schrodinger.application.desmond.constants module

Define common numerical constants, CT and atom property names, and keyword values (enums).

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.constants.Constants

Bases: object

Related constants can inherit from Constants to make them iterable in the order of their declarations.

class schrodinger.application.desmond.constants.MaePropertyName(name: str, **kwargs)

Bases: str

This class defines a container for structure or atom level properties. The property key can be accessed directly, while enum values are accessed via the VAL attribute.

Example usage: CT_TYPE = MaePropertyName(FFIO_DATA_CT_TYPE, FULL_SYSTEM=FFIO_FULL_SYSTEM)

ct.property[CT_TYPE] = CT_TYPE.VAL.FULL_SYSTEM valid_ct_types = list(CT_TYPE.VAL)

__init__(name: str, **kwargs)
class schrodinger.application.desmond.constants.Conversion

Bases: object

KCAL_TO_JOUL = 4184.0
CAL_CM_TO_MPA = 0.48888
AU_TO_KG = 1.6605655
class schrodinger.application.desmond.constants.EXISTING_RESTRAINT

Bases: schrodinger.application.desmond.constants.Constants

RETAIN = 'retain'
IGNORE = 'ignore'
IGNORE_POSRE = 'ignore_posre'
class schrodinger.application.desmond.constants.WATER_MODELS

Bases: schrodinger.application.desmond.constants.Constants

SPC = 'SPC'
SPCE = 'SPCE'
TIP3P = 'TIP3P'
TIP3P_CHARMM = 'TIP3P_CHARMM'
TIP4P = 'TIP4P'
TIP4PEW = 'TIP4PEW'
TIP4P2005 = 'TIP4P2005'
TIP5P = 'TIP5P'
TIP4PD = 'TIP4PD'
class schrodinger.application.desmond.constants.LIPID_BILAYERS

Bases: schrodinger.application.desmond.constants.Constants

POPC = 'POPC'
POPE = 'POPE'
DMPC = 'DMPC'
DPPC = 'DPPC'
class schrodinger.application.desmond.constants.CUSTOM_CHARGE_MODE

Bases: schrodinger.application.desmond.constants.Constants

KEEP = 'keep'
CLEAR = 'clear'
ASSIGN = 'assign'
class schrodinger.application.desmond.constants.FEP_TYPES

Bases: schrodinger.application.desmond.constants.Constants

PRM_PROTEIN_BINDING = 'prm_protein_binding'
PRM_LIGAND_BINDING = 'prm_ligand_binding'
PRM_THERMOSTABILITY = 'prm_thermostability'
PROTEIN_STABILITY = 'prm_stability'
PROTEIN_SELECTIVITY = 'protein_selectivity'
COVALENT_LIGAND = 'covalent_ligand'
SMALL_MOLECULE = 'small_molecule'
METALLOPROTEIN = 'metalloprotein'
LIGAND_SELECTIVITY = 'ligand_selectivity'
ABSOLUTE_BINDING = 'absolute_binding'
SOLUBILITY = 'solubility'
schrodinger.application.desmond.constants.is_combined_protein_fep(fep_type: str)

Return whether the fep_type is one of the combiend protein fep types.

class schrodinger.application.desmond.constants.SIMULATION_PROTOCOL

Bases: schrodinger.application.desmond.constants.Constants

DEFAULT = 'default'
CHARGED = 'charge'
FORMALCHARGED = 'charge0'
COREHOPPING = 'core-hopping'
MACROCYCLE_COREHOPPING = 'macrocycle-core-hopping'
FRAGMENT_LINKING = 'fragment-linking'
class schrodinger.application.desmond.constants.REST_PROPERTIES

Bases: schrodinger.application.desmond.constants.Constants

SOLVENT_HOTREGION = 'i_rest_solvent_hotregion'
COMPLEX_HOTREGION = 'i_rest_complex_hotregion'
class schrodinger.application.desmond.constants.REST_COMPONENT

Bases: schrodinger.application.desmond.constants.Constants

ENVIRONMENT = 'environment'
RECEPTOR = 'receptor'
MEMBRANE = 'membrane'
LIGAND = 'ligand'
COMPLEX = 'complex'
class schrodinger.application.desmond.constants.REST_REGION_RULE

Bases: schrodinger.application.desmond.constants.Constants

DEFAULT = 'default'
ALL = 'all'
class schrodinger.application.desmond.constants.IsotropyPolicy

Bases: schrodinger.application.desmond.constants.Constants

ISOTROPIC = 'isotropic'
SEMI_ISOTROPIC = 'semi_isotropic'
CONSTANT_AXIS_A = 'constant_axis_a'
CONSTANT_AXIS_B = 'constant_axis_b'
CONSTANT_AXIS_C = 'constant_axis_c'
ANISOTROPIC = 'anisotropic'
FLEXIBLE = 'flexible'
class schrodinger.application.desmond.constants.ConfRestraintType

Bases: schrodinger.application.desmond.constants.Constants

BACKBONE = 'backbone'
SIDECHAIN = 'sidechain'
CALPHA_RUNG = 'calpha_rung'
class schrodinger.application.desmond.constants.FepLegTypes

Bases: schrodinger.application.desmond.constants.Constants

Leg types which represent a type of FEP simulation such as the complex leg in small molecule FEP or the hydration leg in FEP solubility.

These leg types are sometimes referred to as alchemical legs.

