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org.xmlcml.cmlimpl.subset
Class AtomSetImpl  

java.lang.Object
  java.util.AbstractCollection
      java.util.AbstractSet
          java.util.HashSet
              org.xmlcml.cmlimpl.subset.ToolHashSetImpl
                  org.xmlcml.cmlimpl.subset.AtomSetImpl

All Implemented Interfaces:

org.xmlcml.cml.subset.AtomSet, java.lang.Cloneable, java.util.Collection, java.lang.Iterable, java.io.Serializable, java.util.Set, org.xmlcml.cml.subset.ToolHashSet

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public class AtomSetImpl

extends ToolHashSetImpl

implements org.xmlcml.cml.subset.AtomSet

a set of atoms. Counts number of times an atom has been added (e.g. for bonds). An AtomSet may have coordinates associated with it which may or may not be related to the molecule. This should make calcuation of fragment geometries easier and therefore assembly less painful

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Field Summary
(package private)  java.util.HashMap	atomCountTable
protected  java.util.HashMap	coordinate2Map

 

Fields inherited from class org.xmlcml.cmlimpl.subset.ToolHashSetImpl

id

 

Fields inherited from class java.util.HashSet

 

Constructor Summary

AtomSetImpl()

AtomSetImpl(org.xmlcml.cml.CMLMolecule molecule)           creates atom set from CMLMolecule

AtomSetImpl(java.util.Vector vector)           creates atom set from Vector of Atoms; if Vector has no elements or they are not Atoms throws CIFException

 

Method Summary
void	addAtom(org.xmlcml.cml.CMLAtom atom)           add an atom.
void	addBond(org.xmlcml.cml.CMLBond bond)           adds both atoms in the bond
org.xmlcml.cml.subset.AtomSet	and(org.xmlcml.cml.subset.AtomSet atomSet)           combines this with AtomSet to find common elements, else null.
org.xmlcml.cml.CMLCoordinate2	getCoord2(org.xmlcml.cml.CMLAtom atom)           convenience get coordinates for atom
java.util.HashMap	getCoordinate2Map()           get atom coordinate map
int	getCount(org.xmlcml.cml.CMLAtom atom)           how many times has atom been added (0 means atom is not in set
org.xmlcml.cml.CMLAtom	getStartingAtom()           get any atom (convenience method for iterative processing) This is not reproducible.
(package private)  void	incrementCount(org.xmlcml.cml.CMLAtom atom)
private  void	init(org.xmlcml.cml.CMLMolecule molecule)
org.xmlcml.cml.subset.AtomSet	not(org.xmlcml.cml.subset.AtomSet atomSet)           combines this with AtomSet to find elements NOT in AtomSet, else null.
org.xmlcml.cml.subset.AtomSet	or(org.xmlcml.cml.subset.AtomSet atomSet)           combines this with AtomSet to find all elements.
void	setCoord2(org.xmlcml.cml.CMLAtom atom, org.xmlcml.cml.CMLCoordinate2 c)           convenience set coordinates for atom
java.lang.String	toString()           Creates a String representation of the Collection.
void	transformBy(Transform2 t2)           transform coordinates of all atoms in the set (rather inefficient)
void	translateBy(org.xmlcml.cml.CMLCoordinate2 offset)           translate coordinates of all atoms in the set
org.xmlcml.cml.subset.AtomSet	xor(org.xmlcml.cml.subset.AtomSet atomSet)           combines this with AtomSet to find elements NOT in common, else null.

 

Methods inherited from class org.xmlcml.cmlimpl.subset.ToolHashSetImpl

and, clone, debug, getId, main, not, or, setId, xor

 

Methods inherited from class java.util.HashSet

add, clear, contains, isEmpty, iterator, remove, size

 

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

 

Methods inherited from class java.util.AbstractCollection

addAll, containsAll, retainAll, toArray, toArray

 

Methods inherited from class java.lang.Object

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

 

Methods inherited from interface org.xmlcml.cml.subset.ToolHashSet

add, addAll, and, clone, contains, debug, getId, iterator, not, or, remove, removeAll, retainAll, setId, size, xor

 

Methods inherited from interface java.util.Set

addAll, containsAll, equals, hashCode, removeAll, retainAll, toArray, toArray

 

Field Detail

atomCountTable

java.util.HashMap atomCountTable

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coordinate2Map

protected java.util.HashMap coordinate2Map

Constructor Detail

AtomSetImpl

public AtomSetImpl()

