Coverage for biobb_chemistry / babelm / babel_add_hydrogens.py: 95%
76 statements
« prev ^ index » next coverage.py v7.13.0, created at 2025-12-22 12:49 +0000
1#!/usr/bin/env python3
3"""Module containing the BabelAddHydrogens class and the command line interface."""
5from typing import Optional
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.tools.file_utils import launchlogger
10from biobb_chemistry.babelm.common import (
11 _from_string_to_list,
12 check_input_path,
13 check_output_path,
14 get_coordinates,
15 get_input_format,
16 get_output_format,
17 get_ph,
18)
21class BabelAddHydrogens(BiobbObject):
22 """
23 | biobb_chemistry BabelAddHydrogens
24 | This class is a wrapper of the Open Babel tool.
25 | Adds hydrogens to a given structure or trajectory. Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. `Visit the official page <http://openbabel.org/wiki/Main_Page>`_.
27 Args:
28 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/babelm/babel.no.H.pdb>`_. Accepted formats: dat (edam:format_1637), ent (edam:format_1476), fa (edam:format_1929), fasta (edam:format_1929), gro (edam:format_2033), inp (edam:format_3878), log (edam:format_2030), mcif (edam:format_1477), mdl (edam:format_3815), mmcif (edam:format_1477), mol (edam:format_3815), mol2 (edam:format_3816), pdb (edam:format_1476), pdbqt (edam:format_1476), png (edam:format_3603), sdf (edam:format_3814), smi (edam:format_1196), smiles (edam:format_1196), txt (edam:format_2033), xml (edam:format_2332), xtc (edam:format_3875).
29 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/babelm/ref_babel.hydrogens.pdb>`_. Accepted formats: ent (edam:format_1476), fa (edam:format_1929), fasta (edam:format_1929), gro (edam:format_2033), inp (edam:format_3878), mcif (edam:format_1477), mdl (edam:format_3815), mmcif (edam:format_1477), mol (edam:format_3815), mol2 (edam:format_3816), pdb (edam:format_1476), pdbqt (edam:format_1476), png (edam:format_3603), sdf (edam:format_3814), smi (edam:format_1196), smiles (edam:format_1196), txt (edam:format_2033).
30 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
31 * **input_format** (*str*) - (None) Format of input file. If not provided, input_path extension will be taken. Values: dat (Information represented in a data record), ent (Protein Data Bank format), fa (FASTA sequence format), fasta (FASTA sequence format), gro (GROMACS structure), inp (AMBER trajectory format), log (Events file), mcif (Entry format of PDB database in mmCIF format), mdl (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mmcif (Entry format of PDB database in mmCIF format), mol (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mol2 (Complete and portable representation of a SYBYL molecule), pdb (Protein Data Bank format), pdbqt (Protein Data Bank format with charges), png (File format for image compression), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), smi (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), smiles (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), txt (Textual format), xml (eXtensible Markup Language), xtc (Portable binary format for trajectories produced by GROMACS package).
32 * **output_format** (*str*) - (None) Format of output file. If not provided, output_path extension will be taken. Values: ent (Protein Data Bank format), fa (FASTA sequence format), fasta (FASTA sequence format), gro (GROMACS structure), inp (AMBER trajectory format), mcif (Entry format of PDB database in mmCIF format), mdl (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mmcif (Entry format of PDB database in mmCIF format), mol (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mol2 (Complete and portable representation of a SYBYL molecule), pdb (Protein Data Bank format), pdbqt (Protein Data Bank format with charges), png (File format for image compression), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), smi (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), smiles (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), txt (Textual format), xtc (Portable binary format for trajectories produced by GROMACS package).
33 * **fs_input** (*list*) - (None) Format-specific input options. Values: b (disable automatic bonding), d (input file is in dlg -AutoDock docking log- format).
34 * **fs_output** (*list*) - (["h"]) Format-specific output options. Values: b (enable automatic bonding), r (output as a rigid molecule), c (combine separate molecular pieces of input into a single rigid molecule), s (output as a flexible residue), p (preserve atom indices from input file), h (preserve hydrogens), n (preserve atom names).
35 * **coordinates** (*int*) - (None) Type of coordinates: 2D or 3D. Values: 2 (2D coordinates), 3 (3D coordinates).
36 * **effort** (*str*) - ("medium") Computational effort wanted to dedicate for the conformer generation coordinates calculations, only for 3D coordinates. Values: fastest (only generate coordinates, no force field or conformer search), fast (perform quick forcefield optimization), medium (forcefield optimization + fast conformer search), better (more optimization + fast conformer search), best (more optimization + significant conformer search).
37 * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH.
38 * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.
39 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
40 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
41 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
42 * **container_path** (*str*) - (None) Container path definition.
43 * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.
44 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
45 * **container_working_dir** (*str*) - (None) Container working directory definition.
46 * **container_user_id** (*str*) - (None) Container user_id definition.
