java.lang.Object
- com.actelion.research.chem.descriptor.flexophore.PPNode
- - com.actelion.research.chem.descriptor.flexophore.PPNodeViz

All Implemented Interfaces:

IPPNode, java.io.Serializable, java.lang.Comparable<PPNode>
```
public class PPNodeViz
extends PPNode
implements java.io.Serializable
```
Pharmacophore node with information about corresponding atoms in the molecule used for construction.

See Also:

Serialized Form

Field Summary
- Fields inherited from class com.actelion.research.chem.descriptor.flexophore.PPNode
  DUMMY_INTERACT_ID, INFO_DEFAULT, MULT_FREQ, NUM_BYTES_INTERACTION_TYPE, SEPARATOR_ATOMS

Constructor Summary

Constructors
Constructor Description

PPNodeViz()

PPNodeViz(PPNode node)

PPNodeViz(PPNodeViz node)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addAtoms(PPNodeViz node)`	Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.
`void`	`addIndexOriginalAtom(int index)`
`void`	`clearInfo()`
`void`	`copy(PPNodeViz node)`	Copy of node into this
`Coordinates`	`getCoordinates()`
`PPNodeViz`	`getCopy()`	node deep copy.
`int`	`getIndex()`
`int`	`getIndexSphereVisualization()`
`java.util.List<java.lang.Integer>`	`getListIndexOriginalAtoms()`
`int`	`getMappingIndex()`
`float`	`getSimilarityMappingNodes()`
`double`	`getX()`
`double`	`getY()`
`double`	`getZ()`
`boolean`	`hasSamePosition(PPNodeViz node)`
`boolean`	`isMarked()`
`void`	`resetInfoColor()`
`void`	`setCoordinates(double x, double y, double z)`
`void`	`setCoordinates(Coordinates c)`
`void`	`setCoordinatesNull()`
`void`	`setIndex(int id)`
`protected void`	`setIndexSphereVisualization(int indexSphereViz)`
`void`	`setMappingIndex(int info)`
`void`	`setMarked(boolean marked)`
`void`	`setSimilarityMappingNodes(float similarityMappingNodes)`
`void`	`setX(double x)`
`void`	`setY(double y)`
`void`	`setZ(double z)`
`java.lang.String`	`toString()`
`java.lang.String`	`toStringShort()`

Methods inherited from class com.actelion.research.chem.descriptor.flexophore.PPNode
add, addAtoms, compareTo, containsInteractionID, copy, equalAtoms, equals, get, getAtomicNo, getAtomicNoFromInteractionType, getDummy, getFractionCarbonInteractions, getHeteroOnlyNode, getInteractionType, getInteractionTypeCount, getInteractionTypeFromByteArray, getModeFlexophore, getNumBytesEntry, hasHeteroAtom, isAromatic, isCarbonExclusiveNode, read, realize, set, setModeFlexophore, sortInteractionTypes, toStringLong, toStringLongHardPPPoint

Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

PPNodeViz
```
public PPNodeViz()
```

PPNodeViz
```
public PPNodeViz(PPNodeViz node)
```

PPNodeViz
```
public PPNodeViz(PPNode node)
```

Method Detail

getIndex
```
public int getIndex()
```

setIndex
```
public void setIndex(int id)
```

addAtoms
```
public void addAtoms(PPNodeViz node)
```
Only atoms are added that are not yet in the list, check PPAtom.equals for comparison.

Parameters:

node -

addIndexOriginalAtom

public void addIndexOriginalAtom(int index)

copy
```
public void copy(PPNodeViz node)
```
Copy of node into this

Parameters:

node -

isMarked
```
public boolean isMarked()
```
Returns:

the marked

setMarked
```
public void setMarked(boolean marked)
```
Parameters:

marked - the marked to set

getCopy
```
public PPNodeViz getCopy()
```
Description copied from class: PPNode

node deep copy.

Overrides:

getCopy in class PPNode

getListIndexOriginalAtoms

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

getMappingIndex
```
public int getMappingIndex()
```

setMappingIndex

public void setMappingIndex(int info)

clearInfo
```
public void clearInfo()
```

hasSamePosition

public boolean hasSamePosition(PPNodeViz node)

resetInfoColor
```
public void resetInfoColor()
```

getCoordinates
```
public Coordinates getCoordinates()
```

setCoordinates

public void setCoordinates(double x,
                           double y,
                           double z)

setCoordinates

public void setCoordinates(Coordinates c)

setCoordinatesNull
```
public void setCoordinatesNull()
```

getX
```
public double getX()
```

getY
```
public double getY()
```

getZ
```
public double getZ()
```

setX
```
public void setX(double x)
```

setY
```
public void setY(double y)
```

setZ
```
public void setZ(double z)
```

getIndexSphereVisualization

public int getIndexSphereVisualization()

setIndexSphereVisualization

protected void setIndexSphereVisualization(int indexSphereViz)

getSimilarityMappingNodes
```
public float getSimilarityMappingNodes()
```
Returns:

the similarityMappingNodes

setSimilarityMappingNodes
```
public void setSimilarityMappingNodes(float similarityMappingNodes)
```
Parameters:

similarityMappingNodes - the similarityMappingNodes to set

toString
```
public java.lang.String toString()
```
Overrides:

toString in class PPNode

toStringShort

public java.lang.String toStringShort()

Constructor	Description
`PPNodeViz()`
`PPNodeViz(PPNode node)`
`PPNodeViz(PPNodeViz node)`

Class PPNodeViz

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Detail

PPNodeViz

PPNodeViz

PPNodeViz

Method Detail

getIndex

setIndex

addAtoms

addIndexOriginalAtom

copy

isMarked

setMarked

getCopy

getListIndexOriginalAtoms

getMappingIndex

setMappingIndex

clearInfo

hasSamePosition

resetInfoColor

getCoordinates

setCoordinates

setCoordinates

setCoordinatesNull

getX

getY

getZ

setX

setY

setZ

getIndexSphereVisualization

setIndexSphereVisualization

getSimilarityMappingNodes

setSimilarityMappingNodes

toString

toStringShort