Coverage for biobb_chemistry/ambertools/reduce_add_hydrogens.py: 75%
110 statements
« prev ^ index » next coverage.py v7.6.12, created at 2025-03-12 09:28 +0000
1#!/usr/bin/env python3
3"""Module containing the ReduceAddHydrogens class and the command line interface."""
4import argparse
5from typing import Optional
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.configuration import settings
8from biobb_common.tools.file_utils import launchlogger
9from biobb_chemistry.ambertools.common import get_binary_path, check_input_path, check_output_path
12class ReduceAddHydrogens(BiobbObject):
13 """
14 | biobb_chemistry ReduceAddHydrogens
15 | This class is a wrapper of the `Ambertools <http://ambermd.org/doc12/AmberTools12.pdf>`_ reduce module for adding hydrogens to a given structure.
16 | Reduce is a program for `adding or removing hydrogens to a Protein DataBank (PDB) molecular structure file <http://ambermd.org/doc12/AmberTools12.pdf>`_.
18 Args:
19 input_path (str): Path to the input file. File type: input. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb>`_. Accepted formats: pdb (edam:format_1476).
20 output_path (str): Path to the output file. File type: output. `Sample file <https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/reference/ambertools/ref_reduce.add.pdb>`_. Accepted formats: pdb (edam:format_1476).
21 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
22 * **flip** (*bool*) - (False) add H and rotate and flip NQH groups
23 * **noflip** (*bool*) - (False) add H and rotate groups with no NQH flips
24 * **nuclear** (*bool*) - (False) use nuclear X-H distances rather than default electron cloud distances
25 * **nooh** (*bool*) - (False) remove hydrogens on OH and SH groups
26 * **oh** (*bool*) - (True) add hydrogens on OH and SH groups (default)
27 * **his** (*bool*) - (False) create NH hydrogens on HIS rings (usually used with -HIS)
28 * **noheth** (*bool*) - (False) do not attempt to add NH proton on Het groups
29 * **rotnh3** (*bool*) - (True) allow lysine NH3 to rotate (default)
30 * **norotnh3** (*bool*) - (False) do not allow lysine NH3 to rotate
31 * **rotexist** (*bool*) - (False) allow existing rotatable groups (OH, SH, Met-CH3) to rotate
32 * **rotexoh** (*bool*) - (False) allow existing OH & SH groups to rotate
33 * **allalt** (*bool*) - (True) process adjustments for all conformations (default)
34 * **onlya** (*bool*) - (False) only adjust 'A' conformations
35 * **charges** (*bool*) - (False) output charge state for appropriate hydrogen records
36 * **dorotmet** (*bool*) - (False) allow methionine methyl groups to rotate (not recommended)
37 * **noadjust** (*bool*) - (False) do not process any rot or flip adjustments
38 * **metal_bump** (*float*) - (None) [0~5|0.005] H 'bumps' metals at radius plus this
39 * **non_metal_bump** (*float*) - (None) [0~5|0.005] 'bumps' nonmetal at radius plus this
40 * **build** (*bool*) - (False) add H, including His sc NH, then rotate and flip groups (except for pre-existing methionine methyl hydrogens)
41 * **binary_path** (*str*) - ("reduce") Path to the reduce executable binary.
42 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
43 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
44 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
45 * **container_path** (*str*) - (None) Container path definition.
46 * **container_image** (*str*) - ('afandiadib/ambertools:serial') Container image definition.
47 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
48 * **container_working_dir** (*str*) - (None) Container working directory definition.
49 * **container_user_id** (*str*) - (None) Container user_id definition.
50 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
52 Examples:
53 This is a use example of how to use the building block from Python::
55 from biobb_chemistry.ambertools.reduce_add_hydrogens import reduce_add_hydrogens
56 prop = {
57 'flip': False,
58 'charges': True,
59 'build': False
60 }
61 reduce_add_hydrogens(input_path='/path/to/myStructure.pdb',
62 output_path='/path/to/newStructure.pdb',
63 properties=prop)
65 Info:
66 * wrapped_software:
67 * name: AmberTools Reduce
68 * version: >=20.0
69 * license: GNU
70 * ontology:
71 * name: EDAM
72 * schema: http://edamontology.org/EDAM.owl
74 """
76 def __init__(self, input_path, output_path,
77 properties=None, **kwargs) -> None:
78 properties = properties or {}
80 # Call parent class constructor
81 super().__init__(properties)
82 self.locals_var_dict = locals().copy()
84 # Input/Output files
85 self.io_dict = {
86 "in": {"input_path": input_path},
87 "out": {"output_path": output_path}
88 }
90 # Properties specific for BB
91 self.flip = properties.get('flip', False)
92 self.noflip = properties.get('noflip', False)
93 self.nuclear = properties.get('nuclear', False)
94 self.nooh = properties.get('nooh', False)
95 self.oh = properties.get('oh', True)
96 self.his = properties.get('his', False)
97 self.noheth = properties.get('noheth', False)
98 self.rotnh3 = properties.get('rotnh3', True)
99 self.norotnh3 = properties.get('norotnh3', False)
