schrodinger.application.desmond.constants module¶

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

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¶