Package org.openscience.cdk.protein.data
Class PDBStructure
- java.lang.Object
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- org.openscience.cdk.ChemObject
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- org.openscience.cdk.protein.data.PDBStructure
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- 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:
- main
- Belongs to CDK module:
- data
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Field Summary
Fields Modifier and Type Field Description static String
HELIX
static String
SHEET
static String
TURN
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Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
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Constructor Summary
Constructors Constructor Description PDBStructure()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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, clear, clone, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
toString
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Field Detail
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HELIX
public static final String HELIX
- See Also:
- Constant Field Values
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SHEET
public static final String SHEET
- See Also:
- Constant Field Values
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TURN
public static final String TURN
- See Also:
- Constant Field Values
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Method Detail
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getEndChainID
public Character getEndChainID()
get the ending Chain identifier of this structure.- Specified by:
getEndChainID
in interfaceIPDBStructure
- Returns:
- the ending Chain identifier of this structure
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setEndChainID
public void setEndChainID(Character endChainID)
set the ending Chain identifier of this structure.- Specified by:
setEndChainID
in interfaceIPDBStructure
- Parameters:
endChainID
- the ending Chain identifier of this structure
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getEndInsertionCode
public Character getEndInsertionCode()
get the ending Code for insertion of residues of this structure.- Specified by:
getEndInsertionCode
in interfaceIPDBStructure
- 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 interfaceIPDBStructure
- Parameters:
endInsertionCode
- the ending Code for insertion of residues of this structure
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getEndSequenceNumber
public Integer getEndSequenceNumber()
get the ending sequence number of this structure.- Specified by:
getEndSequenceNumber
in interfaceIPDBStructure
- Returns:
- the ending sequence number of this structure
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setEndSequenceNumber
public void setEndSequenceNumber(Integer endSequenceNumber)
set the ending sequence number of this structure.- Specified by:
setEndSequenceNumber
in interfaceIPDBStructure
- Parameters:
endSequenceNumber
- the ending sequence number of this structure
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getStartChainID
public Character getStartChainID()
get start Chain identifier of this structure.- Specified by:
getStartChainID
in interfaceIPDBStructure
- Returns:
- the start Chain identifier of this structure
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setStartChainID
public void setStartChainID(Character startChainID)
set the start Chain identifier of this structure.- Specified by:
setStartChainID
in interfaceIPDBStructure
- Parameters:
startChainID
- the start Chain identifier of this structure
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getStartInsertionCode
public Character getStartInsertionCode()
get start Code for insertion of residues of this structure.- Specified by:
getStartInsertionCode
in interfaceIPDBStructure
- Returns:
- the start Code for insertion of residues of this structure
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setStartInsertionCode
public void setStartInsertionCode(Character startInsertionCode)
set the start Chain identifier of this structure.- Specified by:
setStartInsertionCode
in interfaceIPDBStructure
- Parameters:
startInsertionCode
- the start Chain identifier of this structure
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getStartSequenceNumber
public Integer getStartSequenceNumber()
get the start sequence number of this structure.- Specified by:
getStartSequenceNumber
in interfaceIPDBStructure
- Returns:
- the start sequence number of this structure
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setStartSequenceNumber
public void setStartSequenceNumber(Integer startSequenceNumber)
set the start sequence number of this structure.- Specified by:
setStartSequenceNumber
in interfaceIPDBStructure
- Parameters:
startSequenceNumber
- the start sequence number of this structure
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getStructureType
public String getStructureType()
get Structure Type of this structure.- Specified by:
getStructureType
in interfaceIPDBStructure
- Returns:
- the Structure Type of this structure
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setStructureType
public void setStructureType(String structureType)
set the Structure Type of this structure.- Specified by:
setStructureType
in interfaceIPDBStructure
- Parameters:
structureType
- the Structure Type of this structure
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