Package org.biojava.nbio.structure.chem

Class ChemCompBond

java.lang.Object

org.biojava.nbio.structure.chem.ChemCompBond

All Implemented Interfaces:

Serializable, CifBean

public class ChemCompBond
extends Object
implements CifBean

Properties of a bond in a chemical component.

Since:

6.0.0

Author:

Sebastian Bittrich

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
ChemCompBond()

Method Summary

Modifier and Type	Method	Description
String	getAtomId1()
String	getAtomId2()
String	getCompId()
static org.slf4j.Logger	getLogger()
int	getNumericalBondOrder()	Converts this ChemCompBond's value_order attribute into an int using the conversion:
String	getPdbxAromaticFlag()
int	getPdbxOrdinal()
String	getPdbxStereoConfig()
String	getValueOrder()
void	setAtomId1(String atomId1)
void	setAtomId2(String atomId2)
void	setCompId(String compId)
void	setPdbxAromaticFlag(String pdbxAromaticFlag)
void	setPdbxOrdinal(int pdbxOrdinal)
void	setPdbxStereoConfig(String pdbxStereoConfig)
void	setValueOrder(String valueOrder)

Methods inherited from class java.lang.Object

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

Constructor Details

ChemCompBond

public ChemCompBond()

Method Details

getLogger

public static org.slf4j.Logger getLogger()

getCompId

public String getCompId()

setCompId

public void setCompId(String compId)

getAtomId1

public String getAtomId1()

setAtomId1

public void setAtomId1(String atomId1)

getAtomId2

public String getAtomId2()

setAtomId2

public void setAtomId2(String atomId2)

getValueOrder

public String getValueOrder()

setValueOrder

public void setValueOrder(String valueOrder)

getPdbxAromaticFlag

public String getPdbxAromaticFlag()

setPdbxAromaticFlag

public void setPdbxAromaticFlag(String pdbxAromaticFlag)

getPdbxStereoConfig

public String getPdbxStereoConfig()

setPdbxStereoConfig

public void setPdbxStereoConfig(String pdbxStereoConfig)

getPdbxOrdinal

public int getPdbxOrdinal()

setPdbxOrdinal

public void setPdbxOrdinal(int pdbxOrdinal)

getNumericalBondOrder

public int getNumericalBondOrder()

Converts this ChemCompBond's value_order attribute into an int using the conversion:

        SING -> 1
        DOUB -> 2
        TRIP -> 3
        QUAD -> 4
 

Any other values will return -1.

(Source: http://mmcif.rcsb.org/dictionaries/mmcif_mdb.dic/Items/_chem_comp_bond. value_order.html)

Returns:

the numerical value of this ChemCompBond's bond order, or -1 if the value is non-numeric or unknown.