Source code for schrodinger.application.jaguar.solvation_keywords

"""
This module documents all possible Solvation input keywords.
"""

# Contributors: Mark A. Watson

from schrodinger.application.jaguar.workflow_keywords import Choices
from schrodinger.application.jaguar.workflow_keywords import WorkflowKeyword

SOLVATION_KEYWORDS = {}
INPUT_MOLECULE = 'input'
JAG_SOLVATION_METHODS = ['PBF', 'PCM', 'SM8', 'OFF']
MACRO_PKA = 'macro-pka'
EPIKX_PKA = 'epikx'
PKA_METHODS = [MACRO_PKA, EPIKX_PKA]

#------------------------------------------------------------------------------


def keyword(name, valid_type, default, description):
    """
    Convenience function to create a dictionary of SolvationKeyword's
    """

    if name in SOLVATION_KEYWORDS:
        raise ValueError('keyword %s is duplicated' % name)

    # Define all keywords in lower case
    SOLVATION_KEYWORDS[name.lower()] = WorkflowKeyword(name=name.lower(),
                                                       valid_type=valid_type,
                                                       default=default,
                                                       description=description)


def generate_all_keywords():

    from . import solvation_input  # noqa: F401

    #------------------------------------------------------------------------------
    # Add new "list of strings" Solvation keywords here
    #------------------------------------------------------------------------------
    #------------------------------------------------------------------------------
    # Add new "list of float" Solvation keywords here
    #------------------------------------------------------------------------------

    keyword(name='pHs',
            valid_type=[float],
            default=[7.4],
            description='A list of pHs for LogD calculations')

    #------------------------------------------------------------------------------
    # Add new "boolean" Solvation keywords here
    #------------------------------------------------------------------------------

    keyword(name='optimize_phase1',
            valid_type=bool,
            default=True,
            description='If True, optimize input molecule(s) in phase 1.')

    keyword(name='optimize_phase2',
            valid_type=bool,
            default=True,
            description='If True, optimize input molecule(s) in phase 2.')

    keyword(name='optimize_gas',
            valid_type=bool,
            default=True,
            description='If True, optimize input molecule(s) in gas phase.')

    keyword(name='debug',
            valid_type=bool,
            default=False,
            description='Print extra debugging information.')

    keyword(
        name='solvation_energy',
        valid_type=bool,
        default=False,
        description='Compute energy of solvation from gas phase to both phases.'
    )

    keyword(
        name='csrch',
        valid_type=bool,
        default=False,
        description='Do tautomer and conformational search on input molecule.')

    keyword(name='logP',
            valid_type=bool,
            default=False,
            description='Compute the logP between the two phases.')

    keyword(name='logD',
            valid_type=bool,
            default=False,
            description='Compute the logD between the two phases.')

    keyword(
        name='run_alternate_charges',
        valid_type=bool,
        default=True,
        description='Compute the QM logP of charges found in pKa calculation.')

    #------------------------------------------------------------------------------
    # Add new "integer" Solvation keywords here
    #------------------------------------------------------------------------------

    keyword(name='multiplicity',
            valid_type=int,
            default=1,
            description='Overall spin multiplicity of reaction complex.')

    keyword(name='charge',
            valid_type=int,
            default=0,
            description='Overall charge of reaction complex.')

    #------------------------------------------------------------------------------
    # Add new "float" Solvation keywords here
    #------------------------------------------------------------------------------

    keyword(name='temp',
            valid_type=float,
            default=298.15,
            description='Temperature of reactions.')

    #------------------------------------------------------------------------------
    # Add new "string" Solvation keywords here
    #------------------------------------------------------------------------------

    keyword(
        name=INPUT_MOLECULE,
        valid_type=str,
        default='',
        description=
        'A list of full paths (absolute or relative) to Maestro structure files containing individual reactant molecules.'
    )

    keyword(name='phase1',
            valid_type=str,
            default='gas',
            description='The first phase for the input molecules.')

    keyword(name='phase2',
            valid_type=str,
            default='water',
            description='The second phase for the input molecules.')

    keyword(
        name='opt_solvation_method',
        valid_type=Choices(*JAG_SOLVATION_METHODS),
        default='PCM',
        description=
        'The solvation method used for computing geometry optimization of the phases.'
    )

    keyword(
        name='solvation_method',
        valid_type=Choices(*JAG_SOLVATION_METHODS),
        default='SM8',
        description=
        'The solvation method used for final solvation energy of the phases.')

    keyword(name='pka_method',
            valid_type=Choices(*PKA_METHODS),
            default=MACRO_PKA,
            description='The pka predictor to use for LogD calculations.')