Coverage for biobb_cmip / cmip / cmip_titration.py: 26%
69 statements
« prev ^ index » next coverage.py v7.13.0, created at 2025-12-22 12:26 +0000
1#!/usr/bin/env python3
3"""Module containing the Titration class and the command line interface."""
4import os
5from typing import Optional
6from typing import Any
7from pathlib import Path
8from biobb_common.generic.biobb_object import BiobbObject
9from biobb_common.tools import file_utils as fu
10from biobb_common.tools.file_utils import launchlogger
11from biobb_cmip.cmip.common import create_params_file
12from biobb_cmip.cmip.common import params_preset
13from biobb_cmip.cmip.common import get_pdb_total_charge
16class CmipTitration(BiobbObject):
17 """
18 | biobb_cmip Titration
19 | Wrapper class for the CMIP titration module.
20 | The CMIP titration module. CMIP titration module adds water molecules, positive ions (Na+) and negative ions (Cl-) in the energetically most favorable structure locations.
22 Args:
23 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).
24 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).
25 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).
26 input_params_path (str) (Optional): Path to the CMIP input parameters file. File type: input. Accepted formats: txt (edam:format_2330).
27 properties (dict - Python dictionary object containing the tool parameters, not input/output files):
28 * **params** (*dict*) - ({}) CMIP options specification.
29 * **energy_cutoff** (*float*) - (9999.9) Energy cutoff, extremely hight value to enable the addition of all the ions and waters before reaching the cutoff.
30 * **num_wats** (*int*) - (10) Number of water molecules to be added.
31 * **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.
32 * **num_positive_ions** (*int*) - (10) Number of positive ions to be added (Tipatom IP=Na+).
33 * **num_negative_ions** (*int*) - (10) Number of negative ions to be added (Tipatom IM=Cl-).
34 * **binary_path** (*str*) - ("titration") Path to the CMIP Titration executable binary.
35 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
36 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
37 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
38 * **container_path** (*str*) - (None) Path to the binary executable of your container.
39 * **container_image** (*str*) - ("cmip/cmip:latest") Container Image identifier.
40 * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
41 * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
42 * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
43 * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
46 Examples:
47 This is a use example of how to use the building block from Python::
49 from biobb_cmip.cmip.titration import titration
50 prop = { 'binary_path': 'titration' }
51 titration(input_pdb_path='/path/to/myStructure.pdb',
52 output_pdb_path='/path/to/newStructure.pdb',
53 properties=prop)
55 Info:
56 * wrapped_software:
57 * name: CMIP Titration
58 * version: 2.7.0
59 * license: Apache-2.0
60 * ontology:
61 * name: EDAM
62 * schema: http://edamontology.org/EDAM.owl
63 """
65 def __init__(self, input_pdb_path: str, output_pdb_path: str,
66 input_vdw_params_path: Optional[str] = None, input_params_path: Optional[str] = None,
67 properties: Optional[dict] = None, **kwargs) -> None:
68 properties = properties or {}
70 # Call parent class constructor
71 super().__init__(properties)
72 self.locals_var_dict = locals().copy()
74 # Input/Output files
75 self.io_dict = {
76 "in": {"input_pdb_path": input_pdb_path, "input_vdw_params_path": input_vdw_params_path,
77 "input_params_path": input_params_path},
78 "out": {"output_pdb_path": output_pdb_path}
79 }
81 # Properties specific for BB
82 self.neutral = properties.get('neutral', False)
83 self.num_wats = properties.get('num_wats')
84 self.num_positive_ions = properties.get('num_positive_ions')
85 self.num_negative_ions = properties.get('num_negative_ions')
86 self.binary_path = properties.get('binary_path', 'titration')
87 self.output_params_path = properties.get('output_params_path', 'params')
88 if not self.io_dict['in'].get('input_vdw_params_path'):
89 self.io_dict['in']['input_vdw_params_path'] = f"{os.environ.get('CONDA_PREFIX')}/share/cmip/dat/vdwprm"
90 self.params: dict[str, Any] = {k: str(v) for k, v in properties.get('params', dict()).items()}
91 self.energy_cutoff = properties.get('energy_cutoff', 9999.9)
93 # Check the properties
94 self.check_properties(properties)
95 self.check_arguments()
97 @launchlogger
98 def launch(self) -> int:
99 """Execute the :class:`Titration <cmip.titration.Titration>` object."""
