Class CsfReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class CsfReader
    extends MopacSlaterReader
    CSF file reader based on CIF idea -- fluid property fields. note that, like CIF, the order of fields is totally unpredictable in addition, ID numbers are not sequential, requiring atomNames first crack at this 2006/04/13 added DGAUSS, MOPAC, EHT orbital/basis reading 2007/04/09 streamlined CSF dataset reading capabilities 2007/04/09
    Author:
    hansonr
    • Field Detail

      • nAtoms

        private int nAtoms
      • strAtomicNumbers

        private java.lang.String strAtomicNumbers
      • fieldCount

        private int fieldCount
      • nVibrations

        private int nVibrations
      • nGaussians

        private int nGaussians
      • nSlaters

        private int nSlaters
      • htBonds

        private java.util.Map<java.lang.String,​Bond> htBonds
      • propertyItemCounts

        private java.util.Map<java.lang.String,​java.lang.Integer> propertyItemCounts
      • fieldTypes

        private final int[] fieldTypes
      • connectorFields

        private static final java.lang.String[] connectorFields
      • connectorFieldMap

        private static final byte[] connectorFieldMap
      • connectors

        private java.util.Map<java.lang.String,​java.lang.String[]> connectors
      • atomFields

        private static final java.lang.String[] atomFields
      • atomFieldMap

        private static final byte[] atomFieldMap
      • bondFields

        private static final java.lang.String[] bondFields
      • bondFieldMap

        private static final byte[] bondFieldMap
      • vibFields

        private static final java.lang.String[] vibFields
      • vibFieldMap

        private static final byte[] vibFieldMap
      • moFields

        private static final java.lang.String[] moFields
      • moFieldMap

        private static final byte[] moFieldMap
    • Constructor Detail

      • CsfReader

        public CsfReader()
    • Method Detail

      • checkLine

        protected boolean checkLine()
                             throws java.lang.Exception
        Overrides:
        checkLine in class AtomSetCollectionReader
        Returns:
        true if need to read new line
        Throws:
        java.lang.Exception
      • processLocalTransform

        private void processLocalTransform()
                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getPropertyCount

        private int getPropertyCount​(java.lang.String what)
      • parseLineParameters

        private int parseLineParameters​(java.lang.String[] fields,
                                        byte[] fieldMap)
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • fillCsfArray

        private void fillCsfArray​(java.lang.String property,
                                  java.lang.String[] tokens,
                                  int i0,
                                  java.lang.Object f,
                                  boolean isInteger)
                           throws java.lang.Exception
        Throws:
        java.lang.Exception
      • processConnectorObject

        private void processConnectorObject()
                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • setBond

        private void setBond​(Bond bond,
                             java.lang.String[] connect)
      • processAtomObject

        private void processAtomObject()
                                throws java.lang.Exception
        Throws:
        java.lang.Exception
      • processBondObject

        private void processBondObject()
                                throws java.lang.Exception
        Throws:
        java.lang.Exception
      • processVibrationObject

        private void processVibrationObject()
                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • processMolecularOrbitalObject

        private void processMolecularOrbitalObject()
                                            throws java.lang.Exception
        Throws:
        java.lang.Exception
      • processBasisObject

        private void processBasisObject​(java.lang.String sto_gto)
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception