Package com.actelion.research.chem.descriptor.flexophore

Class MolDistHistViz

java.lang.Object

com.actelion.research.chem.descriptor.flexophore.DistHist

com.actelion.research.chem.descriptor.flexophore.MolDistHistViz

All Implemented Interfaces:

IMolDistHist, ICompleteGraph, java.io.Serializable

Direct Known Subclasses:

MolDistHistVizFrag

public class MolDistHistViz
extends DistHist
implements java.io.Serializable, IMolDistHist, ICompleteGraph

Class for Flexophore visualization and atom tracking. Information about corresponding atoms is stored in PPNodeViz.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static int	CAPACITY_INEVITABLE_PPPOINTS
static java.lang.String[]	COLORS	Colors for visualization of the Flexophore mapping.
static int	DESCRIBE_ALL
static int	DESCRIBE_MAPPED	Only mapped atoms are described.
protected Molecule3D	molecule3D
static java.lang.String	TAG_VIZ_INFO_ENCODED

Fields inherited from class com.actelion.research.chem.descriptor.flexophore.DistHist

arrDistHists

Constructor Summary

Constructors

Constructor	Description
MolDistHistViz()
MolDistHistViz(int nNodes)
MolDistHistViz(int nNodes, Molecule3D molecule3D)
MolDistHistViz(MolDistHist mdh)
MolDistHistViz(MolDistHistViz mdhv)

Method Summary

Modifier and Type	Method	Description
void	addInevitablePharmacophorePoint(int indexPPNode)
int	addNode(PPNodeViz node)
void	blurrSingleBinHistograms()
void	calculate()
void	canonize()
boolean	check()
MolDistHistViz	copy()
void	copy(MolDistHistViz copy)
static void	createIndexTables()
void	createNodeIndex()	This index is used to track the fate of the nodes MvK 17.07.2007
boolean	equals(java.lang.Object o)
protected static Molecule3D	finalizeMolecule(Molecule3D mol)	Remove all atoms without connections.
protected static java.lang.String	formatDescription(java.lang.String s)
int	getBondAtom(int index, int bond)
int	getConnAtom(int at, int index)
int	getConnBond(int at, int index)
java.util.List<float[][]>	getDistanceTables()
protected java.util.HashSet<java.lang.Integer>	getHashSetIndexInevitablePPPoints()
int	getIndexFromCoord(double x, double y, double z)
java.util.List<java.lang.Integer>	getInevitablePharmacophorePoints()
int	getInfo(int index)
double	getMaximumDistanceInPPPoint(int indexNode)
MolDistHist	getMolDistHist()
Molecule3D	getMolecule()	The atoms of the ff molecule contain the corresponding PPNode indices in the first field of the PPP vector.
Molecule3D	getMoleculeRemovedUnrelatedAtoms()
java.lang.String	getName()
PPNodeViz	getNode(int i)
java.util.List<PPNodeViz>	getNodes()
int	getNumCExclusiveNodes()
int	getNumHeteroNodes()
int	getNumInevitablePharmacophorePoints()
int	hashCode()
protected void	initHistogramArray(int size)
boolean	isAcceptor(int indexNode)
boolean	isAliphatic(int indexNode)
boolean	isAromatic(int indexNode)
boolean	isChargeNeg(int indexNode)
boolean	isChargePos(int indexNode)
boolean	isDonor(int indexNode)
boolean	isInevitablePharmacophorePoint(int indexNode)
boolean	isMarked(int index)
boolean	isOnlyCarbon(int index)
static void	merge(MolDistHistViz mdhviz, MolDistHist mdh)	Deprecated.
void	realize()
void	recalculateCoordPPPoints()	Recalculates the coordinates off the pharmacophore nodes.
void	removeInevitablePharmacophorePoint(int indexPPNode)
void	resetInevitablePharmacophorePoints()
void	resetInfoColor()
void	set(Molecule3D ff)
void	set(java.util.List<PPNodeViz> liPPNodeViz)
void	setDistanceTables(java.util.List<double[][]> liDistanceTable)	The distance tables which were generated from the conformations.
void	setMappingIndex(int index, int info)
void	setMark(int index, boolean mark)
void	setMarkAll(boolean mark)
void	setModeFlexophore(byte modeFlexophore)
void	setName(java.lang.String name)
void	setSimilarityMappingNodes(int index, float similarityMappingNodes)
static MolDistHistViz	summarizeAlkaneCluster(MolDistHistViz mdh, int maxDistance)	Summarizes alkane cluster.
void	swapNodes(int n1, int n2)
java.lang.String	toString()
java.lang.String	toStringInevitable()
java.lang.String	toStringShort()

