org.openscience.cdk.protein.data

Class PDBStructure

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.protein.data.PDBStructure

All Implemented Interfaces:

Serializable, Cloneable, ICDKObject, IChemObject, IPDBStructure

Direct Known Subclasses:

DebugPDBStructure

public class PDBStructure
extends ChemObject
implements IPDBStructure

Holder for secundary protein structure elements. Lously modeled after the Jmol Structure.java.

Author:

egonw

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

data

Field Summary

Fields

Modifier and Type	Field and Description
static String	HELIX
static String	SHEET
static String	TURN

Constructor Summary

Constructors

Constructor and Description
PDBStructure()

Method Summary

Modifier and Type	Method and Description
Character	getEndChainID() get the ending Chain identifier of this structure.
Character	getEndInsertionCode() get the ending Code for insertion of residues of this structure.
Integer	getEndSequenceNumber() get the ending sequence number of this structure.
Character	getStartChainID() get start Chain identifier of this structure.
Character	getStartInsertionCode() get start Code for insertion of residues of this structure.
Integer	getStartSequenceNumber() get the start sequence number of this structure.
String	getStructureType() get Structure Type of this structure.
void	setEndChainID(Character endChainID) set the ending Chain identifier of this structure.
void	setEndInsertionCode(Character endInsertionCode) set the ending Code for insertion of residues of this structure.
void	setEndSequenceNumber(Integer endSequenceNumber) set the ending sequence number of this structure.
void	setStartChainID(Character startChainID) set the start Chain identifier of this structure.
void	setStartInsertionCode(Character startInsertionCode) set the start Chain identifier of this structure.
void	setStartSequenceNumber(Integer startSequenceNumber) set the start sequence number of this structure.
void	setStructureType(String structureType) set the Structure Type of this structure.

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, clone, compare, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

toString

Field Detail

HELIX

public static final String HELIX

See Also:

Constant Field Values

SHEET

public static final String SHEET

See Also:

Constant Field Values

TURN

public static final String TURN

See Also:

Constant Field Values

Constructor Detail

PDBStructure

public PDBStructure()

Method Detail

getEndChainID

public Character getEndChainID()

get the ending Chain identifier of this structure.

Specified by:

getEndChainID in interface IPDBStructure

Returns:

the ending Chain identifier of this structure

setEndChainID

public void setEndChainID(Character endChainID)

set the ending Chain identifier of this structure.

Specified by:

setEndChainID in interface IPDBStructure

Parameters:

endChainID - the ending Chain identifier of this structure

getEndInsertionCode

public Character getEndInsertionCode()

get the ending Code for insertion of residues of this structure.

Specified by:

getEndInsertionCode in interface IPDBStructure

Returns:

the ending Code for insertion of residues of this structure

setEndInsertionCode

public void setEndInsertionCode(Character endInsertionCode)

set the ending Code for insertion of residues of this structure.

Specified by:

setEndInsertionCode in interface IPDBStructure

Parameters:

endInsertionCode - the ending Code for insertion of residues of this structure

getEndSequenceNumber

public Integer getEndSequenceNumber()

get the ending sequence number of this structure.

Specified by:

getEndSequenceNumber in interface IPDBStructure

Returns:

the ending sequence number of this structure

setEndSequenceNumber

public void setEndSequenceNumber(Integer endSequenceNumber)

set the ending sequence number of this structure.

Specified by:

setEndSequenceNumber in interface IPDBStructure

Parameters:

endSequenceNumber - the ending sequence number of this structure

getStartChainID

public Character getStartChainID()

get start Chain identifier of this structure.

Specified by:

getStartChainID in interface IPDBStructure

Returns:

the start Chain identifier of this structure

setStartChainID

public void setStartChainID(Character startChainID)

set the start Chain identifier of this structure.

Specified by:

setStartChainID in interface IPDBStructure

Parameters:

startChainID - the start Chain identifier of this structure

getStartInsertionCode

public Character getStartInsertionCode()

get start Code for insertion of residues of this structure.

Specified by:

getStartInsertionCode in interface IPDBStructure

Returns:

the start Code for insertion of residues of this structure

setStartInsertionCode

public void setStartInsertionCode(Character startInsertionCode)

set the start Chain identifier of this structure.

Specified by:

setStartInsertionCode in interface IPDBStructure

Parameters:

startInsertionCode - the start Chain identifier of this structure

getStartSequenceNumber

public Integer getStartSequenceNumber()

get the start sequence number of this structure.

Specified by:

getStartSequenceNumber in interface IPDBStructure

Returns:

the start sequence number of this structure

setStartSequenceNumber

public void setStartSequenceNumber(Integer startSequenceNumber)

set the start sequence number of this structure.

Specified by:

setStartSequenceNumber in interface IPDBStructure

Parameters:

startSequenceNumber - the start sequence number of this structure

getStructureType

public String getStructureType()

get Structure Type of this structure.

Specified by:

getStructureType in interface IPDBStructure

Returns:

the Structure Type of this structure

setStructureType

public void setStructureType(String structureType)

set the Structure Type of this structure.

Specified by:

setStructureType in interface IPDBStructure

Parameters:

structureType - the Structure Type of this structure