org.simtk.rnaml
Class RnamlDocument

java.lang.Object
  org.simtk.rnaml.RnamlDocument

public class RnamlDocument
extends java.lang.Object

Field Summary

java.util.Map<java.lang.Integer,NucleicAcid>

rnamlIndexMolecules

Constructor Summary

RnamlDocument(java.io.File rnamlFile, MoleculeCollection molecules)

Method Summary

void	importSecondaryStructures()
boolean	isDeemedNucleotide(Residue res, java.lang.String source)
boolean	isRnaviewNA(Biopolymer mol)

Methods inherited from class java.lang.Object

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

Field Detail

rnamlIndexMolecules

public java.util.Map<java.lang.Integer,NucleicAcid> rnamlIndexMolecules

Constructor Detail

RnamlDocument

public RnamlDocument(java.io.File rnamlFile,
                     MoleculeCollection molecules)
              throws org.jdom.JDOMException,
                     java.io.IOException

Throws:

org.jdom.JDOMException

java.io.IOException

Method Detail

importSecondaryStructures

public void importSecondaryStructures()

isRnaviewNA

public boolean isRnaviewNA(Biopolymer mol)

isDeemedNucleotide

public boolean isDeemedNucleotide(Residue res,
                                  java.lang.String source)