ProGAL.proteins
Class ProteinComplex

java.lang.Object
  ProGAL.geom3d.complex.alphaComplex.AlphaFiltration
      ProGAL.geom3d.complex.alphaComplex.AlphaComplex
          ProGAL.proteins.ProteinComplex

All Implemented Interfaces:

SimplicialComplex

public class ProteinComplex
extends AlphaComplex

Nested Class Summary

class	ProteinComplex.Cavity
class	ProteinComplex.Hole

Field Summary

PDBFile

pdbFile

Constructor Summary

ProteinComplex(PDBFile f)

ProteinComplex(PDBFile f, double waterRad)

Method Summary

PDBFile.AtomRecord	getAtom(Point p)
char	getAtomType(Point p)
java.util.List<ProteinComplex.Cavity>	getCavities()
java.util.List<CEdge>	getEdges()
java.util.List<ProteinComplex.Hole>	getHoles()
java.util.List<ProteinComplex.Hole>	getHoles(double probeRad)
java.util.List<CTetrahedron>	getTetrahedra()
java.util.List<CTriangle>	getTriangles()
CVertex	getVertex(Point p)
boolean	isBuried(CVertex v)
boolean	isBuried(PDBFile.AtomRecord ar)
static void	main(java.lang.String[] args)

Methods inherited from class ProGAL.geom3d.complex.alphaComplex.AlphaComplex

getAllCavities, getAllCavityPaths, getAllDeepestCavityTetrahedra, getAllEdges, getAllSimplices, getAlpha, getCavity, getCavityPath, getDeepestCavityTetrahedron, getDepth, getSimplices, getVoids, setAlpha

Methods inherited from class ProGAL.geom3d.complex.alphaComplex.AlphaFiltration

getAlphaShape, getAttached, getBettiNumbers, getBettiPersistence, getDim, getEdges, getInAlpha, getOnCH, getPairSimplices, getSimplices, getSurfaceTriangles, getTetrahedra, getTetrahedra, getTriangles, getVertexHull, getVertices

Methods inherited from class java.lang.Object

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

Methods inherited from interface ProGAL.geom3d.complex.SimplicialComplex

getVertices

Field Detail

pdbFile

public final PDBFile pdbFile

Constructor Detail

ProteinComplex

public ProteinComplex(PDBFile f)

ProteinComplex

public ProteinComplex(PDBFile f,
                      double waterRad)

Method Detail

getEdges

public java.util.List<CEdge> getEdges()

Specified by:

getEdges in interface SimplicialComplex

Overrides:

getEdges in class AlphaComplex

getTetrahedra

public java.util.List<CTetrahedron> getTetrahedra()

Specified by:

getTetrahedra in interface SimplicialComplex

Overrides:

getTetrahedra in class AlphaComplex

getTriangles

public java.util.List<CTriangle> getTriangles()

Specified by:

getTriangles in interface SimplicialComplex

Overrides:

getTriangles in class AlphaComplex

getVertex

public CVertex getVertex(Point p)

getAtom

public PDBFile.AtomRecord getAtom(Point p)

getAtomType

public char getAtomType(Point p)

isBuried

public boolean isBuried(CVertex v)

isBuried

public boolean isBuried(PDBFile.AtomRecord ar)

getHoles

public java.util.List<ProteinComplex.Hole> getHoles()

getHoles

public java.util.List<ProteinComplex.Hole> getHoles(double probeRad)

getCavities

public java.util.List<ProteinComplex.Cavity> getCavities()

main

public static void main(java.lang.String[] args)