schrodinger.application.prime.residue_interaction module

A Python interface to Prime residue interaction data

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.prime.residue_interaction.InteractionReader(struc)

Bases: object

Read the Prime residue interaction data from a structure

Variables:

• _available_res (set) – A set of residue names for which Prime interaction data has been read
• _energy (dict) – A dictionary of the interaction energy, stored as [energy type][res1][res2]. Note that this dictionary is not symmetric: [energy type][res1][res2] is stored but [energy type][res2][res1] is not. In _buildEnergyDict and getEnergy, res1 is arbitrarily assigned to be less than res2.

BLOCK_NAME = 'm_psp_residue_interaction_energies'

__init__(struc)

Read the Prime residue interaction data

Parameters:struc (schrodinger.structure.Structure) – The structure to read interaction data from Raises:ValueError – If the structure does not have any Prime residue interaction data

classmethod hasData(struc)

Check if the specified structure contains interaction data

Parameters:struc (schrodinger.structure.Structure) – The structure to check Returns:True if the structure has interaction data. False otherwise. Return type:bool

getEnergy(energy_type, res1, res2)

Get the interaction energy between the specified residues

Parameters:

• energy_type (str) – The name of the energy to retrieve, such as “r_psp_Prime_Energy” or “r_psp_Prime_Covalent”
• res1 (schrodinger.structure._Residue or str) – The first residue or residue key (i.e. the string value returned by resKey)
• res2 (schrodinger.structure._Residue or str) – The second residue or residue key (i.e. the string value returned by resKey)

Returns:

The interaction energy between the specified residues

Return type:

float

Raises:

ValueError – If no data is found for the given energy type or residues

static resKey(res)

Get the Prime-formatted residue name for the specified residue

Parameters:res (schrodinger.structure._Residue) – The residue to get the name for Returns:The formatted name Return type:str

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.prime.residue_interaction', '__doc__': '\n Read the Prime residue interaction data from a structure\n\n :ivar _available_res: A set of residue names for which Prime interaction\n data has been read\n :vartype _available_res: set\n\n :ivar _energy: A dictionary of the interaction energy, stored as\n [energy type][res1][res2]. Note that this dictionary is not symmetric:\n [energy type][res1][res2] is stored but [energy type][res2][res1] is not.\n In `_buildEnergyDict` and `getEnergy`, res1 is arbitrarily assigned to be\n less than res2.\n :vartype _energy: dict\n ', 'BLOCK_NAME': 'm_psp_residue_interaction_energies', '__init__': <function InteractionReader.__init__>, 'hasData': <classmethod object>, '_readEnergyMetaData': <function InteractionReader._readEnergyMetaData>, '_openDataHandle': <classmethod object>, '_readEnergyData': <function InteractionReader._readEnergyData>, 'getEnergy': <function InteractionReader.getEnergy>, '_getResKey': <function InteractionReader._getResKey>, 'resKey': <staticmethod object>, '__dict__': <attribute '__dict__' of 'InteractionReader' objects>, '__weakref__': <attribute '__weakref__' of 'InteractionReader' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.prime.residue_interaction'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)