Coverage for biobb_haddock/haddock_restraints/haddock3_actpass_to_ambig.py: 64%
61 statements
« prev ^ index » next coverage.py v7.10.2, created at 2025-08-07 08:48 +0000
1#!/usr/bin/env python3
3"""Module containing the haddock 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.file_utils import launchlogger
13class Haddock3ActpassToAmbig(BiobbObject):
14 """
15 | biobb_haddock Haddock3ActpassToAmbig
16 | Wrapper class for the Haddock-Restraints active_passive_to_ambig module.
17 | `Haddock-Restraints active_passive_to_ambig <https://www.bonvinlab.org/haddock3/clients/haddock.clis.restraints.active_passive_to_ambig.html>`_ generates a corresponding ambig.tbl file to be used by HADDOCK from two given files containing active (in the first line) and passive (second line) residues.
19 Args:
20 input_actpass1_path (str): Path to the first input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/haddock_actpass1.txt>`_. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), in (edam:format_2330), pass (edam:format_2330).
21 input_actpass2_path (str): Path to the second input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/haddock_actpass2.txt>`_. Accepted formats: txt (edam:format_2330), dat (edam:format_2330), in (edam:format_2330), pass (edam:format_2330).
22 output_tbl_path (str): Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/haddock_actpass.tbl>`_. Accepted formats: tbl (edam:format_2330), txt (edam:format_2330), out (edam:format_2330).
23 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
24 * **pass_to_act** (*bool*) - (False) Path to the haddock haddock executable binary.
25 * **segid_one** (*str*) - (None) Segid of the first model.
26 * **segid_two** (*str*) - (None) Segid of the second model.
27 * **binary_path** (*str*) - ("haddock") Path to the haddock haddock executable binary.
28 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
29 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
30 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
31 * **container_path** (*str*) - (None) Path to the binary executable of your container.
32 * **container_image** (*str*) - (None) Container Image identifier.
33 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
34 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
35 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
36 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
39 Examples:
40 This is a use example of how to use the building block from Python::
42 from biobb_haddock.haddock_restraints.haddock3_actpass_to_ambig import haddock3_actpass_to_ambig
43 haddock3_actpass_to_ambig(
44 input_actpass1_path='/path/to/haddock_actpass1.txt',
45 input_actpass2_path='/path/to/haddock_actpass2.txt',
46 output_tbl_path='/path/to/output_AIR.tbl'
47 )
49 Info:
50 * wrapped_software:
51 * name: Haddock33-restraints
52 * version: 2025.5
53 * license: Apache-2.0
54 * ontology:
55 * name: EDAM
56 * schema: http://edamontology.org/EDAM.owl
57 """
59 def __init__(
60 self,
61 input_actpass1_path: str,
62 input_actpass2_path: str,
63 output_tbl_path: str,
64 properties: Optional[dict] = None,
65 **kwargs,
66 ) -> None:
67 properties = properties or {}
69 # Call parent class constructor
70 super().__init__(properties)
72 # Input/Output files
73 self.io_dict = {
74 "in": {
75 "input_actpass1_path": input_actpass1_path,
76 "input_actpass2_path": input_actpass2_path,
77 },
78 "out": {
79 "output_tbl_path": output_tbl_path,
80 },
81 }
83 # Properties specific for BB
84 self.binary_path = properties.get("binary_path", "haddock3-restraints")
85 self.pass_to_act = properties.get("pass_to_act", False)
86 self.segid_one = properties.get("segid_one", None)
87 self.segid_two = properties.get("segid_two", None)
89 # Check the properties
90 self.check_properties(properties)
92 @launchlogger
93 def launch(self) -> int:
94 """Execute the :class:`Haddock3ActpassToAmbig <biobb_haddock.haddock_restraints.haddock3_actpass_to_ambig>` object."""
