties=properties, **kwargs).launch()
122def main():
123 """Command line execution of this building block. Please check the command line documentation."""
124 parser = argparse.ArgumentParser(description="Remove the selected ligand atoms from a 3D structure.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
125 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
127 # Specific args of each building block
128 required_args = parser.add_argument_group('required arguments')
129 required_args.add_argument('-i', '--input_structure_path', required=True, help="Input structure file name")
130 required_args.add_argument('-o', '--output_structure_path', required=True, help="Output structure file name")
132 args = parser.parse_args()
133 config = args.config if args.config else None
134 properties = settings.ConfReader(config=config).get_prop_dic()
136 # Specific call of each building block
137 remove_ligand(input_structure_path=args.input_structure_path,
138 output_structure_path=args.output_structure_path,
139 properties=properties)
142if __name__ == '__main__':
143 main()