Coverage for biobb_chemistry / babelm / babel_convert.py: 94%
79 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 BabelConvert 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 BabelConvert(BiobbObject):
22 """
23 | biobb_chemistry BabelConvert
24 | This class is a wrapper of the Open Babel tool.
25 | Small molecule format conversion for structures or trajectories. 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.smi>`_. 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.convert.mol2>`_. 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*) - (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).
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 * **flex** (*bool*) - (False) Remove all but the largest contiguous fragment (strip salts).
39 * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.
40 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
41 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
42 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
43 * **container_path** (*str*) - (None) Container path definition.
44 * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.
45 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
46 * **container_working_dir** (*str*) - (None) Container working directory definition.
47 * **container_user_id** (*str*) - (None) Container user_id definition.
48 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
50 Examples:
51 This is a use example of how to use the building block from Python::
53 from biobb_chemistry.babelm.babel_convert import babel_convert
54 prop = {
55 'input_format': 'smi',
56 'output_format': 'mol2',
57 'coordinates': 3,
58 'ph': 7.4
59 }
60 babel_convert(input_path='/path/to/my2DMolecule.smi',
61 output_path='/path/to/new3DMolecule.mol2',
62 properties=prop)
64 Info:
65 * wrapped_software:
66 * name: Open Babel
67 * version: 2.4.1
68 * license: GNU
69 * ontology:
70 * name: EDAM
71 * schema: http://edamontology.org/EDAM.owl
73 """
75 def __init__(self, input_path, output_path, properties=None, **kwargs) -> None:
76 properties = properties or {}
78 # Call parent class constructor
79 super().__init__(properties)
80 self.locals_var_dict = locals().copy()
82 # Input/Output files
83 self.io_dict = {
84 "in": {"input_path": input_path},
85 "out": {"output_path": output_path},
86 }
88 # Properties specific for BB
89 self.input_format = properties.get("input_format", "")
90 self.output_format = properties.get("output_format", "")
91 self.fs_input = _from_string_to_list(properties.get("fs_input", None))
92 self.fs_output = _from_string_to_list(properties.get("fs_output", None))
93 self.coordinates = properties.get("coordinates", "")
94 self.effort = properties.get("effort", "medium")
95 self.ph = properties.get("ph", "")
96 self.flex = properties.get("flex", False)
97 self.binary_path = properties.get("binary_path", "obabel")
98 self.properties = properties
100 # Check the properties
101 self.check_properties(properties)
102 self.check_arguments()
104 def check_data_params(self, out_log, err_log):
105 """Checks all the input/output paths and parameters"""
106 self.io_dict["in"]["input_path"] = check_input_path(
107 self.io_dict["in"]["input_path"], out_log, self.__class__.__name__
108 )
109 self.io_dict["out"]["output_path"] = check_output_path(
110 self.io_dict["out"]["output_path"], out_log, self.__class__.__name__
111 )
113 def create_cmd(self, container_io_dict, out_log, err_log):
114 """Creates the command line instruction using the properties file settings"""
115 instructions_list = []
117 # executable path
118 instructions_list.append(self.binary_path)
120 # generating input
121 infr = get_input_format(
122 self.input_format, container_io_dict["in"]["input_path"], out_log
123 )
124 iformat = "-i" + infr
125 instructions_list.append(iformat)
126 ipath = container_io_dict["in"]["input_path"]
127 instructions_list.append(ipath)
129 # generating output
130 oufr = get_output_format(
131 self.output_format, container_io_dict["out"]["output_path"], out_log
132 )
133 oformat = "-o" + oufr
134 instructions_list.append(oformat)
135 opath = "-O" + container_io_dict["out"]["output_path"]
136 instructions_list.append(opath)
138 # adding coordinates
139 crd = get_coordinates(self.coordinates, out_log)
140 coordinates = ""
141 if crd:
142 coordinates = "--gen" + crd + "d"
143 instructions_list.append(coordinates)
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 # flex
153 flex = ""
154 if not self.flex:
155 flex = "-r"
156 instructions_list.append(flex)
158 # fs_input
159 if self.fs_input is not None:
160 for fsi in self.fs_input:
161 instructions_list.append("-a" + fsi)
163 # fs_output
164 if self.fs_output is not None:
165 for fso in self.fs_output:
166 instructions_list.append("-x" + fso)
168 # adding effort (only for 3D coordinates)
169 if crd == "3":
170 instructions_list.append("--" + self.effort)
172 return instructions_list
174 @launchlogger
175 def launch(self) -> int:
176 """Execute the :class:`BabelConvert <babelm.babel_convert.BabelConvert>` babelm.babel_convert.BabelConvert object."""
178 # check input/output paths and parameters
179 self.check_data_params(self.out_log, self.err_log)
181 # Setup Biobb
182 if self.check_restart():
183 return 0
184 self.stage_files()
186 # create command line instruction
187 self.cmd = self.create_cmd(self.stage_io_dict, self.out_log, self.err_log)
189 # Run Biobb block
190 self.run_biobb()
192 # Copy files to host
193 self.copy_to_host()
195 # remove temporary folder(s)
196 self.remove_tmp_files()
198 self.check_arguments(output_files_created=True, raise_exception=False)
200 return self.return_code
203def babel_convert(
204 input_path: str, output_path: str, properties: Optional[dict] = None, **kwargs
205) -> int:
206 """Create the :class:`BabelConvert <babelm.babel_convert.BabelConvert>` class and
207 execute the :meth:`launch() <babelm.babel_convert.BabelConvert.launch>` method."""
208 return BabelConvert(**dict(locals())).launch()
211babel_convert.__doc__ = BabelConvert.__doc__
212main = BabelConvert.get_main(babel_convert, "Small molecule format conversion.")
215if __name__ == "__main__":
216 main()