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AtomSetImpl

public AtomSetImpl(org.xmlcml.cml.CMLMolecule molecule)

creates atom set from CMLMolecule

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AtomSetImpl

public AtomSetImpl(java.util.Vector vector)
            throws org.xmlcml.cml.CMLException

creates atom set from Vector of Atoms; if Vector has no elements or they are not Atoms throws CIFException

Method Detail

init

private void init(org.xmlcml.cml.CMLMolecule molecule)

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addAtom

public void addAtom(org.xmlcml.cml.CMLAtom atom)
             throws org.xmlcml.cml.CMLException

add an atom. If atom already present, increments count

Specified by:

addAtom in interface org.xmlcml.cml.subset.AtomSet

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addBond

public void addBond(org.xmlcml.cml.CMLBond bond)
             throws org.xmlcml.cml.CMLException

adds both atoms in the bond

Specified by:

addBond in interface org.xmlcml.cml.subset.AtomSet

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and

public org.xmlcml.cml.subset.AtomSet and(org.xmlcml.cml.subset.AtomSet atomSet)
                                  throws org.xmlcml.cml.CMLException

combines this with AtomSet to find common elements, else null.

Specified by:

and in interface org.xmlcml.cml.subset.AtomSet

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xor

public org.xmlcml.cml.subset.AtomSet xor(org.xmlcml.cml.subset.AtomSet atomSet)
                                  throws org.xmlcml.cml.CMLException

combines this with AtomSet to find elements NOT in common, else null.

Specified by:

xor in interface org.xmlcml.cml.subset.AtomSet

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not

public org.xmlcml.cml.subset.AtomSet not(org.xmlcml.cml.subset.AtomSet atomSet)
                                  throws org.xmlcml.cml.CMLException

combines this with AtomSet to find elements NOT in AtomSet, else null.

Specified by:

not in interface org.xmlcml.cml.subset.AtomSet

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or

public org.xmlcml.cml.subset.AtomSet or(org.xmlcml.cml.subset.AtomSet atomSet)
                                 throws org.xmlcml.cml.CMLException

combines this with AtomSet to find all elements.

Specified by:

or in interface org.xmlcml.cml.subset.AtomSet

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getCount

public int getCount(org.xmlcml.cml.CMLAtom atom)

how many times has atom been added (0 means atom is not in set

Specified by:

getCount in interface org.xmlcml.cml.subset.AtomSet

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incrementCount

void incrementCount(org.xmlcml.cml.CMLAtom atom)

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getCoordinate2Map

public java.util.HashMap getCoordinate2Map()

get atom coordinate map

Specified by:

getCoordinate2Map in interface org.xmlcml.cml.subset.AtomSet

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setCoord2

public void setCoord2(org.xmlcml.cml.CMLAtom atom,
                      org.xmlcml.cml.CMLCoordinate2 c)
               throws org.xmlcml.cml.CMLException

convenience set coordinates for atom

Specified by:

setCoord2 in interface org.xmlcml.cml.subset.AtomSet

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getCoord2

public org.xmlcml.cml.CMLCoordinate2 getCoord2(org.xmlcml.cml.CMLAtom atom)

convenience get coordinates for atom

Specified by:

getCoord2 in interface org.xmlcml.cml.subset.AtomSet

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transformBy

public void transformBy(Transform2 t2)

transform coordinates of all atoms in the set (rather inefficient)

Specified by:

transformBy in interface org.xmlcml.cml.subset.AtomSet

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translateBy

public void translateBy(org.xmlcml.cml.CMLCoordinate2 offset)

translate coordinates of all atoms in the set

Specified by:

translateBy in interface org.xmlcml.cml.subset.AtomSet

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getStartingAtom

public org.xmlcml.cml.CMLAtom getStartingAtom()

get any atom (convenience method for iterative processing) This is not reproducible. If none left,return null

Specified by:

getStartingAtom in interface org.xmlcml.cml.subset.AtomSet

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toString

public java.lang.String toString()

Description copied from class: java.util.AbstractCollection

Creates a String representation of the Collection. The string returned is of the form "[a, b, ...]" where a and b etc are the results of calling toString on the elements of the collection. This implementation obtains an Iterator over the Collection and adds each element to a StringBuffer as it is returned by the iterator. "" is inserted when the collection contains itself (only works for direct containment, not for collections inside collections).

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> xmlcml >> cmlimpl >> [ subset overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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