Coverage for biobb_cmip/cmip/cmip_titration.py: 23%
82 statements
« prev ^ index » next coverage.py v7.6.10, created at 2025-01-28 09:52 +0000
1#!/usr/bin/env python3
3"""Module containing the Titration class and the command line interface."""
4import os
5import argparse
6from typing import Optional
7from typing import Any
8from pathlib import Path
9from biobb_common.generic.biobb_object import BiobbObject
10from biobb_common.configuration import settings
11from biobb_common.tools import file_utils as fu
12from biobb_common.tools.file_utils import launchlogger
13from biobb_cmip.cmip.common import create_params_file
14from biobb_cmip.cmip.common import params_preset
15from biobb_cmip.cmip.common import get_pdb_total_charge
18class CmipTitration(BiobbObject):
19 """
20 | biobb_cmip Titration
21 | Wrapper class for the CMIP titration module.
22 | The CMIP titration module. CMIP titration module adds water molecules, positive ions (Na+) and negative ions (Cl-) in the energetically most favorable structure locations.
24 Args:
25 input_pdb_path (str): Path to the input PDB file. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_cmip/master/biobb_cmip/test/data/cmip/1kim_h.pdb>`_. Accepted formats: pdb (edam:format_1476).
26 output_pdb_path (str): Path to the output PDB file. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_cmip/master/biobb_cmip/test/reference/cmip/1kim_neutral.pdb>`_. Accepted formats: pdb (edam:format_1476).
27 input_vdw_params_path (str) (Optional): Path to the CMIP input Van der Waals force parameters, if not provided the CMIP conda installation one is used ("$CONDA_PREFIX/share/cmip/dat/vdwprm"). File type: input. Accepted formats: txt (edam:format_2330).
28 input_params_path (str) (Optional): Path to the CMIP input parameters file. File type: input. Accepted formats: txt (edam:format_2330).
29 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
30 * **params** (*dict*) - ({}) CMIP options specification.
31 * **energy_cutoff** (*float*) - (9999.9) Energy cutoff, extremely hight value to enable the addition of all the ions and waters before reaching the cutoff.
32 * **num_wats** (*int*) - (10) Number of water molecules to be added.
33 * **neutral** (*bool*) - (False) Neutralize the charge of the system. If selected *num_positive_ions* and *num_negative_ions* values will not be taken into account.
34 * **num_positive_ions** (*int*) - (10) Number of positive ions to be added (Tipatom IP=Na+).
35 * **num_negative_ions** (*int*) - (10) Number of negative ions to be added (Tipatom IM=Cl-).
36 * **binary_path** (*str*) - ("titration") Path to the CMIP Titration 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) Path to the binary executable of your container.
41 * **container_image** (*str*) - ("cmip/cmip:latest") Container Image identifier.
42 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
43 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
44 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
45 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
48 Examples:
49 This is a use example of how to use the building block from Python::
51 from biobb_cmip.cmip.titration import titration
52 prop = { 'binary_path': 'titration' }
53 titration(input_pdb_path='/path/to/myStructure.pdb',
54 output_pdb_path='/path/to/newStructure.pdb',
55 properties=prop)
57 Info:
58 * wrapped_software:
59 * name: CMIP Titration
60 * version: 2.7.0
61 * license: Apache-2.0
62 * ontology:
63 * name: EDAM
64 * schema: http://edamontology.org/EDAM.owl
65 """
67 def __init__(self, input_pdb_path: str, output_pdb_path: str,
68 input_vdw_params_path: Optional[str] = None, input_params_path: Optional[str] = None,
69 properties: Optional[dict] = None, **kwargs) -> None:
70 properties = properties or {}
72 # Call parent class constructor
73 super().__init__(properties)
74 self.locals_var_dict = locals().copy()
76 # Input/Output files
77 self.io_dict = {
78 "in": {"input_pdb_path": input_pdb_path, "input_vdw_params_path": input_vdw_params_path,
79 "input_params_path": input_params_path},
80 "out": {"output_pdb_path": output_pdb_path}
81 }
83 # Properties specific for BB
84 self.neutral = properties.get('neutral', False)
85 self.num_wats = properties.get('num_wats')
86 self.num_positive_ions = properties.get('num_positive_ions')
87 self.num_negative_ions = properties.get('num_negative_ions')
88 self.binary_path = properties.get('binary_path', 'titration')
89 self.output_params_path = properties.get('output_params_path', 'params')
90 if not self.io_dict['in'].get('input_vdw_params_path'):
91 self.io_dict['in']['input_vdw_params_path'] = f"{os.environ.get('CONDA_PREFIX')}/share/cmip/dat/vdwprm"
92 self.params: dict[str, Any] = {k: str(v) for k, v in properties.get('params', dict()).items()}
93 self.energy_cutoff = properties.get('energy_cutoff', 9999.9)
95 # Check the properties
96 self.check_properties(properties)
97 self.check_arguments()
99 @launchlogger
100 def launch(self) -> int:
101 """Execute the :class:`Titration <cmip.titration.Titration>` object."""
