de.bioforscher.singa.structure.parser.plip

Class PlipShellGenerator

java.lang.Object

de.bioforscher.singa.structure.parser.plip.PlipShellGenerator

public class PlipShellGenerator
extends Object

Calculates the shell of residues in indirect contact with the ligand utilizing PLIP interaction data. According to:

 Brodkin, HR, DeLateur, NA, Somarowthu, S, Mills, CL, Novak, WR, Beuning, PJ, Ringe, D, Ondrechen, MJ (2015).
 Prediction of distal residue participation in enzyme catalysis.
 Protein Sci., 24, 5:762-78.
 

Author:

fk

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PlipShellGenerator.InteractionShell

Method Summary

Modifier and Type	Method and Description
GenericGraph<LeafSubstructure<?>>	getGraph()
static PlipShellGenerator	getInteractionShellsForLigand(Chain chain, LeafSubstructure<?> reference, InteractionContainer interChainInteractions, InteractionContainer referenceInteractions)
Map<PlipShellGenerator.InteractionShell,List<LeafSubstructure<?>>>	getShells()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getInteractionShellsForLigand

public static PlipShellGenerator getInteractionShellsForLigand(Chain chain,
                                                               LeafSubstructure<?> reference,
                                                               InteractionContainer interChainInteractions,
                                                               InteractionContainer referenceInteractions)

getShells

public Map<PlipShellGenerator.InteractionShell,List<LeafSubstructure<?>>> getShells()

getGraph

public GenericGraph<LeafSubstructure<?>> getGraph()