Coverage for biobb_gromacs / gromacs_extra / ndx2resttop.py: 75%
111 statements
« prev ^ index » next coverage.py v7.13.4, created at 2026-03-05 08:26 +0000
1#!/usr/bin/env python3
3"""Module containing the Ndx2resttop class and the command line interface."""
4import fnmatch
5from typing import Optional
6from typing import Any
7from pathlib import Path
8from biobb_common.generic.biobb_object import BiobbObject
9from biobb_common.tools import file_utils as fu
10from biobb_common.tools.file_utils import launchlogger
13class Ndx2resttop(BiobbObject):
14 """
15 | biobb_gromacs Ndx2resttop
16 | Generate a restrained topology from an index NDX file.
17 | This module automatizes the process of restrained topology generation starting from an index NDX file.
19 Args:
20 input_ndx_path (str): Path to the input NDX index file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs_extra/ndx2resttop.ndx>`_. Accepted formats: ndx (edam:format_2033).
21 input_top_zip_path (str): Path the input TOP topology in zip format. 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).
22 output_top_zip_path (str): Path the output TOP topology in zip format. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs_extra/ref_ndx2resttop.zip>`_. Accepted formats: zip (edam:format_3987).
23 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
24 * **posres_names** (*list*) - ("CUSTOM_POSRES") String with names of the position restraints to be included in the topology file separated by spaces. If provided it should match the length of the ref_rest_chain_triplet_list.
25 * **force_constants** (*str*) - ("500 500 500") Array of three floats defining the force constants.
26 * **ref_rest_chain_triplet_list** (*str*) - (None) Triplet list composed by (reference group, restrain group, chain) list.
28 Examples:
29 This is a use example of how to use the building block from Python::
31 from biobb_gromacs.gromacs_extra.ndx2resttop import ndx2resttop
32 prop = { 'ref_rest_chain_triplet_list': '( Chain_A, Chain_A_noMut, A ), ( Chain_B, Chain_B_noMut, B ), ( Chain_C, Chain_C_noMut, C ), ( Chain_D, Chain_D_noMut, D )' }
33 ndx2resttop(input_ndx_path='/path/to/myIndex.ndx',
34 input_top_zip_path='/path/to/myTopology.zip',
35 output_top_zip_path='/path/to/newTopology.zip',
36 properties=prop)
38 Info:
39 * wrapped_software:
40 * name: In house
41 * license: Apache-2.0
42 * ontology:
43 * name: EDAM
44 * schema: http://edamontology.org/EDAM.owl
45 """
47 def __init__(self, input_ndx_path: str, input_top_zip_path: str, output_top_zip_path: str,
48 properties: Optional[dict] = None, **kwargs) -> None:
49 properties = properties or {}
51 # Call parent class constructor
52 super().__init__(properties)
53 self.locals_var_dict = locals().copy()
55 # Input/Output files
56 self.io_dict = {
57 "in": {"input_ndx_path": input_ndx_path, "input_top_zip_path": input_top_zip_path},
58 "out": {"output_top_zip_path": output_top_zip_path}
59 }
61 # Properties specific for BB
62 self.posres_names = properties.get('posres_names')
63 self.force_constants = properties.get('force_constants', '500 500 500')
64 self.ref_rest_chain_triplet_list = properties.get('ref_rest_chain_triplet_list')
66 # Check the properties
67 self.check_properties(properties)
68 self.check_arguments()
70 @launchlogger
71 def launch(self) -> int:
72 """Execute the :class:`Ndx2resttop <gromacs_extra.ndx2resttop.Ndx2resttop>` object."""
73 # Setup Biobb
74 if self.check_restart():
75 return 0
77 top_file = fu.unzip_top(zip_file=self.io_dict['in'].get("input_top_zip_path", ""), out_log=self.out_log)
79 # Create group dictionary from the ndx index file
80 # Each group will have a list with its starting and ending lines in the ndx file
81 groups_dic: dict[str, Any] = {}
82 current_group = ''
83 previous_group = ''
85 # Iterate over the lines of the ndx file
86 ndx_lines = open(self.io_dict['in'].get("input_ndx_path", "")).read().splitlines()
87 for index, line in enumerate(ndx_lines):
89 # Found a new group in the index file
90 if line.startswith('['):
91 current_group = line
93 # Set the starting line of the new group
94 groups_dic[current_group] = [index, 0]
96 # Check if there was a previous group to set its ending line
97 if previous_group != '':
98 groups_dic[previous_group][1] = index
100 # Update the previous group variable
101 previous_group = current_group
103 # If we reach the last line of the file, set the ending line of the last group
104 if index == len(ndx_lines)-1:
105 groups_dic[current_group][1] = index
107 # Catch groups with just one line
108 for group_name in groups_dic.keys():
109 if (groups_dic[group_name][0]+1) == groups_dic[group_name][1]:
110 groups_dic[group_name][1] += 1
112 fu.log('groups_dic: '+str(groups_dic), self.out_log, self.global_log)
114 self.ref_rest_chain_triplet_list = [tuple(elem.strip(' ()').replace(' ', '').split(',')) for elem in str(self.ref_rest_chain_triplet_list).split('),')]
115 fu.log('ref_rest_chain_triplet_list: ' + str(self.ref_rest_chain_triplet_list), self.out_log, self.global_log)
117 if self.posres_names:
118 self.posres_names = [elem.strip() for elem in self.posres_names.split()]
119 fu.log('posres_names: ' + str(self.posres_names), self.out_log, self.global_log)