96 # Setup Biobb
97 if self.check_restart():
98 return 0
99 self.stage_files()
101 if self.pass_to_act:
102 with open(self.stage_io_dict['in']['input_actpass1_path'], 'r') as file1, \
103 open(self.stage_io_dict['in']['input_actpass2_path'], 'r') as file2:
104 actpass1_lines = file1.readlines()
105 actpass2_lines = file2.readlines()
107 with open(self.stage_io_dict['in']['input_actpass1_path'], 'w') as file1, \
108 open(self.stage_io_dict['in']['input_actpass2_path'], 'w') as file2:
109 file1.writelines([actpass1_lines[1], actpass1_lines[0], '\n'])
110 file2.writelines([actpass2_lines[1], actpass2_lines[0], '\n'])
112 # haddock3-restraints active_passive_to_ambig haddock_actpass.txt
113 self.cmd = [self.binary_path, "active_passive_to_ambig", self.stage_io_dict['in']
114 ['input_actpass1_path'], self.stage_io_dict['in']['input_actpass2_path']]
116 if self.segid_one is not None:
117 self.cmd.extend(["--segid-one", self.segid_one])
118 if self.segid_two is not None:
119 self.cmd.extend(["--segid-two", self.segid_two])
121 self.cmd.append(">")
122 self.cmd.append(self.stage_io_dict['out']['output_tbl_path'])
123 self.cmd.append("2>&1")
125 # Run Biobb block
126 self.run_biobb()
128 # Remove deprecation warning if present
129 with open(self.stage_io_dict['out']['output_tbl_path'], 'r') as file:
130 lines = file.readlines()
131 if lines and "DEPRECATION NOTICE" in lines[0]:
132 with open(self.stage_io_dict['out']['output_tbl_path'], 'w') as file:
133 file.writelines(lines[1:])
135 # Copy files to host
136 self.copy_to_host()
138 # Remove temporal files
139 self.tmp_files.extend([self.stage_io_dict["unique_dir"]])
140 self.remove_tmp_files()
142 return self.return_code
145def haddock3_actpass_to_ambig(
146 input_actpass1_path: str,
147 input_actpass2_path: str,
148 output_tbl_path: str,
149 properties: Optional[dict] = None,
150 **kwargs,
151) -> int:
152 """Create :class:`Haddock3ActpassToAmbig <biobb_haddock.haddock_restraints.haddock3_actpass_to_ambig>` class and
153 execute the :meth:`launch() <biobb_haddock.haddock_restraints.haddock3_actpass_to_ambig.launch>` method."""
155 return Haddock3ActpassToAmbig(
156 input_actpass1_path=input_actpass1_path,
157 input_actpass2_path=input_actpass2_path,
158 output_tbl_path=output_tbl_path,
159 properties=properties,
160 **kwargs,
161 ).launch()
164haddock3_actpass_to_ambig.__doc__ = Haddock3ActpassToAmbig.__doc__
167def main():
168 parser = argparse.ArgumentParser(
169 description="Wrapper of the haddock-restraints active_passive_to_ambig module.",
170 formatter_class=lambda prog: argparse.RawTextHelpFormatter(
171 prog, width=99999),
172 )
173 parser.add_argument(
174 "-c",
175 "--config",
176 required=False,
177 help="This file can be a YAML file, JSON file or JSON string",
178 )
180 # Specific args of each building block
181 required_args = parser.add_argument_group("required arguments")
182 required_args.add_argument("--input_actpass1_path", required=True)
183 required_args.add_argument("--input_actpass2_path", required=True)
184 required_args.add_argument("--output_tbl_path", required=True)
186 args = parser.parse_args()
187 config = args.config if args.config else None
188 properties = settings.ConfReader(config=config).get_prop_dic()
190 # Specific call of each building block
191 haddock3_actpass_to_ambig(
192 input_actpass1_path=args.input_actpass1_path,
193 input_actpass2_path=args.input_actpass2_path,
194 output_tbl_path=args.output_tbl_path,
195 properties=properties,
196 )
199if __name__ == "__main__":
200 main()