#!/usr/bin/env python3
"""Module containing the Titration class and the command line interface."""
import os
from typing import Optional
from typing import Any
from pathlib import Path, PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_cmip.cmip.common import create_params_file
from biobb_cmip.cmip.common import params_preset
from biobb_cmip.cmip.common import get_pdb_total_charge
[docs]
class CmipTitration(BiobbObject):
"""
| biobb_cmip Titration
| Wrapper class for the CMIP titration module.
| The CMIP titration module. CMIP titration module adds water molecules, positive ions (Na+) and negative ions (Cl-) in the energetically most favorable structure locations.
Args:
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).
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).
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).
input_params_path (str) (Optional): Path to the CMIP input parameters file. File type: input. Accepted formats: txt (edam:format_2330).
properties (dict - Python dictionary object containing the tool parameters, not input/output files):
* **params** (*dict*) - ({}) CMIP options specification.
* **energy_cutoff** (*float*) - (9999.9) Energy cutoff, extremely hight value to enable the addition of all the ions and waters before reaching the cutoff.
* **num_wats** (*int*) - (10) Number of water molecules to be added.
* **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.
* **num_positive_ions** (*int*) - (10) Number of positive ions to be added (Tipatom IP=Na+).
* **num_negative_ions** (*int*) - (10) Number of negative ions to be added (Tipatom IM=Cl-).
* **binary_path** (*str*) - ("titration") Path to the CMIP Titration executable binary.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
* **container_path** (*str*) - (None) Path to the binary executable of your container.
* **container_image** (*str*) - ("cmip/cmip:latest") Container Image identifier.
* **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
* **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
* **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
* **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.
Examples:
This is a use example of how to use the building block from Python::
from biobb_cmip.cmip.titration import titration
prop = { 'binary_path': 'titration' }
titration(input_pdb_path='/path/to/myStructure.pdb',
output_pdb_path='/path/to/newStructure.pdb',
properties=prop)
Info:
* wrapped_software:
* name: CMIP Titration
* version: 2.7.0
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, input_pdb_path: str, output_pdb_path: str,
input_vdw_params_path: Optional[str] = None, input_params_path: Optional[str] = None,
properties: Optional[dict] = None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {"input_pdb_path": input_pdb_path, "input_vdw_params_path": input_vdw_params_path,
"input_params_path": input_params_path},
"out": {"output_pdb_path": output_pdb_path}
}
# Properties specific for BB
self.neutral = properties.get('neutral', False)
self.num_wats = properties.get('num_wats')
self.num_positive_ions = properties.get('num_positive_ions')
self.num_negative_ions = properties.get('num_negative_ions')
self.binary_path = properties.get('binary_path', 'titration')
self.output_params_path = properties.get('output_params_path', 'params')
if not self.io_dict['in'].get('input_vdw_params_path'):
self.io_dict['in']['input_vdw_params_path'] = f"{os.environ.get('CONDA_PREFIX')}/share/cmip/dat/vdwprm"
self.params: dict[str, Any] = {k: str(v) for k, v in properties.get('params', dict()).items()}
self.energy_cutoff = properties.get('energy_cutoff', 9999.9)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`Titration <cmip.titration.Titration>` object."""
# Setup Biobb
if self.check_restart():
return 0
# Check if output_pdb_path ends with ".pdb"
if not self.io_dict['out']['output_pdb_path'].endswith('.pdb'):
fu.log('ERROR: output_pdb_path name must end in .pdb', self.out_log, self.global_log)
raise ValueError("ERROR: output_pdb_path name must end in .pdb")
# Adding neutral, num_negative_ions, num_positive_ions, num_wats, cutoff
if self.num_wats:
self.params['titwat'] = str(self.num_wats)
if self.num_positive_ions:
self.params['titip'] = str(self.num_positive_ions)
if self.num_negative_ions:
self.params['titim'] = str(self.num_negative_ions)
if self.neutral:
charge = get_pdb_total_charge(self.io_dict['in']['input_pdb_path'])
self.params['titip'] = '0'
self.params['titim'] = '0'
if int(round(charge)) > 0:
self.params['titim'] = str(int(round(charge)))
elif int(round(charge)) < 0:
self.params['titip'] = abs(int(round(charge)))
else:
fu.log(f'Neutral flag activated however no positive or negative ions will be added because the system '
f'is already neutralized. System charge: {round(charge, 3)}', self.out_log, self.global_log)
fu.log(f'Neutral flag activated. Current system charge: {round(charge, 3)}, '
f'positive ions to be added: {self.params["titip"]}, '
f'negative ions to be added: {self.params["titim"]}, '
f'final residual charge: {round(charge + int(self.params["titip"]) - int(self.params["titim"]), 3)}',
self.out_log, self.global_log)
if self.energy_cutoff:
self.params['titcut'] = str(self.energy_cutoff)
combined_params_dir = fu.create_unique_dir()
self.io_dict['in']['combined_params_path'] = create_params_file(
output_params_path=str(Path(combined_params_dir).joinpath(self.output_params_path)),
input_params_path=self.io_dict['in']['input_params_path'],
params_preset_dict=params_preset(execution_type='titration'),
params_properties_dict=self.params)
self.stage_files()
self.cmd = ["cd",
self.stage_io_dict["unique_dir"],
";",
self.binary_path,
'-i', PurePath(self.stage_io_dict['in']['combined_params_path']).name,
'-vdw', PurePath(self.stage_io_dict['in']['input_vdw_params_path']).name,
'-hs', PurePath(self.stage_io_dict['in']['input_pdb_path']).name,
'-outpdb', PurePath(self.stage_io_dict['out']['output_pdb_path'][:-4]).name]
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# remove temporary folder(s)
self.tmp_files.append(combined_params_dir)
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]
def cmip_titration(input_pdb_path: str, output_pdb_path: str,
input_vdw_params_path: Optional[str] = None, input_params_path: Optional[str] = None,
properties: Optional[dict] = None, **kwargs) -> int:
"""Create :class:`Titration <cmip.titration.Titration>` class and
execute the :meth:`launch() <cmip.titration.Titration.launch>` method."""
return CmipTitration(input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path,
input_vdw_params_path=input_vdw_params_path, input_params_path=input_params_path,
properties=properties, **kwargs).launch()
cmip_titration.__doc__ = CmipTitration.__doc__
main = CmipTitration.get_main(cmip_titration, "Wrapper of the CMIP Titration module.")
if __name__ == '__main__':
main()