120 else:
121 self.posres_names = ['CUSTOM_POSRES']*len(self.ref_rest_chain_triplet_list)
122 fu.log('posres_names: ' + str(self.posres_names), self.out_log, self.global_log)
124 # Check if the number of posres_names matches the number of ref_rest_chain_triplet_list
125 if len(self.posres_names) != len(self.ref_rest_chain_triplet_list):
126 raise ValueError("If posres_names is provided, it should match the number of ref_rest_chain_triplet_list")
128 for triplet, posre_name in zip(self.ref_rest_chain_triplet_list, self.posres_names):
130 reference_group, restrain_group, chain = triplet
132 fu.log('Reference group: '+reference_group, self.out_log, self.global_log)
133 fu.log('Restrain group: '+restrain_group, self.out_log, self.global_log)
134 fu.log('Chain: '+chain, self.out_log, self.global_log)
135 self.io_dict['out']["output_itp_path"] = fu.create_name(path=str(Path(top_file).parent), prefix=self.prefix, step=self.step, name=restrain_group+'_posre.itp')
137 # Mapping atoms from absolute enumeration to Chain relative enumeration
138 fu.log('reference_group_index: start_closed:'+str(groups_dic['[ '+reference_group+' ]'][0]+1)+' stop_open: '+str(groups_dic['[ '+reference_group+' ]'][1]), self.out_log, self.global_log)
139 reference_group_list = [int(elem) for line in ndx_lines[groups_dic['[ '+reference_group+' ]'][0]+1: groups_dic['[ '+reference_group+' ]'][1]] for elem in line.split()]
140 fu.log('restrain_group_index: start_closed:'+str(groups_dic['[ '+restrain_group+' ]'][0]+1)+' stop_open: '+str(groups_dic['[ '+restrain_group+' ]'][1]), self.out_log, self.global_log)
141 restrain_group_list = [int(elem) for line in ndx_lines[groups_dic['[ '+restrain_group+' ]'][0]+1: groups_dic['[ '+restrain_group+' ]'][1]] for elem in line.split()]
142 selected_list = [reference_group_list.index(atom)+1 for atom in restrain_group_list]
143 # Creating new ITP with restrains
144 with open(self.io_dict['out'].get("output_itp_path", ''), 'w') as f:
145 fu.log('Creating: '+str(f)+' and adding the selected atoms force constants', self.out_log, self.global_log)
146 f.write('[ position_restraints ]\n')
147 f.write('; atom type fx fy fz\n')
148 for atom in selected_list:
149 f.write(str(atom)+' 1 '+self.force_constants+'\n')
151 multi_chain = False
152 # For multi-chain topologies
153 # Including new ITP in the corresponding ITP-chain file
154 for file_dir in Path(top_file).parent.iterdir():
155 if "posre" not in file_dir.name and not file_dir.name.endswith("_pr.itp"):
156 if fnmatch.fnmatch(str(file_dir), "*_chain_"+chain+".itp"):
157 multi_chain = True
158 with open(str(file_dir), 'a') as f:
159 fu.log('Opening: '+str(f)+' and adding the ifdef include statement', self.out_log, self.global_log)
160 f.write('\n')
161 f.write('; Include Position restraint file\n')
162 f.write('#ifdef '+str(posre_name)+'\n')
163 f.write('#include "'+str(Path(self.io_dict['out'].get("output_itp_path", "")).name)+'"\n')
164 f.write('#endif\n')
165 f.write('\n')
167 # For single-chain topologies
168 # Including new ITP in the TOP file
169 if not multi_chain:
171 # Read all lines of the top file
172 with open(top_file, 'r') as f:
173 lines = f.readlines()
175 main_chain = False
176 index = 0
178 # Find the index of the line where the custom position restraints are going to be included
179 for line in lines:
181 # Find the moleculetype directive of the main chain
182 if line.startswith('Protein_chain_'+chain):
183 main_chain = True
184 index = lines.index(line) + 3
186 # Find the end of the moleculetype directive of the main chain
187 if main_chain:
188 if line.startswith('[system]') or line.startswith('[molecules]') or line.startswith('#include ') or line.startswith('#ifdef POSRES'):
189 index = lines.index(line) - 1
190 break
192 if index == 0:
193 raise ValueError(f"Protein_chain_{chain} not found in the topology file")
195 # Include the custom position restraints in the top file
196 lines.insert(index, '\n')
197 lines.insert(index + 1, '; Include Position restraint file\n')
198 lines.insert(index + 2, '#ifdef '+str(posre_name)+'\n')
199 lines.insert(index + 3, '#include "'+str(Path(self.io_dict['out'].get("output_itp_path", "")).name)+'"\n')
200 lines.insert(index + 4, '#endif\n')
202 # Write the new top file
203 with open(top_file, 'w') as f:
204 f.writelines(lines)
206 # zip topology
207 fu.zip_top(zip_file=self.io_dict['out'].get("output_top_zip_path", ""), top_file=top_file, out_log=self.out_log, remove_original_files=self.remove_tmp)
209 # Remove temporal files
210 self.remove_tmp_files()
212 self.check_arguments(output_files_created=True, raise_exception=False)
213 return 0
216def ndx2resttop(input_ndx_path: str, input_top_zip_path: str, output_top_zip_path: str,
217 properties: Optional[dict] = None, **kwargs) -> int:
218 """Create :class:`Ndx2resttop <gromacs_extra.ndx2resttop.Ndx2resttop>` class and
219 execute the :meth:`launch() <gromacs_extra.ndx2resttop.Ndx2resttop.launch>` method."""
220 return Ndx2resttop(**dict(locals())).launch()
223ndx2resttop.__doc__ = Ndx2resttop.__doc__
224main = Ndx2resttop.get_main(ndx2resttop, "Generate a restrained topology from an index NDX file.")
227if __name__ == '__main__':
228 main()