47 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
49 Examples:
50 This is a use example of how to use the building block from Python::
52 from biobb_chemistry.babelm.babel_add_hydrogens import babel_add_hydrogens
53 prop = {
54 'input_format': 'pdb',
55 'output_format': 'pdb',
56 'coordinates': 3,
57 'ph': 7.4
58 }
59 babel_add_hydrogens(input_path='/path/to/myStructure.pdb',
60 output_path='/path/to/newStructure.pdb',
61 properties=prop)
63 Info:
64 * wrapped_software:
65 * name: Open Babel
66 * version: 2.4.1
67 * license: GNU
68 * ontology:
69 * name: EDAM
70 * schema: http://edamontology.org/EDAM.owl
72 """
74 def __init__(self, input_path, output_path, properties=None, **kwargs) -> None:
75 properties = properties or {}
77 # Call parent class constructor
78 super().__init__(properties)
79 self.locals_var_dict = locals().copy()
81 # Input/Output files
82 self.io_dict = {
83 "in": {"input_path": input_path},
84 "out": {"output_path": output_path},
85 }
87 # Properties specific for BB
88 self.input_format = properties.get("input_format", "")
89 self.output_format = properties.get("output_format", "")
90 self.fs_input = _from_string_to_list(properties.get("fs_input", None))
91 self.fs_output = _from_string_to_list(properties.get("fs_output", ["h"]))
92 self.coordinates = properties.get("coordinates", "")
93 self.effort = properties.get("effort", "medium")
94 self.ph = properties.get("ph", "")
95 self.binary_path = properties.get("binary_path", "obabel")
96 self.properties = properties
98 # Check the properties
99 self.check_properties(properties)
100 self.check_arguments()
102 def check_data_params(self, out_log, err_log):
103 """Checks all the input/output paths and parameters"""
104 self.io_dict["in"]["input_path"] = check_input_path(
105 self.io_dict["in"]["input_path"], out_log, self.__class__.__name__
106 )
107 self.io_dict["out"]["output_path"] = check_output_path(
108 self.io_dict["out"]["output_path"], out_log, self.__class__.__name__
109 )
111 def create_cmd(self, container_io_dict, out_log, err_log):
112 """Creates the command line instruction using the properties file settings"""
113 instructions_list = []
115 # executable path
116 instructions_list.append(self.binary_path)
118 # generating input
119 infr = get_input_format(
120 self.input_format, container_io_dict["in"]["input_path"], out_log
121 )
122 iformat = "-i" + infr
123 instructions_list.append(iformat)
124 ipath = container_io_dict["in"]["input_path"]
125 instructions_list.append(ipath)
127 # generating output
128 oufr = get_output_format(
129 self.output_format, container_io_dict["out"]["output_path"], out_log
130 )
131 oformat = "-o" + oufr
132 instructions_list.append(oformat)
133 opath = "-O" + container_io_dict["out"]["output_path"]
134 instructions_list.append(opath)
136 # adding coordinates
137 crd = get_coordinates(self.coordinates, out_log)
138 coordinates = ""
139 if crd:
140 coordinates = "--gen" + crd + "d"
141 instructions_list.append(coordinates)
143 # checking pH
144 p = get_ph(self.ph, out_log)
146 # adding H
147 hydrogens = "-h"
149 # adding pH
150 ph = ""
151 if p:
152 ph = "-p " + p
153 instructions_list.append(ph)
154 else:
155 instructions_list.append(hydrogens)
157 # fs_input
158 if self.fs_input is not None:
159 for fsi in self.fs_input:
160 instructions_list.append("-a" + fsi)
162 # fs_output
163 if self.fs_output is not None:
164 for fso in self.fs_output:
165 instructions_list.append("-x" + fso)
167 # adding effort (only for 3D coordinates)
168 if crd == "3":
169 instructions_list.append("--" + self.effort)
171 return instructions_list
173 @launchlogger
174 def launch(self) -> int:
175 """Execute the :class:`BabelAddHydrogens <babelm.babel_add_hydrogens.BabelAddHydrogens>` babelm.babel_add_hydrogens.BabelAddHydrogens object."""
177 # check input/output paths and parameters
178 self.check_data_params(self.out_log, self.err_log)
180 # Setup Biobb
181 if self.check_restart():
182 return 0
183 self.stage_files()
185 # create command line instruction
186 self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log)
188 # Run Biobb block
189 self.run_biobb()
191 # Copy files to host
192 self.copy_to_host()
194 # remove temporary folder(s)
195 self.remove_tmp_files()
197 self.check_arguments(output_files_created=True, raise_exception=False)
199 return self.return_code
202def babel_add_hydrogens(
203 input_path: str, output_path: str, properties: Optional[dict] = None, **kwargs
204) -> int:
205 """Create the :class:`BabelAddHydrogens <babelm.babel_add_hydrogens.BabelAddHydrogens>` class and
206 execute the :meth:`launch() <babelm.babel_add_hydrogens.BabelAddHydrogens.launch>` method."""
207 return BabelAddHydrogens(**dict(locals())).launch()
210babel_add_hydrogens.__doc__ = BabelAddHydrogens.__doc__
211main = BabelAddHydrogens.get_main(babel_add_hydrogens, "Adds hydrogen atoms to small molecules.")
214if __name__ == "__main__":
215 main()