org.simtk.molecularstructure
Class MoleculeCollection

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

All Implemented Interfaces:

MassBody, Chemical, Molecular

public class MoleculeCollection
extends MolecularClass

Constructor Summary

MoleculeCollection()

Method Summary

Vector3D	getCenterOfMass()
java.lang.String	getInputStructureFileName()
double	getMass()
Molecule	getMolecule(int i)
java.lang.String	getPdbId()
java.lang.String	getTitle()
void	loadPDBFormat(java.io.InputStream is)
void	loadPDBFormat(java.lang.String fileName)
void	loadPDBFormat(java.net.URL url)
java.util.Collection<Molecule>	molecules()
void	setInputStructureFileName(java.lang.String s)
void	setPdbId(java.lang.String i)
void	setTitle(java.lang.String t)

Methods inherited from class org.simtk.molecularstructure.MolecularClass

atoms, bestPlane3D

Methods inherited from class java.lang.Object

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

Constructor Detail

MoleculeCollection

public MoleculeCollection()

Method Detail

getTitle

public java.lang.String getTitle()

setTitle

public void setTitle(java.lang.String t)

getPdbId

public java.lang.String getPdbId()

setPdbId

public void setPdbId(java.lang.String i)

getInputStructureFileName

public java.lang.String getInputStructureFileName()

setInputStructureFileName

public void setInputStructureFileName(java.lang.String s)

getMass

public double getMass()

Specified by:

getMass in interface MassBody

Overrides:

getMass in class MolecularClass

getCenterOfMass

public Vector3D getCenterOfMass()

Specified by:

getCenterOfMass in interface MassBody

Overrides:

getCenterOfMass in class MolecularClass

molecules

public java.util.Collection<Molecule> molecules()

getMolecule

public Molecule getMolecule(int i)

loadPDBFormat

public void loadPDBFormat(java.lang.String fileName)
                   throws java.io.FileNotFoundException,
                          java.io.IOException,
                          java.lang.InterruptedException

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.InterruptedException

loadPDBFormat

public void loadPDBFormat(java.net.URL url)
                   throws java.io.IOException,
                          java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

loadPDBFormat

public void loadPDBFormat(java.io.InputStream is)
                   throws java.io.IOException,
                          java.lang.InterruptedException

Parameters:

is -

Throws:

java.io.IOException

java.lang.InterruptedException