100 self.rotexist = properties.get('rotexist', False)
101 self.rotexoh = properties.get('rotexoh', False)
102 self.allalt = properties.get('allalt', True)
103 self.onlya = properties.get('onlya', False)
104 self.charges = properties.get('charges', False)
105 self.dorotmet = properties.get('dorotmet', False)
106 self.noadjust = properties.get('noadjust', False)
107 self.build = properties.get('build', False)
108 self.metal_bump = properties.get('metal_bump', None)
109 self.non_metal_bump = properties.get('non_metal_bump', None)
110 self.binary_path = get_binary_path(properties, 'binary_path')
111 self.properties = properties
113 # Check the properties
114 self.check_properties(properties)
115 self.check_arguments()
117 def check_data_params(self, out_log, err_log):
118 """ Checks all the input/output paths and parameters """
119 self.io_dict["in"]["input_path"] = check_input_path(self.io_dict["in"]["input_path"], out_log, self.__class__.__name__)
120 self.io_dict["out"]["output_path"] = check_output_path(self.io_dict["out"]["output_path"], out_log, self.__class__.__name__)
122 def create_cmd(self, container_io_dict, out_log, err_log):
123 """Creates the command line instruction using the properties file settings"""
124 instructions_list = []
126 # executable path
127 instructions_list.append(self.binary_path)
129 if self.flip:
130 instructions_list.append('-FLIP')
131 if self.noflip:
132 instructions_list.append('-NOFLIP')
133 if self.nuclear:
134 instructions_list.append('-NUClear')
135 if self.nooh:
136 instructions_list.append('-NOOH')
137 if self.oh:
138 instructions_list.append('-OH')
139 if self.his:
140 instructions_list.append('-HIS')
141 if self.noheth:
142 instructions_list.append('-NOHETh')
143 if self.rotnh3:
144 instructions_list.append('-ROTNH3')
145 if self.norotnh3:
146 instructions_list.append('-NOROTNH3')
147 if self.rotexist:
148 instructions_list.append('-ROTEXist')
149 if self.rotexoh:
150 instructions_list.append('-ROTEXOH')
151 if self.allalt:
152 instructions_list.append('-ALLALT')
153 if self.onlya:
154 instructions_list.append('-ONLYA')
155 if self.charges:
156 instructions_list.append('-CHARGEs')
157 if self.dorotmet:
158 instructions_list.append('-DOROTMET')
159 if self.noadjust:
160 instructions_list.append('-NOADJust')
161 if self.build:
162 instructions_list.append('-BUILD')
164 if self.metal_bump:
165 instructions_list.append('-METALBump ' + str(self.metal_bump))
167 if self.non_metal_bump:
168 instructions_list.append('-NONMETALBump ' + str(self.non_metal_bump))
170 instructions_list.append(container_io_dict["in"]["input_path"])
171 instructions_list.append('>')
172 instructions_list.append(container_io_dict["out"]["output_path"])
174 return instructions_list
176 @launchlogger
177 def launch(self) -> int:
178 """Execute the :class:`ReduceAddHydrogens <ambertools.reduce_add_hydrogens.ReduceAddHydrogens>` ambertools.reduce_add_hydrogens.ReduceAddHydrogens object."""
180 # check input/output paths and parameters
181 self.check_data_params(self.out_log, self.err_log)
183 # Setup Biobb
184 if self.check_restart():
185 return 0
186 self.stage_files()
188 # create command line instruction
189 self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log)
191 # Run Biobb block
192 self.run_biobb()
194 # Copy files to host
195 self.copy_to_host()
197 # remove temporary folder(s)
198 '''self.tmp_files.extend([
199 self.stage_io_dict.get("unique_dir", "")
200 ])'''
201 self.remove_tmp_files()
203 self.check_arguments(output_files_created=True, raise_exception=False)
205 return self.return_code
208def reduce_add_hydrogens(input_path: str, output_path: str, properties: Optional[dict] = None, **kwargs) -> int:
209 """Execute the :class:`ReduceAddHydrogens <ambertools.reduce_add_hydrogens.ReduceAddHydrogens>` class and
210 execute the :meth:`launch() <ambertools.reduce_add_hydrogens.ReduceAddHydrogens.launch>` method."""
212 return ReduceAddHydrogens(input_path=input_path,
213 output_path=output_path,
214 properties=properties, **kwargs).launch()
216 reduce_add_hydrogens.__doc__ = ReduceAddHydrogens.__doc__
219def main():
220 """Command line execution of this building block. Please check the command line documentation."""
221 parser = argparse.ArgumentParser(description="Adds hydrogen atoms to small molecules.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
222 parser.add_argument('--config', required=False, help='Configuration file')
224 # Specific args of each building block
225 required_args = parser.add_argument_group('required arguments')
226 required_args.add_argument('--input_path', required=True, help='Path to the input file. Accepted formats: pdb.')
227 required_args.add_argument('--output_path', required=True, help='Path to the output file. Accepted formats: pdb.')
229 args = parser.parse_args()
230 args.config = args.config or "{}"
231 properties = settings.ConfReader(config=args.config).get_prop_dic()
233 # Specific call of each building block
234 reduce_add_hydrogens(input_path=args.input_path,
235 output_path=args.output_path,
236 properties=properties)
239if __name__ == '__main__':
240 main()