Coverage for biobb_gromacs/gromacs_extra/append_ligand.py: 66%
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« 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 AppendLigand class and the command line interface."""
5import argparse
6import re
7import shutil
8from pathlib import Path
9from typing import Optional
11from biobb_common.configuration import settings
12from biobb_common.generic.biobb_object import BiobbObject
13from biobb_common.tools import file_utils as fu
14from biobb_common.tools.file_utils import launchlogger
17class AppendLigand(BiobbObject):
18 """
19 | biobb_gromacs AppendLigand
20 | This class takes a ligand ITP file and inserts it in a topology.
21 | This module automatizes the process of inserting a ligand ITP file in a GROMACS topology.
23 Args:
24 input_top_zip_path (str): Path the input topology TOP and ITP files zipball. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.zip>`_. Accepted formats: zip (edam:format_3987).
25 input_itp_path (str): Path to the ligand ITP file to be inserted in the topology. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs_extra/pep_ligand.itp>`_. Accepted formats: itp (edam:format_3883).
26 output_top_zip_path (str): Path/Name the output topology TOP and ITP files zipball. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs_extra/ref_appendligand.zip>`_. Accepted formats: zip (edam:format_3987).
27 input_posres_itp_path (str) (Optional): Path to the position restriction ITP file. File type: input. Accepted formats: itp (edam:format_3883).
28 properties (dic):
29 * **posres_name** (*str*) - ("POSRES_LIGAND") String to be included in the ifdef clause.
30 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
31 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
32 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
34 Examples:
35 This is a use example of how to use the building block from Python::
37 from biobb_gromacs.gromacs_extra.append_ligand import append_ligand
38 prop = { 'posres_name': 'POSRES_LIGAND' }
39 append_ligand(input_top_zip_path='/path/to/myTopology.zip',
40 input_itp_path='/path/to/myTopologyAddOn.itp',
41 output_top_zip_path='/path/to/newTopology.zip',
42 properties=prop)
44 Info:
45 * wrapped_software:
46 * name: In house
47 * license: Apache-2.0
48 * ontology:
49 * name: EDAM
50 * schema: http://edamontology.org/EDAM.owl
51 """
53 def __init__(
54 self,
55 input_top_zip_path: str,
56 input_itp_path: str,
57 output_top_zip_path: str,
58 input_posres_itp_path: Optional[str] = None,
59 properties: Optional[dict] = None,
60 **kwargs,
61 ) -> None:
62 properties = properties or {}
64 # Call parent class constructor
65 super().__init__(properties)
66 self.locals_var_dict = locals().copy()
68 # Input/Output files
69 self.io_dict = {
70 "in": {
71 "input_top_zip_path": input_top_zip_path,
72 "input_itp_path": input_itp_path,
73 "input_posres_itp_path": input_posres_itp_path,
74 },
75 "out": {"output_top_zip_path": output_top_zip_path},
76 }
78 # Properties specific for BB
79 self.posres_name = properties.get("posres_name", "POSRES_LIGAND")
81 # Check the properties
82 self.check_properties(properties)
83 self.check_arguments()
85 @launchlogger
86 def launch(self) -> int:
87 """Execute the :class:`AppendLigand <gromacs_extra.append_ligand.AppendLigand>` object."""
