Package org.biojava.nbio.structure.chem

Class ChemComp

java.lang.Object

org.biojava.nbio.structure.chem.ChemComp

All Implemented Interfaces:

Serializable, Comparable<ChemComp>, CifBean

public class ChemComp
extends Object
implements CifBean, Comparable<ChemComp>

Properties of a chemical component.

Since:

6.0.0

Author:

Sebastian Bittrich

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
ChemComp()

Method Summary

Modifier and Type	Method	Description
int	compareTo(ChemComp arg0)
boolean	equals(Object o)
List<ChemCompAtom>	getAtoms()
List<ChemCompBond>	getBonds()
List<ChemCompDescriptor>	getDescriptors()
static ChemComp	getEmptyChemComp()	Creates a new instance of the dummy empty ChemComp.
String	getFormula()
double	getFormulaWeight()
String	getId()
String	getMonNstdFlag()
String	getMonNstdParentCompId()
String	getName()
String	getOneLetterCode()
String	getPdbxAmbiguousFlag()
int	getPdbxFormalCharge()
String	getPdbxIdealCoordinatesDetails()
String	getPdbxIdealCoordinatesMissingFlag()
String	getPdbxInitialDate()
String	getPdbxModelCoordinatesDbCode()
String	getPdbxModelCoordinatesDetails()
String	getPdbxModelCoordinatesMissingFlag()
String	getPdbxModifiedDate()
String	getPdbxProcessingSite()
String	getPdbxReleaseStatus()
String	getPdbxReplacedBy()
String	getPdbxReplaces()
String	getPdbxSubcomponentList()
String	getPdbxSynonyms()
String	getPdbxType()
PolymerType	getPolymerType()
ResidueType	getResidueType()
String	getThreeLetterCode()
String	getType()
int	hashCode()
boolean	hasParent()
boolean	isEmpty()	Indicates whether this compound was created with
boolean	isStandard()
void	setAtoms(List<ChemCompAtom> atoms)
void	setBonds(List<ChemCompBond> bonds)
void	setDescriptors(List<ChemCompDescriptor> descriptors)
void	setFormula(String formula)
void	setFormulaWeight(double formulaWeight)
void	setId(String id)
void	setMonNstdFlag(String monNstdFlag)
void	setMonNstdParentCompId(String monNstdParentCompId)
void	setName(String name)
void	setOneLetterCode(String oneLetterCode)
void	setPdbxAmbiguousFlag(String pdbxAmbiguousFlag)
void	setPdbxFormalCharge(int pdbxFormalCharge)
void	setPdbxIdealCoordinatesDetails(String pdbxIdealCoordinatesDetails)
void	setPdbxIdealCoordinatesMissingFlag(String pdbxIdealCoordinatesMissingFlag)
void	setPdbxInitialDate(String pdbxInitialDate)
void	setPdbxModelCoordinatesDbCode(String pdbxModelCoordinatesDbCode)
void	setPdbxModelCoordinatesDetails(String pdbxModelCoordinatesDetails)
void	setPdbxModelCoordinatesMissingFlag(String pdbxModelCoordinatesMissingFlag)
void	setPdbxModifiedDate(String pdbxModifiedDate)
void	setPdbxProcessingSite(String pdbxProcessingSite)
void	setPdbxReleaseStatus(String pdbxReleaseStatus)
void	setPdbxReplacedBy(String pdbxReplacedBy)
void	setPdbxReplaces(String pdbxReplaces)
void	setPdbxSubcomponentList(String pdbxSubcomponentList)
void	setPdbxSynonyms(String pdbxSynonyms)
void	setPdbxType(String pdbxType)
void	setPolymerType(PolymerType polymerType)
void	setResidueType(ResidueType residueType)
void	setThreeLetterCode(String threeLetterCode)
void	setType(String type)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

ChemComp

public ChemComp()

Method Details

toString

public String toString()

