org.simtk.molecularstructure
Class MoleculeClass

java.lang.Object
  org.simtk.molecularstructure.MolecularClass
      org.simtk.molecularstructure.MoleculeClass

All Implemented Interfaces:

MassBody, Chemical, Molecular, Molecule

Direct Known Subclasses:

BiopolymerClass

public class MoleculeClass
extends MolecularClass
implements Molecule

Field Summary

protected java.lang.String	chainId
protected java.util.Collection<SecondaryStructureClass.SourceType>	displaySourceTypes

Constructor Summary

MoleculeClass(char chainId)

Method Summary

static Molecule	createFactoryPDBMolecule(java.io.LineNumberReader reader) Read one molecule from a PDB format stream.
static Molecule	createFactoryPDBMolecule(java.lang.String fileName)
static Molecule	createFactoryPDBMolecule(java.net.URL url)
java.util.Collection<SecondaryStructureClass.SourceType>	getDisplaySourceTypes()
java.lang.String	getPdbChainId()
boolean	isSolvent()
void	setDisplaySourceTypes(java.util.Collection<SecondaryStructureClass.SourceType> displaySourceTypes)
protected void	setPdbChainId(java.lang.String c)

Methods inherited from class org.simtk.molecularstructure.MolecularClass

atoms, bestPlane3D, getCenterOfMass, getMass

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.simtk.molecularstructure.Molecular

atoms, bestPlane3D

Methods inherited from interface org.simtk.geometry3d.MassBody

getCenterOfMass, getMass

Field Detail

chainId

protected java.lang.String chainId

displaySourceTypes

protected java.util.Collection<SecondaryStructureClass.SourceType> displaySourceTypes

Constructor Detail

MoleculeClass

public MoleculeClass(char chainId)

Method Detail

getPdbChainId

public java.lang.String getPdbChainId()

Specified by:

getPdbChainId in interface Molecule

getDisplaySourceTypes

public java.util.Collection<SecondaryStructureClass.SourceType> getDisplaySourceTypes()

Specified by:

getDisplaySourceTypes in interface Molecule

setDisplaySourceTypes

public void setDisplaySourceTypes(java.util.Collection<SecondaryStructureClass.SourceType> displaySourceTypes)

Specified by:

setDisplaySourceTypes in interface Molecule

setPdbChainId

protected void setPdbChainId(java.lang.String c)

isSolvent

public boolean isSolvent()

Specified by:

isSolvent in interface Molecule

createFactoryPDBMolecule

public static Molecule createFactoryPDBMolecule(java.net.URL url)
                                         throws java.io.IOException

Throws:

java.io.IOException

createFactoryPDBMolecule

public static Molecule createFactoryPDBMolecule(java.lang.String fileName)
                                         throws java.io.IOException

Throws:

java.io.IOException

createFactoryPDBMolecule

public static Molecule createFactoryPDBMolecule(java.io.LineNumberReader reader)
                                         throws java.io.IOException

Read one molecule from a PDB format stream. Stop before the first atom of the next molecule.

Parameters:

reader -

Returns:

a newly created Molecule object

Throws:

java.io.IOException