102 # Setup Biobb
103 if self.check_restart():
104 return 0
106 # Check if output_pdb_path ends with ".pdb"
107 if not self.io_dict['out']['output_pdb_path'].endswith('.pdb'):
108 fu.log('ERROR: output_pdb_path name must end in .pdb', self.out_log, self.global_log)
109 raise ValueError("ERROR: output_pdb_path name must end in .pdb")
111 # Adding neutral, num_negative_ions, num_positive_ions, num_wats, cutoff
112 if self.num_wats:
113 self.params['titwat'] = str(self.num_wats)
114 if self.num_positive_ions:
115 self.params['titip'] = str(self.num_positive_ions)
116 if self.num_negative_ions:
117 self.params['titim'] = str(self.num_negative_ions)
118 if self.neutral:
119 charge = get_pdb_total_charge(self.io_dict['in']['input_pdb_path'])
120 self.params['titip'] = '0'
121 self.params['titim'] = '0'
122 if int(round(charge)) > 0:
123 self.params['titim'] = str(int(round(charge)))
124 elif int(round(charge)) < 0:
125 self.params['titip'] = abs(int(round(charge)))
126 else:
127 fu.log(f'Neutral flag activated however no positive or negative ions will be added because the system '
128 f'is already neutralized. System charge: {round(charge, 3)}', self.out_log, self.global_log)
129 fu.log(f'Neutral flag activated. Current system charge: {round(charge, 3)}, '
130 f'positive ions to be added: {self.params["titip"]}, '
131 f'negative ions to be added: {self.params["titim"]}, '
132 f'final residual charge: {round(charge + int(self.params["titip"]) - int(self.params["titim"]), 3)}',
133 self.out_log, self.global_log)
134 if self.energy_cutoff:
135 self.params['titcut'] = str(self.energy_cutoff)
137 combined_params_dir = fu.create_unique_dir()
138 self.io_dict['in']['combined_params_path'] = create_params_file(
139 output_params_path=str(Path(combined_params_dir).joinpath(self.output_params_path)),
140 input_params_path=self.io_dict['in']['input_params_path'],
141 params_preset_dict=params_preset(execution_type='titration'),
142 params_properties_dict=self.params)
144 self.stage_files()
146 self.cmd = [self.binary_path,
147 '-i', self.stage_io_dict['in']['combined_params_path'],
148 '-vdw', self.stage_io_dict['in']['input_vdw_params_path'],
149 '-hs', self.stage_io_dict['in']['input_pdb_path'],
150 '-outpdb', self.stage_io_dict['out']['output_pdb_path'][:-4]]
152 # Run Biobb block
153 self.run_biobb()
155 # Copy files to host
156 self.copy_to_host()
158 # remove temporary folder(s)
159 self.tmp_files.extend([
160 # self.stage_io_dict.get("unique_dir", ""),
161 combined_params_dir
162 ])
163 self.remove_tmp_files()
165 self.check_arguments(output_files_created=True, raise_exception=False)
166 return self.return_code
169def cmip_titration(input_pdb_path: str, output_pdb_path: str,
170 input_vdw_params_path: Optional[str] = None, input_params_path: Optional[str] = None,
171 properties: Optional[dict] = None, **kwargs) -> int:
172 """Create :class:`Titration <cmip.titration.Titration>` class and
173 execute the :meth:`launch() <cmip.titration.Titration.launch>` method."""
175 return CmipTitration(input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path,
176 input_vdw_params_path=input_vdw_params_path, input_params_path=input_params_path,
177 properties=properties, **kwargs).launch()
179 cmip_titration.__doc__ = CmipTitration.__doc__
182def main():
183 parser = argparse.ArgumentParser(description="Wrapper of the CMIP Titration module.",
184 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
185 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
187 # Specific args of each building block
188 required_args = parser.add_argument_group('required arguments')
189 required_args.add_argument('--input_pdb_path', required=True)
190 required_args.add_argument('--output_pdb_path', required=True)
191 parser.add_argument('--input_vdw_params_path', required=False)
192 parser.add_argument('--input_params_path', required=False)
194 args = parser.parse_args()
195 config = args.config if args.config else None
196 properties = settings.ConfReader(config=config).get_prop_dic()
198 # Specific call of each building block
199 cmip_titration(input_pdb_path=args.input_pdb_path, output_pdb_path=args.output_pdb_path,
200 input_vdw_params_path=args.input_vdw_params_path, input_params_path=args.input_params_path,
201 properties=properties)
204if __name__ == '__main__':
205 main()