Source code for schrodinger.application.jaguar.solvation_keywords

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

# Contributors: Mark A. Watson

from voluptuous import Any
from voluptuous import MultipleInvalid
from voluptuous import Required
from voluptuous import Schema

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

SOLVATION_KEYWORDS = {}
INPUT_MOLECULE = 'input'
JAG_SOLVATION_METHODS = ['PBF', 'PCM', 'SM8']

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


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
    #------------------------------------------------------------------------------
    # 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.')

    #------------------------------------------------------------------------------
    # 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='PBF',
        description=
        'The solvation method used for final solvation energy of the phases.')