COMPLEX = 'complex'
SOLVENT = 'solvent'
FRAGMENT = 'fragment'
VACUUM = 'vacuum'
SUBLIMATION = 'sublimation'
HYDRATION = 'hydration'
SOLVATION = 'solvation'
FRAGMENT_HYDRATION = 'solvent_fragment_hydration'
RESTRAINED_FRAGMENT_HYDRATION = 'solvent_restrained_fragment_hydration'
MD = 'md'
class schrodinger.application.desmond.constants.PhysicalLegTypes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.StrEnum

Leg types which represent physical processes such as ligand binding or dissolution.

A given physical leg type generally corresponds to a consistent set of simulation types (which are sometimes referred to as alchemical leg types,) and which here are denoted as comments next to each value.

BINDING = 'binding'
FOLDING = 'folding'
SOLVATION = 'solvation'
AQUEOUS_DISSOLUTION = 'aqueous_dissolution'
SOLUBILITY_SOLVATION = 'solubility_solvation'
HYDRATION = 'hydration'
class schrodinger.application.desmond.constants.KineticsLegTypes(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.StrEnum

Leg types which represent steps in the Unbinding Kinetics workflow.

MD = 'md'
RAMD = 'ramd'
UNBIND = 'unbind'
class schrodinger.application.desmond.constants.Ensembles

Bases: schrodinger.application.desmond.constants.Constants

NVE = 'NVE'
NVT = 'NVT'
NPT = 'NPT'
MUVT = 'muVT'
NPgammaT = 'NPgT'
class schrodinger.application.desmond.constants.RestrainTypes

Bases: schrodinger.application.desmond.constants.Constants

POS = 'pos'
POS_FBHW = 'posfbhw'
STRETCH_FBHW = 'stretchfbhw'
ANGLE_FBHW = 'anglefbhw'
IMPROPER_FBHW = 'improperfbhw'
class schrodinger.application.desmond.constants.Schedule

Bases: schrodinger.application.desmond.constants.Constants

DEFAULT = 'default'
FLEXIBLE = 'flexible'
CHARGE = 'charge'
class schrodinger.application.desmond.constants.IdConversion

Bases: schrodinger.application.desmond.constants.Constants

COMPONENT_TO_COMBINED = 'component_to_combined'
ATOM_TOTAL = 'atom_total'
PSEUDO_END = 'pseudo_end'
PARENT2PSEUDO = 'parent_to_pseudo'
PSEUDO2PARENT = 'pseudo_to_parent'
TOPOLOGY = 'topology'
class schrodinger.application.desmond.constants.DefaultFEPSimulationTimes

Bases: schrodinger.application.desmond.constants.Constants

SIMULATION = 5000.0
EQUILIBRATION = 20.0
COMPLEX_EQUILIBRATION = 20.0
COMPLEX_EQUILIBRATION_MUVT = 240.0
class schrodinger.application.desmond.constants.CorrectionTerm

Bases: schrodinger.application.desmond.constants.Constants

PKA = 'pKa'
STATE_PENALTY = 'State Penalty'
UNKNOWN = 'Unknown'
BORESCH_RESTRAINT = 'Boresch Restraint'
FRAGMENT_SOLVATION = 'Fragment Solvation'
POPULATION = 'Population'
class schrodinger.application.desmond.constants.FEP_STATE_KEYS

Bases: schrodinger.application.desmond.constants.Constants

WT = 'wt'
MUT = 'mut'
class schrodinger.application.desmond.constants.ENERGY_GROUPS

Bases: schrodinger.application.desmond.constants.Constants

PRESSURE_TENSOR = 'pressure_tensor'
CORR_ENERGY = 'corr_energy'
SELF_ENERGY_ONLY = 'self_energy_only'
CROSS_ENERGY_ONLY = 'cross_energy_only'
GCMC_INFO = 'gcmc_info'
SIMULATION_BOX = 'simulation_box'
class schrodinger.application.desmond.constants.SystemType

Bases: schrodinger.application.desmond.constants.Constants

ALCHEMICAL = 1
BINDING = 2
OTHER = 0
class schrodinger.application.desmond.constants.PRODUCT

Bases: schrodinger.application.desmond.constants.Constants

FEP = 'fep'
CONSTANT_PH = 'constant_ph'
IFD_MD = 'ifd-md'
class schrodinger.application.desmond.constants.UiMode(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

NEW = 1
RESTART = 2
EXTEND = 3
class schrodinger.application.desmond.constants.BUILD_GEOMETRY

Bases: schrodinger.application.desmond.constants.Constants

NAME = 'build_geometry'
REMOVE_OVERLAPPED_SOLVENT = 'remove_overlapped_solvent'
class schrodinger.application.desmond.constants.SYSTEM_BUILDER_INP

Bases: schrodinger.application.desmond.constants.Constants

CHECK_SOLVENT_OVERLAP = 'check_solvent_overlap'
class schrodinger.application.desmond.constants.SkipFepReason(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

HIGH_RMSD = 'High ligand RMSD in binding site'
class schrodinger.application.desmond.constants.SidedError

Bases: object

Types of sided errors. It’s used in the context of the experimental dg to indicate whether the measured experimental dg is an upper bound, lower bound or within the range of the measurement procedure.

  • TOP: the measured experimental dg is a lower bound, and the actual value

    can be higher

  • BOTTOM: the measured experimental dg is an upper bound, and the actual

    value can be lower

  • CENTER: the experimental dg is within the range of the measurement

  • ALL: all sided errors.

TOP = 1

Error to +inf

CENTER = 0

no sided error

BOTTOM = -1

Error to -inf

ALL = (1, 0, -1)
class schrodinger.application.desmond.constants.DRUDE_INVERSE_FORCE_CONSTANT_SCALING

Bases: schrodinger.application.desmond.constants.Constants

FULLY_RESTRAINED = 0.0
NONE = 1.0