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JavaGenes, NASA Ames. Written largely by Al Globus | |||||||||
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java.lang.Objectgov.nasa.alsUtility.Mark
gov.nasa.javaGenes.graph.GraphElement
gov.nasa.javaGenes.graph.Vertex
gov.nasa.javaGenes.chemistry.Atom
Represent a chemical atom.
Nested Class Summary | |
protected static class |
Atom.ExtendedTypeKey
Represents the extended type of this atom for use as a hashtable key. |
Field Summary | |
protected Element |
element
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Fields inherited from class gov.nasa.javaGenes.graph.Vertex |
edges, extendedTypeCache, number, xyz |
Constructor Summary | |
Atom(Atom atom)
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Atom(Element e)
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Atom(int number)
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Atom(java.lang.String symbol)
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Method Summary | |
int |
bondValenceSum()
What portion of the valence is used by existing bonds? |
boolean |
canAcceptEdge()
Will adding another bond exceed valence? |
boolean |
canAcceptEdge(Edge e)
Will attaching to this bond exceed valence? |
boolean |
canAcceptEdgesOf(Vertex v)
can all of the edges of v be connected to this? |
int |
getAtomicNumber()
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Bond |
getBond(int i)
Return the i'th bond |
java.lang.Object |
getExtendedTypeObject()
returns a ExtendedTypeKey (a internal class) to represent the extended type of this atom, usually as a hashtable key. |
java.lang.String |
getExtendedTypeString()
Create a string to represent the extended type of this atom. |
int |
getValence()
Return the valence of this element |
boolean |
isElement(java.lang.String symbol)
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boolean |
isIn(Atom[] array)
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boolean |
isSame(Vertex v)
is v exactly this? |
int |
remainingValence()
return the amount of valence unused by existing bonds |
java.lang.String |
toString()
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void |
translateWithNeighbors(Vector3d translation,
Atom[] keepStationary)
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Methods inherited from class gov.nasa.javaGenes.graph.Vertex |
add, clone, getAngleBetween, getDistanceTo, getEdge, getEdgeIterator, getLocationVector, getNumber, getTypeString, getXyz, hasEdgeTo, moveInsideInterval, removeEdge, scaleBy, setNumber, setXyz, setXyz, shallowCopyVertex, stateChange, stealEdges, translate, walkAll, walkVertices |
Methods inherited from class gov.nasa.alsUtility.Mark |
getMark, isMarked, setMark |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
protected Element element
Constructor Detail |
public Atom(int number)
public Atom(Element e)
public Atom(java.lang.String symbol)
public Atom(Atom atom)
Method Detail |
public boolean isElement(java.lang.String symbol)
public void translateWithNeighbors(Vector3d translation, Atom[] keepStationary)
public boolean isIn(Atom[] array)
public boolean canAcceptEdge()
canAcceptEdge
in class Vertex
public boolean canAcceptEdgesOf(Vertex v)
canAcceptEdgesOf
in class Vertex
public boolean canAcceptEdge(Edge e)
canAcceptEdge
in class Vertex
e
- must be a Bond
public int bondValenceSum()
public boolean isSame(Vertex v)
isSame
in class Vertex
public java.lang.String getExtendedTypeString()
getExtendedTypeString
in class Vertex
public java.lang.Object getExtendedTypeObject()
This provides an efficiency advantage over the String returned by getExtendedTypeString() but requires a little bit of care. Don't modify the returned object in any way. And ExtendedTypeKey is not thread safe
getExtendedTypeObject
in class Vertex
Atom
public int remainingValence()
public int getValence()
public int getAtomicNumber()
public Bond getBond(int i)
public java.lang.String toString()
toString
in class Vertex
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JavaGenes, NASA Ames. Written largely by Al Globus | |||||||||
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