denoptim.graph.rings.RingClosingConformations Class Reference

Serializable object to store/get a list of conformations that allow to close a ring from an open chain of atoms. More...

Inheritance diagram for denoptim.graph.rings.RingClosingConformations:

Collaboration diagram for denoptim.graph.rings.RingClosingConformations:

Public Member Functions
	RingClosingConformations ()
	Constructs an empty RingClosure. More...
	RingClosingConformations (String chainID, ArrayList< ArrayList< Double > > lstConfs)
	Constructs a RingClosure from data. More...
String	getChainID ()
int	getNumberOfConformations ()
ArrayList< ArrayList< Double > >	getListOfConformations ()
String	toString ()

Private Attributes
String	chainID
	The identifier of the chain. More...
ArrayList< ArrayList< Double > >	lstConfs
	List of conformations (each as list of dihedrals) More...

Static Private Attributes
static final long	serialVersionUID = 1L
	Version ID. More...

Detailed Description

Serializable object to store/get a list of conformations that allow to close a ring from an open chain of atoms.

Fragment ID and Attachment point ID are used to identify the chain. Each closable conformation is recorded as the ordered vector of dihedral angles calculated from the reference points is the chain. Note that the angles do NOT necessarily refer to the torsion in the chain, in fact they constitute a standardized representation of the conformation of a bond and can be used to compare different chains that involve the same bond. For instance, interdependent non-same chains of atoms. The definition of the standard reference points for the calculation of the dihedral angles is performed in the parent object representing the chain. See here.

Author

Marco Foscato

Definition at line 41 of file RingClosingConformations.java.

Constructor & Destructor Documentation

RingClosingConformations() [1/2]

denoptim.graph.rings.RingClosingConformations.RingClosingConformations

(

)

Constructs an empty RingClosure.

Definition at line 64 of file RingClosingConformations.java.

RingClosingConformations() [2/2]

denoptim.graph.rings.RingClosingConformations.RingClosingConformations	(	String	chainID,
		ArrayList< ArrayList< Double > >	lstConfs
	)

Constructs a RingClosure from data.

Parameters

chainID	the computer-generated string identifier of the chain
lstConfs	the list of closable conformations

Definition at line 78 of file RingClosingConformations.java.

References denoptim.graph.rings.RingClosingConformations.chainID, and denoptim.graph.rings.RingClosingConformations.lstConfs.

Member Function Documentation

getChainID()

String denoptim.graph.rings.RingClosingConformations.getChainID

(

)

Definition at line 87 of file RingClosingConformations.java.

References denoptim.graph.rings.RingClosingConformations.chainID.

getListOfConformations()

ArrayList< ArrayList< Double > > denoptim.graph.rings.RingClosingConformations.getListOfConformations

(

)

Definition at line 101 of file RingClosingConformations.java.

References denoptim.graph.rings.RingClosingConformations.lstConfs.

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkClosabilityOfInterdependentPaths().

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getNumberOfConformations()

int denoptim.graph.rings.RingClosingConformations.getNumberOfConformations

(

)

Definition at line 94 of file RingClosingConformations.java.

References denoptim.graph.rings.RingClosingConformations.lstConfs.

toString()

String denoptim.graph.rings.RingClosingConformations.toString

(

)

Definition at line 109 of file RingClosingConformations.java.

References denoptim.graph.rings.RingClosingConformations.chainID, and denoptim.graph.rings.RingClosingConformations.lstConfs.

Member Data Documentation

chainID

String denoptim.graph.rings.RingClosingConformations.chainID

private

The identifier of the chain.

Definition at line 51 of file RingClosingConformations.java.

Referenced by denoptim.graph.rings.RingClosingConformations.getChainID(), denoptim.graph.rings.RingClosingConformations.RingClosingConformations(), and denoptim.graph.rings.RingClosingConformations.toString().

lstConfs

ArrayList<ArrayList<Double> > denoptim.graph.rings.RingClosingConformations.lstConfs

private

List of conformations (each as list of dihedrals)

Definition at line 56 of file RingClosingConformations.java.

Referenced by denoptim.graph.rings.RingClosingConformations.getListOfConformations(), denoptim.graph.rings.RingClosingConformations.getNumberOfConformations(), denoptim.graph.rings.RingClosingConformations.RingClosingConformations(), and denoptim.graph.rings.RingClosingConformations.toString().

serialVersionUID

final long denoptim.graph.rings.RingClosingConformations.serialVersionUID = 1L

staticprivate

Version ID.

Definition at line 46 of file RingClosingConformations.java.

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The documentation for this class was generated from the following file:

• /github/workspace/src/main/java/denoptim/graph/rings/RingClosingConformations.java