Coverage for biobb_chemistry / babelm / babel_remove_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 BabelRemoveHydrogens class and the command line interface."""
4from typing import Optional
5from biobb_common.generic.biobb_object import BiobbObject
6from biobb_common.tools.file_utils import launchlogger
8from biobb_chemistry.babelm.common import (
9 _from_string_to_list,
10 check_input_path,
11 check_output_path,
12 get_coordinates,
13 get_input_format,
14 get_output_format,
15 get_ph,
16)
19class BabelRemoveHydrogens(BiobbObject):
20 """
21 | biobb_chemistry BabelRemoveHydrogens
22 | This class is a wrapper of the Open Babel tool.
23 | Removes 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>`_.
25 Args:
26 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.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).
27 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.nohydrogens.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).
28 properties (dic - Python dictionary object containing the tool parameters, not input/output files):
29 * **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).
30 * **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).
31 * **fs_input** (*list*) - (None) Format-specific input options. Values: b (disable automatic bonding), d (input file is in dlg -AutoDock docking log- format).
32 * **fs_output** (*list*) - (None) 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).
33 * **coordinates** (*int*) - (None) Type of coordinates: 2D or 3D. Values: 2 (2D coordinates), 3 (3D coordinates).
34 * **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).
35 * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH.
36 * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.
37 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
38 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
39 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
40 * **container_path** (*str*) - (None) Container path definition.
41 * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.
42 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
43 * **container_working_dir** (*str*) - (None) Container working directory definition.
44 * **container_user_id** (*str*) - (None) Container user_id definition.
45 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
47 Examples:
48 This is a use example of how to use the building block from Python::
50 from biobb_chemistry.babelm.babel_remove_hydrogens import babel_remove_hydrogens
51 prop = {
52 'input_format': 'pdb',
53 'output_format': 'pdb',
54 'coordinates': 3,
55 'ph': 7.4
56 }
57 babel_remove_hydrogens(input_path='/path/to/myStructure.pdb',
58 output_path='/path/to/newStructure.pdb',
59 properties=prop)
61 Info:
62 * wrapped_software:
63 * name: Open Babel
64 * version: 2.4.1
65 * license: GNU
66 * ontology:
67 * name: EDAM
68 * schema: http://edamontology.org/EDAM.owl
70 """
72 def __init__(self, input_path, output_path, properties=None, **kwargs) -> None:
73 properties = properties or {}
75 # Call parent class constructor
76 super().__init__(properties)
77 self.locals_var_dict = locals().copy()
79 # Input/Output files
80 self.io_dict = {
81 "in": {"input_path": input_path},
82 "out": {"output_path": output_path},
83 }
85 # Properties specific for BB
86 self.input_format = properties.get("input_format", "")
87 self.output_format = properties.get("output_format", "")
88 self.fs_input = _from_string_to_list(properties.get("fs_input", None))
89 self.fs_output = _from_string_to_list(properties.get("fs_output", None))
90 self.coordinates = properties.get("coordinates", "")
91 self.effort = properties.get("effort", "medium")
92 self.ph = properties.get("ph", "")
93 self.binary_path = properties.get("binary_path", "obabel")
94 self.properties = properties
96 # Check the properties
97 self.check_properties(properties)
98 self.check_arguments()
100 def check_data_params(self, out_log, err_log):
101 """Checks all the input/output paths and parameters"""
102 self.io_dict["in"]["input_path"] = check_input_path(
103 self.io_dict["in"]["input_path"], out_log, self.__class__.__name__
104 )
105 self.io_dict["out"]["output_path"] = check_output_path(
106 self.io_dict["out"]["output_path"], out_log, self.__class__.__name__
107 )
109 def create_cmd(self, container_io_dict, out_log, err_log):
110 """Creates the command line instruction using the properties file settings"""
111 instructions_list = []
113 # executable path
114 instructions_list.append(self.binary_path)
116 # generating input
117 infr = get_input_format(
118 self.input_format, container_io_dict["in"]["input_path"], out_log
119 )
120 iformat = "-i" + infr
121 instructions_list.append(iformat)
122 ipath = container_io_dict["in"]["input_path"]
123 instructions_list.append(ipath)
125 # generating output
126 oufr = get_output_format(
127 self.output_format, container_io_dict["out"]["output_path"], out_log
128 )
129 oformat = "-o" + oufr
130 instructions_list.append(oformat)
131 opath = "-O" + container_io_dict["out"]["output_path"]
132 instructions_list.append(opath)
134 # adding coordinates
135 crd = get_coordinates(self.coordinates, out_log)
136 coordinates = ""
137 if crd:
138 coordinates = "--gen" + crd + "d"
139 instructions_list.append(coordinates)
141 hydrogens = "-d"
143 instructions_list.append(hydrogens)
145 # adding pH
146 p = get_ph(self.ph, out_log)
147 ph = ""
148 if p:
149 ph = "-p " + p
150 instructions_list.append(ph)
152 # fs_input
153 if self.fs_input is not None:
154 for fsi in self.fs_input:
155 instructions_list.append("-a" + fsi)
157 # fs_output
158 if self.fs_output is not None:
159 for fso in self.fs_output:
160 instructions_list.append("-x" + fso)
162 # adding effort (only for 3D coordinates)
163 if crd == "3":
164 instructions_list.append("--" + self.effort)
166 return instructions_list
168 @launchlogger
169 def launch(self) -> int:
170 """Execute the :class:`BabelRemoveHydrogens <babelm.babel_remove_hydrogens.BabelRemoveHydrogens>` babelm.babel_remove_hydrogens.BabelRemoveHydrogens object."""
172 # check input/output paths and parameters
173 self.check_data_params(self.out_log, self.err_log)
175 # Setup Biobb
176 if self.check_restart():
177 return 0
178 self.stage_files()
180 # create command line instruction
181 self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log)
183 # Run Biobb block
184 self.run_biobb()
186 # Copy files to host
187 self.copy_to_host()
189 # remove temporary folder(s)
190 self.remove_tmp_files()
192 self.check_arguments(output_files_created=True, raise_exception=False)
194 return self.return_code
197def babel_remove_hydrogens(
198 input_path: str, output_path: str, properties: Optional[dict] = None, **kwargs
199) -> int:
200 """Create the :class:`BabelRemoveHydrogens <babelm.babel_remove_hydrogens.BabelRemoveHydrogens>` class and
201 execute the :meth:`launch() <babelm.babel_remove_hydrogens.BabelRemoveHydrogens.launch>` method."""
202 return BabelRemoveHydrogens(**dict(locals())).launch()
205babel_remove_hydrogens.__doc__ = BabelRemoveHydrogens.__doc__
206main = BabelRemoveHydrogens.get_main(babel_remove_hydrogens, "Removes hydrogen atoms to small molecules.")
209if __name__ == "__main__":
210 main()