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.
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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_win : int
- Number of lambda windows
- charge_div : float 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_div : float 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.
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bonded_div
= None¶
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__init__
(n_win: int, charge_div: Optional[float] = None) → None¶ Initialize self. See help(type(self)) for accurate signature.
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n_win
= None¶
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charge_div
= None¶
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get_lambda
()¶
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class
schrodinger.application.desmond.fep_schedule.
FepScheduleAlchemical
(n_win: int, charge_div: Optional[float] = None)¶ Bases:
schrodinger.application.desmond.fep_schedule.FepSchedule
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vdw
¶
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coulomb
¶
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vdwA
¶
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vdwB
¶
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chargeA
¶
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chargeB
¶
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bondedA
¶
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bondedB
¶
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__init__
(n_win: int, charge_div: Optional[float] = None) → None¶ Initialize self. See help(type(self)) for accurate signature.
-
bonded_div
= None¶
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charge_div
= None¶
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get_lambda
()¶
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n_win
= None¶
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class
schrodinger.application.desmond.fep_schedule.
FepScheduleBinding
(n_win: int, charge_div: Optional[float] = None)¶ Bases:
schrodinger.application.desmond.fep_schedule.FepSchedule
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vdw
¶
-
coulomb
¶
-
vdwA
¶
-
vdwB
¶
-
chargeA
¶
-
chargeB
¶
-
bondedA
¶
-
bondedB
¶
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__init__
(n_win: int, charge_div: Optional[float] = None) → None¶ Initialize self. See help(type(self)) for accurate signature.
-
bonded_div
= None¶
-
charge_div
= None¶
-
get_lambda
()¶
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n_win
= None¶
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class
schrodinger.application.desmond.fep_schedule.
FepSchemeMixIn
¶ Bases:
object
Configure schedule of FEP schedule.
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charge_div
= 2.5¶
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bonded_div
= inf¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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class
schrodinger.application.desmond.fep_schedule.
FepSchemeChargeMixIn
¶ Bases:
schrodinger.application.desmond.fep_schedule.FepSchemeMixIn
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charge_div
= 1.5¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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bonded_div
= inf¶
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class
schrodinger.application.desmond.fep_schedule.
FepSchemeQuickchargeMixIn
¶ Bases:
schrodinger.application.desmond.fep_schedule.FepSchemeMixIn
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charge_div
= 5.0¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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bonded_div
= inf¶
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class
schrodinger.application.desmond.fep_schedule.
FepSchemeSuperquickchargeMixIn
¶ Bases:
schrodinger.application.desmond.fep_schedule.FepSchemeMixIn
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charge_div
= 10.0¶
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bonded_div
= 10.0¶
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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 – Type of FEP simulation. Can be either ‘alchemical’
(default) or ‘binding’. :type fep_type: str :param scheme: Simulation scheme. Can be one of ‘default’, ‘flexible’, ‘charge’, ‘quickcharge’, or ‘superquickcharge’. :type scheme: str
Returns: Concrete schedule of the specified type, scheme, and number of windows. :rtype: FepSchedule
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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.
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__init__
(n_win: int, charge_div: Optional[float] = None) → None¶ Initialize self. See help(type(self)) for accurate signature.
-
bondedA
¶
-
bondedB
¶
-
bonded_div
= inf¶
-
chargeA
¶
-
chargeB
¶
-
charge_div
= 2.5¶
-
coulomb
¶
-
get_lambda
()¶
-
n_win
= None¶
-
vdw
¶
-
vdwA
¶
-
vdwB
¶
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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.
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__init__
(n_win: int, charge_div: Optional[float] = None) → None¶ Initialize self. See help(type(self)) for accurate signature.
-
bondedA
¶
-
bondedB
¶
-
bonded_div
= inf¶
-
chargeA
¶
-
chargeB
¶
-
charge_div
= 1.5¶
-
coulomb
¶
-
get_lambda
()¶
-
n_win
= None¶
-
vdw
¶
-
vdwA
¶
-
vdwB
¶
-
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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.
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__init__
(n_win: int, charge_div: Optional[float] = None) → None¶ Initialize self. See help(type(self)) for accurate signature.
-
bondedA
¶
-
bondedB
¶
-
bonded_div
= inf¶
-
chargeA
¶
-
chargeB
¶
-
charge_div
= 2.5¶
-
coulomb
¶
-
get_lambda
()¶
-
n_win
= None¶
-
vdw
¶
-
vdwA
¶
-
vdwB
¶
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