Source code for schrodinger.application.jaguar.hydrokinetic_keywords

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

# Contributors: Mark A. Watson

import schrodinger.application.jaguar.hydrokinetic_input_constants as constants
import schrodinger.application.jaguar.autots_input_constants as autots_constants
from schrodinger.application.jaguar.workflow_keywords import Choices, WorkflowKeyword

HYDROKINETIC_KEYWORDS = {}

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


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

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

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


def generate_all_keywords():

    #------------------------------------------------------------------------------
    # Add new "list of int" Hydrokinetic keywords here
    #------------------------------------------------------------------------------

    keyword(name='protonatable_positions',
            valid_type=[int],
            default=[],
            description='A list of atom indices to protonate.')

    #------------------------------------------------------------------------------
    # Add new "list of float" Hydrokinetic keywords here
    #------------------------------------------------------------------------------

    keyword(name='pHs',
            valid_type=[float],
            default=[5.0, 7.0, 9.0],
            description=
            'A list of pHs to consider for the determination of half-lives.')

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

    keyword(
        name='optimize_inputs',
        valid_type=bool,
        default=True,
        description='If True, optimize initial complexes.  This parameter will '
        'be automatically set to False if the parameters reactant_complex '
        'and product_complex are set.')

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

    keyword(name='debug_autots',
            valid_type=bool,
            default=False,
            description='Print extra debugging information in AutoTS subjobs.')

    keyword(name='skip_pka',
            valid_type=bool,
            default=False,
            description='Do not compute pKas of structures')

    keyword(name='csrch',
            valid_type=bool,
            default=True,
            description='Run conformational search in macro-pka calculation')

    keyword(name='ph_aware_mechs',
            valid_type=bool,
            default=True,
            description='Use the requested pHs to limit mechanisms considered '
            'e.g. do not consider hydroxide catalyzed reactions at pH 3')

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

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

    keyword(name='max_halflife',
            valid_type=float,
            default=315360000.0,
            description=
            'Maximum half-life to allow for further reactive elaboration.')

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

    keyword(name=constants.JOBTYPE,
            valid_type=Choices(*constants.JOBTYPE_CHOICES),
            default=constants.JOBTYPE_STD,
            description='Jobtype for Hydrokinetic to run.')

    keyword(
        name=constants.INPUT_MOLECULE,
        valid_type=str,
        default='',
        description=
        'Path to Maestro structure file containing an individual reactant molecule.'
    )

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

    keyword(
        name='spectator_esp',
        valid_type=Choices(*autots_constants.SPECTATOR_ESPS),
        default=autots_constants.ESP_JAGUAR,
        description=
        'Methodology used to position spectator molecules in reactant and product complexes.'
    )