Methods inherited from class com.actelion.research.chem.descriptor.flexophore.DistHist

copy, getBonds, getClusterCenter, getDistHist, getDistHist, getDistHists, getIdentifier, getIndex, getIndexPosStartForDistHist, getMaxDistInHist, getMinDist, getNumPPNodes, getRelMaxDistInHist, getRelMaxDistInHist, getSizeBytes, getValueAtAbsolutePosition, setDistHist, setDistHists, setIdentifier, toStringHistsIndexed

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface com.actelion.research.util.graph.complete.ICompleteGraph

getNumPPNodes

Methods inherited from interface com.actelion.research.chem.descriptor.flexophore.IMolDistHist

getDistHist, getRelMaxDistInHist

Field Detail

DESCRIBE_ALL

public static final int DESCRIBE_ALL

See Also:

Constant Field Values

DESCRIBE_MAPPED

public static final int DESCRIBE_MAPPED

Only mapped atoms are described.

See Also:

Constant Field Values

CAPACITY_INEVITABLE_PPPOINTS

public static final int CAPACITY_INEVITABLE_PPPOINTS

See Also:

Constant Field Values

TAG_VIZ_INFO_ENCODED

public static final java.lang.String TAG_VIZ_INFO_ENCODED

See Also:

Constant Field Values

COLORS

public static final transient java.lang.String[] COLORS

Colors for visualization of the Flexophore mapping.

molecule3D

protected Molecule3D molecule3D

Constructor Detail

MolDistHistViz

public MolDistHistViz()

MolDistHistViz

public MolDistHistViz(int nNodes)

MolDistHistViz

public MolDistHistViz(int nNodes,
                      Molecule3D molecule3D)

MolDistHistViz

public MolDistHistViz(MolDistHistViz mdhv)

MolDistHistViz

public MolDistHistViz(MolDistHist mdh)

Method Detail

createIndexTables

public static void createIndexTables()

addInevitablePharmacophorePoint

public void addInevitablePharmacophorePoint(int indexPPNode)

removeInevitablePharmacophorePoint

public void removeInevitablePharmacophorePoint(int indexPPNode)

setModeFlexophore

public void setModeFlexophore(byte modeFlexophore)

setMarkAll

public void setMarkAll(boolean mark)

setMark

public void setMark(int index,
                    boolean mark)

isMarked

public boolean isMarked(int index)

addNode

public int addNode(PPNodeViz node)

Parameters:

node -

Returns:

index of the node.

check

public boolean check()

initHistogramArray

protected void initHistogramArray(int size)

Overrides:

initHistogramArray in class DistHist

copy

public MolDistHistViz copy()

copy

public void copy(MolDistHistViz copy)

Parameters:

copy - This is written into copy.

recalculateCoordPPPoints

public void recalculateCoordPPPoints()

Recalculates the coordinates off the pharmacophore nodes. Has to be called after changing the coordinates for the Molecule3D.

resetInevitablePharmacophorePoints

public void resetInevitablePharmacophorePoints()

resetInfoColor

public void resetInfoColor()

createNodeIndex

public void createNodeIndex()

This index is used to track the fate of the nodes MvK 17.07.2007

getBondAtom

public int getBondAtom(int index,
                       int bond)

