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2017-1 Schrodinger Python API
Package schrodinger :: Package application :: Package bioluminate :: Module interaction_calculator :: Class Interactions
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Class Interactions

object --+
         |
        Interactions

Store data about all the interactions made by a single residue

Instance Methods [hide private]
 
__init__(self)
Initialize an instance of this class with 0 interactions
 
_createInteractionsDict(self)
Create self._interactions that contains all of the specific interaction counters
 
__repr__(self)
Generate a string that can be used to reproduce this object
 
__eq__(self, other)
Test two Interactions objects for equality.
 
__ne__(self, other)
Test two Interactions objects for inequality.
int
numHbonds(self)
Return the number of hydrogen bonds
int
numPiStacks(self)
Return the number of pi stacks
int
numSaltBridges(self)
Return the number of salt bridges
int
numDisulfides(self)
Return the number of disulfide bonds
int
numClashs(self)
Return the number of steric clashes
int
numSpecificInteractions(self)
Return the total number of specific interactions (i.e.
set
allInteractingResidues(self)
Return a list of all residues that this one interacts with (not counting nearby residues)
str
interactionSummary(self)
Create the interaction summary to display in the specific interactions column.
tuple
nearbyRes(self)
Return the nearby residues

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Methods [hide private]
Interactions
init(cls, **kwargs)
Initialize a class instance from existing interaction dictionaries.
Class Variables [hide private]
  H_BOND = 'hb'
  PI_STACK = 'pi stack'
  SALT_BRIDGE = 'salt bridge'
  CLASH = 'clash'
  DISULFIDE = 's-s'
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

 

Initialize an instance of this class with 0 interactions

Overrides: object.__init__

init(cls, **kwargs)
Class Method

 

Initialize a class instance from existing interaction dictionaries. This function allows for the output of __repr__() to be evaluated and is intended for use in testing.

Returns: Interactions
The initialized instance

__repr__(self)
(Representation operator)

 

Generate a string that can be used to reproduce this object

Overrides: object.__repr__

__eq__(self, other)
(Equality operator)

 

Test two Interactions objects for equality. Note that nearby residue distances are compared for approximate equality since they're floats.

numHbonds(self)

 

Return the number of hydrogen bonds

Returns: int
The number of hydrogen bonds

numPiStacks(self)

 

Return the number of pi stacks

Returns: int
The number of pi stacks

numSaltBridges(self)

 

Return the number of salt bridges

Returns: int
The number of salt bridges

numDisulfides(self)

 

Return the number of disulfide bonds

Returns: int
The number of disulfide bonds

numClashs(self)

 

Return the number of steric clashes

Returns: int
The number of steric clashes

numSpecificInteractions(self)

 

Return the total number of specific interactions (i.e. ignoring non- specific interactions such as buried SASA)

Returns: int
The total number of specific interactions

allInteractingResidues(self)

 

Return a list of all residues that this one interacts with (not counting nearby residues)

Returns: set
A set of ResTuple objects

interactionSummary(self)

 

Create the interaction summary to display in the specific interactions column.

Returns: str
The interaction summary

nearbyRes(self)

 

Return the nearby residues

Returns: tuple
A tuple of
  • The nearby residues (as strings), sorted by distance
  • The sorted residue distances (floats)

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2017-1 Schrodinger Python API
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