schrodinger.application.desmond.fep_schedule module

This module handles the allocation of lambda windows for FEP simulations.

Different schemes of FEP simulations and interactions require different schedules of lambda windows. The FepSchedule class abstracts the creation of these schedules. This class is meant to be instantiated via its derived classes (with mixins) or, preferably, using the get_fep_schedule function.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.fep_schedule.FepSchedule(n_win: int, charge_div: Optional[float] = None)

Bases: object

Lambda schedule for FEP calculations.

This class should not be instantiated directly. Instead, subclass it combining the mixins below.

n_winint

Number of lambda windows

charge_divfloat or None

Determines the fraction of lambda windows devoted to turning on electrostatic interactions. This should be overriden by a mix-in class or by the user.

bonded_divfloat or None

Determines the fraction of lambda windows devoted to turning on bonded interactions. This should be overriden by a mix-in class or by the user.

bonded_div: Optional[float] = None

__init__(n_win: int, charge_div: Optional[float] = None) → None

n_win: Optional[int] = None

charge_div: Optional[float] = None

get_lambda()

class schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical(n_win: int, charge_div: Optional[float] = None)

Bases: schrodinger.application.desmond.fep_schedule.FepSchedule

property vdw

property coulomb

property vdwA

property vdwB

property chargeA

property chargeB

property bondedA

property bondedB

__init__(n_win: int, charge_div: Optional[float] = None) → None

bonded_div: Optional[float] = None

charge_div: Optional[float] = None

get_lambda()

n_win: Optional[int] = None

class schrodinger.application.desmond.fep_schedule.FepScheduleBinding(n_win: int, charge_div: Optional[float] = None)

Bases: schrodinger.application.desmond.fep_schedule.FepSchedule

property vdw

property coulomb

property vdwA

property vdwB

property chargeA

property chargeB

property bondedA

property bondedB

__init__(n_win: int, charge_div: Optional[float] = None) → None

bonded_div: Optional[float] = None

charge_div: Optional[float] = None

get_lambda()

n_win: Optional[int] = None

class schrodinger.application.desmond.fep_schedule.FepSchemeMixIn

Bases: object

Configure schedule of FEP schedule.

charge_div = 2.5

bonded_div = inf

class schrodinger.application.desmond.fep_schedule.FepSchemeChargeMixIn

Bases: schrodinger.application.desmond.fep_schedule.FepSchemeMixIn

charge_div = 1.5

bonded_div = inf

class schrodinger.application.desmond.fep_schedule.FepSchemeQuickchargeMixIn

Bases: schrodinger.application.desmond.fep_schedule.FepSchemeMixIn

charge_div = 5.0

bonded_div = inf

class schrodinger.application.desmond.fep_schedule.FepSchemeSuperquickchargeMixIn

Bases: schrodinger.application.desmond.fep_schedule.FepSchemeMixIn

charge_div = 10.0

bonded_div = 10.0

schrodinger.application.desmond.fep_schedule.get_fep_schedule_class(fep_type: str = 'alchemical', scheme: str = 'default') → Type[schrodinger.application.desmond.fep_schedule.FepSchedule]

Return FEP schedule class.

get_fep_schedule

schrodinger.application.desmond.fep_schedule.get_fep_schedule(n_win: int, fep_type: str = 'alchemical', scheme: str = 'default') → schrodinger.application.desmond.fep_schedule.FepSchedule

Instantiate FEP schedule.

Return a class encapsulating a concrete lambda schedule for the specified FEP simulation type and scheme.

Parameters

• n_win (int) – Number of lambda windows.

• fep_type (str) – Type of FEP simulation. Can be either ‘alchemical’ (default) or ‘binding’.

• scheme (str) – Simulation scheme. Can be one of ‘default’, ‘flexible’, ‘charge’, ‘quickcharge’, or ‘superquickcharge’.

Returns

Concrete schedule of the specified type, scheme, and number of windows.

Return type

FepSchedule

class schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalDefault(n_win: int, charge_div: Optional[float] = None)

Bases: schrodinger.application.desmond.fep_schedule.FepSchemeMixIn, schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical

Convenience class for the alchemical schedule with the default scheme.

__init__(n_win: int, charge_div: Optional[float] = None) → None

property bondedA

property bondedB

bonded_div: Optional[float] = inf

property chargeA

property chargeB

charge_div: Optional[float] = 2.5

property coulomb

get_lambda()

n_win: Optional[int] = None

property vdw

property vdwA

property vdwB

class schrodinger.application.desmond.fep_schedule.FepScheduleAlchemicalCharge(n_win: int, charge_div: Optional[float] = None)

Bases: schrodinger.application.desmond.fep_schedule.FepSchemeChargeMixIn, schrodinger.application.desmond.fep_schedule.FepScheduleAlchemical

Convenience class for the alchemical schedule with the charge scheme.

__init__(n_win: int, charge_div: Optional[float] = None) → None

property bondedA

property bondedB

bonded_div: Optional[float] = inf

property chargeA

property chargeB

charge_div: Optional[float] = 1.5

property coulomb

get_lambda()

n_win: Optional[int] = None

property vdw

property vdwA

property vdwB

class schrodinger.application.desmond.fep_schedule.FepScheduleBindingDefault(n_win: int, charge_div: Optional[float] = None)

Bases: schrodinger.application.desmond.fep_schedule.FepSchemeMixIn, schrodinger.application.desmond.fep_schedule.FepScheduleBinding

Convenience class for the binding schedule with the default scheme.

__init__(n_win: int, charge_div: Optional[float] = None) → None

property bondedA

property bondedB

bonded_div: Optional[float] = inf

property chargeA

property chargeB

charge_div: Optional[float] = 2.5

property coulomb

get_lambda()

n_win: Optional[int] = None

property vdw

property vdwA

property vdwB

schrodinger.application.desmond.fep_schedule.get_absolute_binding_num_lambda_windows(protocol: schrodinger.application.desmond.constants.SIMULATION_PROTOCOL, restrained: bool) → Tuple[int, int]

Get the number of lambda windows in the absolute binding lambda schedules. These are derived from the lambda schedules in mmshare/data/desmond/abfep

Returns

A tuple of # of complex windows, # of solvent windows