Overrides:

toString in class Object

hasParent

public boolean hasParent()

isStandard

public boolean isStandard()

getId

public String getId()

setId

public void setId(String id)

getName

public String getName()

setName

public void setName(String name)

getType

public String getType()

setType

public void setType(String type)

getResidueType

public ResidueType getResidueType()

setResidueType

public void setResidueType(ResidueType residueType)

getPolymerType

public PolymerType getPolymerType()

setPolymerType

public void setPolymerType(PolymerType polymerType)

getPdbxType

public String getPdbxType()

setPdbxType

public void setPdbxType(String pdbxType)

getFormula

public String getFormula()

setFormula

public void setFormula(String formula)

getMonNstdParentCompId

public String getMonNstdParentCompId()

setMonNstdParentCompId

public void setMonNstdParentCompId(String monNstdParentCompId)

getPdbxSynonyms

public String getPdbxSynonyms()

setPdbxSynonyms

public void setPdbxSynonyms(String pdbxSynonyms)

getPdbxFormalCharge

public int getPdbxFormalCharge()

setPdbxFormalCharge

public void setPdbxFormalCharge(int pdbxFormalCharge)

getPdbxInitialDate

public String getPdbxInitialDate()

setPdbxInitialDate

public void setPdbxInitialDate(String pdbxInitialDate)

getPdbxModifiedDate

public String getPdbxModifiedDate()

setPdbxModifiedDate

public void setPdbxModifiedDate(String pdbxModifiedDate)

getPdbxAmbiguousFlag

public String getPdbxAmbiguousFlag()

setPdbxAmbiguousFlag

public void setPdbxAmbiguousFlag(String pdbxAmbiguousFlag)

getPdbxReleaseStatus

public String getPdbxReleaseStatus()

setPdbxReleaseStatus

public void setPdbxReleaseStatus(String pdbxReleaseStatus)

getPdbxReplacedBy

public String getPdbxReplacedBy()

setPdbxReplacedBy

public void setPdbxReplacedBy(String pdbxReplacedBy)

getPdbxReplaces

public String getPdbxReplaces()

setPdbxReplaces

public void setPdbxReplaces(String pdbxReplaces)

getFormulaWeight

public double getFormulaWeight()

setFormulaWeight

public void setFormulaWeight(double formulaWeight)

getOneLetterCode

public String getOneLetterCode()

setOneLetterCode

public void setOneLetterCode(String oneLetterCode)

getThreeLetterCode

public String getThreeLetterCode()

setThreeLetterCode

public void setThreeLetterCode(String threeLetterCode)

getPdbxModelCoordinatesDetails

public String getPdbxModelCoordinatesDetails()

setPdbxModelCoordinatesDetails

public void setPdbxModelCoordinatesDetails(String pdbxModelCoordinatesDetails)

getPdbxModelCoordinatesMissingFlag

public String getPdbxModelCoordinatesMissingFlag()

setPdbxModelCoordinatesMissingFlag

public void setPdbxModelCoordinatesMissingFlag(String pdbxModelCoordinatesMissingFlag)

getPdbxIdealCoordinatesDetails

public String getPdbxIdealCoordinatesDetails()

setPdbxIdealCoordinatesDetails

public void setPdbxIdealCoordinatesDetails(String pdbxIdealCoordinatesDetails)

getPdbxIdealCoordinatesMissingFlag

public String getPdbxIdealCoordinatesMissingFlag()

setPdbxIdealCoordinatesMissingFlag

public void setPdbxIdealCoordinatesMissingFlag(String pdbxIdealCoordinatesMissingFlag)

getPdbxModelCoordinatesDbCode

public String getPdbxModelCoordinatesDbCode()

setPdbxModelCoordinatesDbCode

public void setPdbxModelCoordinatesDbCode(String pdbxModelCoordinatesDbCode)

getPdbxSubcomponentList

public String getPdbxSubcomponentList()

setPdbxSubcomponentList

public void setPdbxSubcomponentList(String pdbxSubcomponentList)

getPdbxProcessingSite

public String getPdbxProcessingSite()

setPdbxProcessingSite

public void setPdbxProcessingSite(String pdbxProcessingSite)

getMonNstdFlag

public String getMonNstdFlag()

setMonNstdFlag

public void setMonNstdFlag(String monNstdFlag)

getDescriptors

public List<ChemCompDescriptor> getDescriptors()

setDescriptors

public void setDescriptors(List<ChemCompDescriptor> descriptors)

getBonds

public List<ChemCompBond> getBonds()

setBonds

public void setBonds(List<ChemCompBond> bonds)

getAtoms

public List<ChemCompAtom> getAtoms()

setAtoms

public void setAtoms(List<ChemCompAtom> atoms)

compareTo

public int compareTo(ChemComp arg0)

Specified by:

compareTo in interface Comparable<ChemComp>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getEmptyChemComp

public static ChemComp getEmptyChemComp()

Creates a new instance of the dummy empty ChemComp.

Returns:

a ChemComp

isEmpty

public boolean isEmpty()

Indicates whether this compound was created with

Returns:

a boolean