Package org.biojava.nbio.structure.chem

Class ChemicalComponentDictionary

java.lang.Object

org.biojava.nbio.structure.chem.ChemicalComponentDictionary

public class ChemicalComponentDictionary
extends Object

A representation of the Chemical Component Dictionary.

Since:

1.7

Author:

Andreas Prlic

See Also:

• link into mmCIF dictionary

Constructor Summary

Constructors

Constructor	Description
ChemicalComponentDictionary()

Method Summary

Modifier and Type	Method	Description
void	addChemComp(ChemComp comp)	Add a new component to the dictionary
ChemComp	getChemComp(String id)
ChemComp	getParent(ChemComp c)	Get the parent of a component.
ChemComp	getReplaced(String id)
ChemComp	getReplaced(ChemComp c)	If ChemComp is replacing another one, get the old version otherwise return the same ChemComp again.
ChemComp	getReplacer(String id)
ChemComp	getReplacer(ChemComp c)	If ChemComp is replaced by another one, get the newer version otherwise return the same ChemComp again.
boolean	isReplaced(String id)
boolean	isReplaced(ChemComp c)
boolean	isReplacer(String id)
boolean	isReplacer(ChemComp c)
int	size()	Returns the number of ChemComps in this dictionary

Methods inherited from class java.lang.Object

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

Constructor Details

ChemicalComponentDictionary

public ChemicalComponentDictionary()

Method Details

isReplaced

public boolean isReplaced(ChemComp c)

isReplaced

public boolean isReplaced(String id)

isReplacer

public boolean isReplacer(ChemComp c)

isReplacer

public boolean isReplacer(String id)

getReplacer

public ChemComp getReplacer(ChemComp c)

If ChemComp is replaced by another one, get the newer version otherwise return the same ChemComp again.

Parameters:

c -

Returns:

get the component that replaced ChemComp.

getReplacer

public ChemComp getReplacer(String id)

getReplaced

public ChemComp getReplaced(ChemComp c)

If ChemComp is replacing another one, get the old version otherwise return the same ChemComp again.

Parameters:

c - the ChemComp for which older versions should be looked up.

getReplaced

public ChemComp getReplaced(String id)

getParent

public ChemComp getParent(ChemComp c)

Get the parent of a component. If component has no parent, return null

Parameters:

c -

Returns:

get the parent component or null if ChemComp has no parent.

addChemComp

public void addChemComp(ChemComp comp)

Add a new component to the dictionary

Parameters:

comp -

size

public int size()

Returns the number of ChemComps in this dictionary

Returns:

nr. of ChemComps

getChemComp

public ChemComp getChemComp(String id)