Parameters:

index - 0 or 1

bond - index of the bond array

Returns:

the atom index

getConnAtom

public int getConnAtom(int at,
                       int index)

getConnBond

public int getConnBond(int at,
                       int index)

getIndexFromCoord

public int getIndexFromCoord(double x,
                             double y,
                             double z)

getInfo

public int getInfo(int index)

getNode

public PPNodeViz getNode(int i)

Specified by:

getNode in interface IMolDistHist

getNodes

public java.util.List<PPNodeViz> getNodes()

Returns:

shallow copy.

set

public void set(java.util.List<PPNodeViz> liPPNodeViz)

set

public void set(Molecule3D ff)

Parameters:

ff - has to be the molecule the descriptor was derived from.

setMappingIndex

public void setMappingIndex(int index,
                            int info)

setSimilarityMappingNodes

public void setSimilarityMappingNodes(int index,
                                      float similarityMappingNodes)

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)

isOnlyCarbon

public boolean isOnlyCarbon(int index)

canonize

public void canonize()

swapNodes

public void swapNodes(int n1,
                      int n2)

getNumCExclusiveNodes

public int getNumCExclusiveNodes()

getNumHeteroNodes

public int getNumHeteroNodes()

getInevitablePharmacophorePoints

public java.util.List<java.lang.Integer> getInevitablePharmacophorePoints()

getHashSetIndexInevitablePPPoints

protected java.util.HashSet<java.lang.Integer> getHashSetIndexInevitablePPPoints()

getNumInevitablePharmacophorePoints

public int getNumInevitablePharmacophorePoints()

Specified by:

getNumInevitablePharmacophorePoints in interface IMolDistHist

isInevitablePharmacophorePoint

public boolean isInevitablePharmacophorePoint(int indexNode)

Specified by:

isInevitablePharmacophorePoint in interface IMolDistHist

isAliphatic

public boolean isAliphatic(int indexNode)

isAcceptor

public boolean isAcceptor(int indexNode)

isDonor

public boolean isDonor(int indexNode)

isAromatic

public boolean isAromatic(int indexNode)

isChargePos

public boolean isChargePos(int indexNode)

isChargeNeg

public boolean isChargeNeg(int indexNode)

realize

public void realize()

blurrSingleBinHistograms

public void blurrSingleBinHistograms()

calculate

public void calculate()

finalizeMolecule

protected static Molecule3D finalizeMolecule(Molecule3D mol)

Remove all atoms without connections.

Parameters:

mol -

Returns:

getMolDistHist

public MolDistHist getMolDistHist()

Returns:

deep object.

getMaximumDistanceInPPPoint

public double getMaximumDistanceInPPPoint(int indexNode)

getMolecule

public Molecule3D getMolecule()

The atoms of the ff molecule contain the corresponding PPNode indices in the first field of the PPP vector.

Returns:

getMoleculeRemovedUnrelatedAtoms

public Molecule3D getMoleculeRemovedUnrelatedAtoms()

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toStringInevitable

public java.lang.String toStringInevitable()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toStringShort

public java.lang.String toStringShort()

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

setDistanceTables

public void setDistanceTables(java.util.List<double[][]> liDistanceTable)

The distance tables which were generated from the conformations.

Parameters:

liDistanceTable -

getDistanceTables

public java.util.List<float[][]> getDistanceTables()

formatDescription

protected static java.lang.String formatDescription(java.lang.String s)

merge

public static void merge(MolDistHistViz mdhviz,
                         MolDistHist mdh)

Deprecated.

Merges the histograms from mdh into mdhviz.

Parameters:

mdhviz - has new histograms afterwards.

mdh - stays unchanged.

summarizeAlkaneCluster

public static MolDistHistViz summarizeAlkaneCluster(MolDistHistViz mdh,
                                                    int maxDistance)

Summarizes alkane cluster. The central node may not be a alkane cluster. The interaction types of the cluster members are added to the interaction types of the center node.

Parameters:

mdh -

maxDistance -

Returns: