Package org.jmol.adapter.readers.more

Class JcampdxReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader, JmolJDXMOLReader
    public class JcampdxReader
extends MolReader
implements JmolJDXMOLReader
    A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS= acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ... 17 14 1 0 0 0 M END 17 1 Energy: -1454.38826 Freq: 3199.35852 C -1.693100 0.007800 0.000000 -0.000980 0.000120 0.000000 ... -- All XML data should be line-oriented in the above fashion. Leading spaces will be ignored. -- Any number of segments can be present -- The first model is referred to as the "base" model -- The base model: -- will generally be of type MOL, but any known type is acceptable -- will be used to generate bonding for later models that have no bonding information -- will be the only model for NMR -- Additional models can represent vibrations (XYZ format) or MS fragmentation (MOL format, probably) ##$PEAKS= ... -- peak record must be a single line of information because Jmol will use line.trim() as a key to pass information to JSpecView.

    • Field Detail

      • selectedModel

        private int selectedModel

      • acdMolFile

        private java.lang.String acdMolFile

      • nPeaks

        private int nPeaks

      • acdAssignments

        private javajs.util.Lst<java.lang.String[]> acdAssignments

      • title

        private java.lang.String title

      • nucleus

        private java.lang.String nucleus

      • type

        private java.lang.String type

      • peakData

        private javajs.util.Lst<java.lang.String> peakData

      • allTypes

        private java.lang.String allTypes

    • Constructor Detail

      • JcampdxReader

        public JcampdxReader()

    • Method Detail

      • initializeReader

        public void initializeReader()
                      throws java.lang.Exception
        Overrides:
        initializeReader in class MolReader
        Throws:
        java.lang.Exception

      • checkLine

        public boolean checkLine()
                  throws java.lang.Exception
        Overrides:
        checkLine in class MolReader
        Returns:
        true if need to read new line
        Throws:
        java.lang.Exception

      • finalizeSubclassReader

        public void finalizeSubclassReader()
                            throws java.lang.Exception
        Description copied from class: AtomSetCollectionReader
        optional reader-specific method run first.
        Overrides:
        finalizeSubclassReader in class MolReader
        Throws:
        java.lang.Exception

      • processModelData

        public void processModelData​(java.lang.String data,
                             java.lang.String id,
                             java.lang.String type,
                             java.lang.String base,
                             java.lang.String last,
                             float modelScale,
                             float vibScale,
                             boolean isFirst)
                      throws java.lang.Exception
        Specified by:
        processModelData in interface JmolJDXMOLReader
        Throws:
        java.lang.Exception

      • setBonding

        private void setBonding​(AtomSetCollection a,
                        int ibase)
        add bonding to a set of ModelData based on a MOL file only if the this set has no bonding already
        Parameters:
        a -
        ibase -

      • updateModelIDs

        private void updateModelIDs​(java.lang.String id,
                            int model0,
                            boolean isFirst)
        The first model set is allowed to be a single model and given no extension. All other model sets are given .1 .2 .3 ... extensions to their IDs.
        Parameters:
        id -
        model0 -
        isFirst -

      • processPeakData

        private void processPeakData()
        integrate the records into the associated models, and delete unreferenced n.m models

      • findModelById

        private int findModelById​(java.lang.String modelID)

      • addType

        private void addType​(int imodel,
                     java.lang.String type)
        sets an auxiliaryInfo string to "HNMR 13CNMR" or "IR" or "MS"
        Parameters:
        imodel -
        type -

      • addTypeStr

        private java.lang.String addTypeStr​(java.lang.String types,
                                    java.lang.String type)

      • processPeakSelectAtom

        private void processPeakSelectAtom​(int i,
                                   java.lang.String key,
                                   java.lang.String data)

      • processPeakSelectModel

        private boolean processPeakSelectModel​(int i,
                                       java.lang.String title)

      • setSpectrumPeaks

        public void setSpectrumPeaks​(int nH,
                             java.lang.String piUnitsX,
                             java.lang.String piUnitsY)
        Specified by:
        setSpectrumPeaks in interface JmolJDXMOLReader

      • removeAtomSet

        private void removeAtomSet​(int imodel)
        note that sets must be iterated from LAST to FIRST not a general method -- would mess up if we had unit cells
        Parameters:
        imodel -