Package edu.duke.cs.osprey.structure

Class AtomNeighbors

java.lang.Object

edu.duke.cs.osprey.structure.AtomNeighbors

Direct Known Subclasses:

ProbeAtomNeighbors

public class AtomNeighbors
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	AtomNeighbors.Type

Constructor Summary

Constructors

Constructor	Description
AtomNeighbors(Atom mainAtom)

Method Summary

Modifier and Type	Method	Description
AtomNeighbors.Type	classifyAtom(Atom atom)
static List<int[]>	getPairIndicesByType(List<Atom> atoms1, List<Atom> atoms2, boolean internalE, AtomNeighbors.Type type)
static List<Atom[]>	getPairs14(List<Atom[]> atomPairs)
static List<Atom[]>	getPairs14(List<Atom> atoms1, List<Atom> atoms2, boolean internalE)
static List<Atom[]>	getPairsByType(List<Atom[]> atomPairs, AtomNeighbors.Type type)
static List<Atom[]>	getPairsByType(List<Atom> atoms1, List<Atom> atoms2, boolean internalE, AtomNeighbors.Type type)
static List<Atom[]>	getPairsNonBonded(List<Atom[]> atomPairs)
static List<Atom[]>	getPairsNonBonded(List<Atom> atoms1, List<Atom> atoms2, boolean internalE)

Methods inherited from class java.lang.Object

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

Constructor Details

AtomNeighbors

public AtomNeighbors(Atom mainAtom)

Method Details

classifyAtom

public AtomNeighbors.Type classifyAtom(Atom atom)

getPairs14

public static List<Atom[]> getPairs14(List<Atom> atoms1,
 List<Atom> atoms2,
 boolean internalE)

getPairsNonBonded

public static List<Atom[]> getPairsNonBonded(List<Atom> atoms1,
 List<Atom> atoms2,
 boolean internalE)

getPairsByType

public static List<Atom[]> getPairsByType(List<Atom> atoms1,
 List<Atom> atoms2,
 boolean internalE,
 AtomNeighbors.Type type)

getPairIndicesByType

public static List<int[]> getPairIndicesByType(List<Atom> atoms1,
 List<Atom> atoms2,
 boolean internalE,
 AtomNeighbors.Type type)

getPairsByType

public static List<Atom[]> getPairsByType(List<Atom[]> atomPairs,
 AtomNeighbors.Type type)

getPairs14

public static List<Atom[]> getPairs14(List<Atom[]> atomPairs)

getPairsNonBonded

public static List<Atom[]> getPairsNonBonded(List<Atom[]> atomPairs)