100 # Setup Biobb
101 if self.check_restart():
102 return 0
104 # Check if output_pdb_path ends with ".pdb"
105 if not self.io_dict['out']['output_pdb_path'].endswith('.pdb'):
106 fu.log('ERROR: output_pdb_path name must end in .pdb', self.out_log, self.global_log)
107 raise ValueError("ERROR: output_pdb_path name must end in .pdb")
109 # Adding neutral, num_negative_ions, num_positive_ions, num_wats, cutoff
110 if self.num_wats:
111 self.params['titwat'] = str(self.num_wats)
112 if self.num_positive_ions:
113 self.params['titip'] = str(self.num_positive_ions)
114 if self.num_negative_ions:
115 self.params['titim'] = str(self.num_negative_ions)
116 if self.neutral:
117 charge = get_pdb_total_charge(self.io_dict['in']['input_pdb_path'])
118 self.params['titip'] = '0'
119 self.params['titim'] = '0'
120 if int(round(charge)) > 0:
121 self.params['titim'] = str(int(round(charge)))
122 elif int(round(charge)) < 0:
123 self.params['titip'] = abs(int(round(charge)))
124 else:
125 fu.log(f'Neutral flag activated however no positive or negative ions will be added because the system '
126 f'is already neutralized. System charge: {round(charge, 3)}', self.out_log, self.global_log)
127 fu.log(f'Neutral flag activated. Current system charge: {round(charge, 3)}, '
128 f'positive ions to be added: {self.params["titip"]}, '
129 f'negative ions to be added: {self.params["titim"]}, '
130 f'final residual charge: {round(charge + int(self.params["titip"]) - int(self.params["titim"]), 3)}',
131 self.out_log, self.global_log)
132 if self.energy_cutoff:
133 self.params['titcut'] = str(self.energy_cutoff)
135 combined_params_dir = fu.create_unique_dir()
136 self.io_dict['in']['combined_params_path'] = create_params_file(
137 output_params_path=str(Path(combined_params_dir).joinpath(self.output_params_path)),
138 input_params_path=self.io_dict['in']['input_params_path'],
139 params_preset_dict=params_preset(execution_type='titration'),
140 params_properties_dict=self.params)
142 self.stage_files()
144 self.cmd = [self.binary_path,
145 '-i', self.stage_io_dict['in']['combined_params_path'],
146 '-vdw', self.stage_io_dict['in']['input_vdw_params_path'],
147 '-hs', self.stage_io_dict['in']['input_pdb_path'],
148 '-outpdb', self.stage_io_dict['out']['output_pdb_path'][:-4]]
150 # Run Biobb block
151 self.run_biobb()
153 # Copy files to host
154 self.copy_to_host()
156 # remove temporary folder(s)
157 self.tmp_files.append(combined_params_dir)
158 self.remove_tmp_files()
160 self.check_arguments(output_files_created=True, raise_exception=False)
161 return self.return_code
164def cmip_titration(input_pdb_path: str, output_pdb_path: str,
165 input_vdw_params_path: Optional[str] = None, input_params_path: Optional[str] = None,
166 properties: Optional[dict] = None, **kwargs) -> int:
167 """Create :class:`Titration <cmip.titration.Titration>` class and
168 execute the :meth:`launch() <cmip.titration.Titration.launch>` method."""
169 return CmipTitration(input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path,
170 input_vdw_params_path=input_vdw_params_path, input_params_path=input_params_path,
171 properties=properties, **kwargs).launch()
174cmip_titration.__doc__ = CmipTitration.__doc__
175main = CmipTitration.get_main(cmip_titration, "Wrapper of the CMIP Titration module.")
177if __name__ == '__main__':
178 main()