88 # Setup Biobb
89 if self.check_restart():
90 return 0
92 # Unzip topology
93 top_file = fu.unzip_top(
94 zip_file=str(self.io_dict["in"].get("input_top_zip_path")),
95 out_log=self.out_log,
96 )
97 top_dir = str(Path(top_file).parent)
98 itp_name = str(Path(str(self.io_dict["in"].get("input_itp_path"))).name)
100 with open(top_file) as top_f:
101 top_lines = top_f.readlines()
102 top_f.close()
103 fu.rm(top_file)
105 forcefield_pattern = r"#include.*forcefield.itp\""
106 if top_lines:
107 for ff_index, line in enumerate(top_lines):
108 if re.search(forcefield_pattern, line):
109 break
110 else:
111 fu.log(
112 f'FATAL: Input topfile {top_file} from input_top_zip_path {self.io_dict["in"].get("input_top_zip_path")} is empty.',
113 self.out_log,
114 self.global_log,
115 )
116 return 1
118 ligand_itp_path = self.io_dict["in"].get("input_itp_path")
120 # Read ligand itp contents
121 with open(ligand_itp_path, 'r') as itp_file:
122 ligand_itp_contents = itp_file.readlines()
124 # Separate ligand [ atomtypes ] section from the rest
125 lig_atomtypes_section = []
126 remaining_itp_contents = []
127 in_atomtypes_section = False
128 for line in ligand_itp_contents:
129 if line.strip().startswith("[ atomtypes ]"):
130 in_atomtypes_section = True
131 lig_atomtypes_section.append(line)
132 elif in_atomtypes_section:
133 if line.strip() == "" or line.startswith("["):
134 in_atomtypes_section = False
135 remaining_itp_contents.append(line)
136 else:
137 lig_atomtypes_section.append(line)
138 else:
139 remaining_itp_contents.append(line)
141 # If the ligand itp contains an [ atomtypes ] section, merge it into the main topology
142 if lig_atomtypes_section:
144 # Look for the [ atomtypes ] section in the main topology
145 top_atomtypes_section = []
146 in_atomtypes_section = False
147 for line in top_lines:
148 if line.strip().startswith("[ atomtypes ]"):
149 in_atomtypes_section = True
150 top_atomtypes_section.append(line)
151 elif in_atomtypes_section:
152 if line.strip() == "" or line.startswith("["):
153 in_atomtypes_section = False
154 else:
155 top_atomtypes_section.append(line)
157 # If there is already an [ atomtypes ] section in the main topology
158 if top_atomtypes_section:
160 # Remove the header and comments of the ligand [ atomtypes ] section
161 lig_atomtypes_section = lig_atomtypes_section[2:]
163 # Remove the [ atomtypes ] section from top_lines
164 top_lines = [line for line in top_lines if line not in top_atomtypes_section]
166 # NOTE: Check for repeated atoms in the [ atomtypes ] section
167 # NOTE: raise error if there are conflicts - atoms named equally with different parameters
168 # NOTE: raise error if there are different number of columns in the atomtypes sections
170 top_lines.insert(ff_index + 1, "\n")
172 # Merge both [ atomtypes ] sections
173 atomtype_section = top_atomtypes_section + lig_atomtypes_section
175 # Write the merged [ atomtypes ] section into the main topology after the forcefield include
176 for atomtype_index in range(len(atomtype_section)):
177 top_lines.insert(ff_index + atomtype_index + 2, atomtype_section[atomtype_index])
179 # Update the index for the remaining directives
180 at_index = ff_index + atomtype_index + 2
181 else:
182 at_index = ff_index
184 top_lines.insert(at_index + 1, "\n")
185 top_lines.insert(at_index + 2, "; Including ligand ITP\n")
186 top_lines.insert(at_index + 3, '#include "' + itp_name + '"\n')
187 top_lines.insert(at_index + 4, "\n")
188 if self.io_dict["in"].get("input_posres_itp_path"):
189 top_lines.insert(at_index + 5, "; Ligand position restraints" + "\n")
190 top_lines.insert(at_index + 6, "#ifdef " + self.posres_name + "\n")
191 top_lines.insert(
192 at_index + 7,
193 '#include "' + str(Path(self.io_dict["in"].get("input_posres_itp_path", "")).name) + '"\n'
194 )
195 top_lines.insert(at_index + 8, "#endif" + "\n")
196 top_lines.insert(at_index + 9, "\n")
198 inside_moleculetype_section = False
199 with open(self.io_dict["in"].get("input_itp_path", "")) as itp_file:
200 moleculetype_pattern = r"\[ moleculetype \]"
201 for line in itp_file:
202 if re.search(moleculetype_pattern, line):
203 inside_moleculetype_section = True
204 continue
205 if inside_moleculetype_section and not line.startswith(";"):
206 moleculetype = line.strip().split()[0].strip()
207 break
209 molecules_pattern = r"\[ molecules \]"
210 inside_molecules_section = False
211 index_molecule = None
212 molecule_string = (
213 str(moleculetype) + int(20 - len(moleculetype)) * " " + "1" + "\n"
214 )
215 for index, line in enumerate(top_lines):
216 if re.search(molecules_pattern, line):
217 inside_molecules_section = True
218 continue
219 if (
220 inside_molecules_section and not line.startswith(";") and line.upper().startswith("PROTEIN")
221 ):
222 index_molecule = index
224 if index_molecule:
225 top_lines.insert(index_molecule + 1, molecule_string)
226 else:
227 top_lines.append(molecule_string)
229 new_top = fu.create_name(
230 path=top_dir, prefix=self.prefix, step=self.step, name="ligand.top"
231 )
233 with open(new_top, "w") as new_top_f:
234 new_top_f.write("".join(top_lines))
236 # Create a new itp ligand file without the [ atomtypes ] section
237 new_ligand_tip_path = str(Path(top_dir) / itp_name)
238 with open(new_ligand_tip_path, 'w') as new_itp_file:
239 new_itp_file.write("".join(remaining_itp_contents))
241 if self.io_dict["in"].get("input_posres_itp_path"):
242 shutil.copy2(self.io_dict["in"].get("input_posres_itp_path", ""), top_dir)
244 # zip topology
245 fu.log(
246 "Compressing topology to: %s"
247 % self.io_dict["out"].get("output_top_zip_path"),
248 self.out_log,
249 self.global_log,
250 )
251 fu.zip_top(
252 zip_file=self.io_dict["out"].get("output_top_zip_path", ""),
253 top_file=new_top,
254 out_log=self.out_log,
255 remove_original_files=self.remove_tmp
256 )
258 # Remove temporal files
259 self.tmp_files.append(top_dir)
260 self.remove_tmp_files()
262 self.check_arguments(output_files_created=True, raise_exception=False)
263 return 0
266def append_ligand(
267 input_top_zip_path: str,
268 input_itp_path: str,
269 output_top_zip_path: str,
270 input_posres_itp_path: Optional[str] = None,
271 properties: Optional[dict] = None,
272 **kwargs,
273) -> int:
274 """Create :class:`AppendLigand <gromacs_extra.append_ligand.AppendLigand>` class and
275 execute the :meth:`launch() <gromacs_extra.append_ligand.AppendLigand.launch>` method."""
276 return AppendLigand(
277 input_top_zip_path=input_top_zip_path,
278 input_itp_path=input_itp_path,
279 output_top_zip_path=output_top_zip_path,
280 input_posres_itp_path=input_posres_itp_path,
281 properties=properties,
282 **kwargs,
283 ).launch()
286append_ligand.__doc__ = AppendLigand.__doc__
289def main():
290 """Command line execution of this building block. Please check the command line documentation."""
291 parser = argparse.ArgumentParser(
292 description="Wrapper of the GROMACS editconf module.",
293 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
294 )
295 parser.add_argument(
296 "-c",
297 "--config",
298 required=False,
299 help="This file can be a YAML file, JSON file or JSON string",
300 )
302 # Specific args of each building block
303 required_args = parser.add_argument_group("required arguments")
304 required_args.add_argument("--input_top_zip_path", required=True)
305 required_args.add_argument("--input_itp_path", required=True)
306 required_args.add_argument("--output_top_zip_path", required=True)
307 parser.add_argument("--input_posres_itp_path", required=False)
309 args = parser.parse_args()
310 config = args.config if args.config else None
311 properties = settings.ConfReader(config=config).get_prop_dic()
313 # Specific call of each building block
314 append_ligand(
315 input_top_zip_path=args.input_top_zip_path,
316 input_itp_path=args.input_itp_path,
317 output_top_zip_path=args.output_top_zip_path,
318 input_posres_itp_path=args.input_posres_itp_path,
319 properties=properties,
320 )
323if __name__ == "__main__":
324 main()