org.jmol.adapter.readers.more
Class CsfReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.MopacDataReader
          extended by org.jmol.adapter.readers.more.CsfReader

public class CsfReader
extends MopacDataReader

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 Summary
(package private) static byte anum
           
(package private) static byte[] atomFieldMap
           
(package private) static java.lang.String[] atomFields
           
(package private)  java.lang.String atomicNumbers
           
(package private) static byte bfxn_ang
           
(package private) static byte[] bondFieldMap
           
(package private) static java.lang.String[] bondFields
           
(package private) static byte bondType
           
(package private) static byte chrg
           
(package private) static byte coef_indices
           
(package private) static byte[] connectorFieldMap
           
(package private) static java.lang.String[] connectorFields
           
(package private)  java.util.Hashtable connectors
           
(package private) static byte contractions
           
(package private) static byte eig_val
           
(package private) static byte eig_vec
           
(package private) static byte eig_vec_compressed
           
(package private)  int fieldCount
           
(package private)  int[] fieldTypes
           
(package private) static byte gto_exp
           
private  java.util.Hashtable htBonds
           
(package private) static byte ID
           
(package private) static byte mo_occ
           
(package private) static byte[] moFieldMap
           
(package private) static java.lang.String[] moFields
           
(package private)  int nAtoms
           
(package private)  int nBonds
           
(package private)  int nGaussians
           
(package private) static byte normalMode
           
(package private)  int nSlaters
           
(package private)  int nVibrations
           
(package private) static byte objCls1
           
(package private) static byte objCls2
           
(package private) static byte objID1
           
(package private) static byte objID2
           
(package private) static byte pchrg
           
private  java.util.Hashtable propertyItemCounts
           
(package private) static byte shell
           
(package private) static byte sto_exp
           
(package private) static byte sym
           
(package private) static byte transitionDipole
           
(package private) static byte vibEnergy
           
(package private) static byte[] vibFieldMap
           
(package private) static java.lang.String[] vibFields
           
(package private) static byte xyz_coordinates
           
 
Fields inherited from class org.jmol.adapter.readers.more.MopacDataReader
dValues, floatinfo, intinfo, MIN_COEF, moData, nOrbitals, orbitals
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount
 
Constructor Summary
CsfReader()
           
 
Method Summary
(package private)  void createSlaterByType(int iAtom, int atomicNumber, java.lang.String type, float zeta, float coef)
           
private  void fillCsfArray(java.lang.String property, java.lang.String[] tokens, int i0, java.lang.Object f)
           
(package private)  int getPropertyCount(java.lang.String what)
           
private  int parseLineParameters(java.lang.String[] fields, byte[] fieldMap)
           
(package private)  void processAtomObject()
           
(package private)  void processBasisObject(java.lang.String sto_gto)
           
(package private)  void processBondObject()
           
(package private)  void processConnectorObject()
           
private  void processLocalTransform()
           
(package private)  void processMolecularOrbitalObject()
           
private  void processObjectClass()
           
(package private)  void processVibrationObject()
           
 void readAtomSetCollection(java.io.BufferedReader reader)
           
private  void setBond(Bond bond, int[] connect)
           
 
Methods inherited from class org.jmol.adapter.readers.more.MopacDataReader
addSlater, setMOs, setSlaters
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

nAtoms

int nAtoms

atomicNumbers

java.lang.String atomicNumbers

fieldCount

int fieldCount

nVibrations

int nVibrations

nGaussians

int nGaussians

nSlaters

int nSlaters

htBonds

private java.util.Hashtable htBonds

propertyItemCounts

private java.util.Hashtable propertyItemCounts

fieldTypes

int[] fieldTypes

objCls1

static final byte objCls1
See Also:
Constant Field Values

objID1

static final byte objID1
See Also:
Constant Field Values

objCls2

static final byte objCls2
See Also:
Constant Field Values

objID2

static final byte objID2
See Also:
Constant Field Values

connectorFields

static final java.lang.String[] connectorFields

connectorFieldMap

static final byte[] connectorFieldMap

connectors

java.util.Hashtable connectors

ID

static final byte ID
See Also:
Constant Field Values

sym

static final byte sym
See Also:
Constant Field Values

anum

static final byte anum
See Also:
Constant Field Values

chrg

static final byte chrg
See Also:
Constant Field Values

xyz_coordinates

static final byte xyz_coordinates
See Also:
Constant Field Values

pchrg

static final byte pchrg
See Also:
Constant Field Values

atomFields

static final java.lang.String[] atomFields

atomFieldMap

static final byte[] atomFieldMap

bondType

static final byte bondType
See Also:
Constant Field Values

bondFields

static final java.lang.String[] bondFields

bondFieldMap

static final byte[] bondFieldMap

nBonds

int nBonds

normalMode

static final byte normalMode
See Also:
Constant Field Values

vibEnergy

static final byte vibEnergy
See Also:
Constant Field Values

transitionDipole

static final byte transitionDipole
See Also:
Constant Field Values

vibFields

static final java.lang.String[] vibFields

vibFieldMap

static final byte[] vibFieldMap

eig_val

static final byte eig_val
See Also:
Constant Field Values

mo_occ

static final byte mo_occ
See Also:
Constant Field Values

eig_vec

static final byte eig_vec
See Also:
Constant Field Values

eig_vec_compressed

static final byte eig_vec_compressed
See Also:
Constant Field Values

coef_indices

static final byte coef_indices
See Also:
Constant Field Values

bfxn_ang

static final byte bfxn_ang
See Also:
Constant Field Values

sto_exp

static final byte sto_exp
See Also:
Constant Field Values

contractions

static final byte contractions
See Also:
Constant Field Values

gto_exp

static final byte gto_exp
See Also:
Constant Field Values

shell

static final byte shell
See Also:
Constant Field Values

moFields

static final java.lang.String[] moFields

moFieldMap

static final byte[] moFieldMap
Constructor Detail

CsfReader

public CsfReader()
Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader)
Specified by:
readAtomSetCollection in class MopacDataReader

processObjectClass

private void processObjectClass()
                         throws java.lang.Exception
Throws:
java.lang.Exception

processLocalTransform

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

getPropertyCount

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)
                   throws java.lang.Exception
Throws:
java.lang.Exception

processConnectorObject

void processConnectorObject()
                      throws java.lang.Exception
Throws:
java.lang.Exception

setBond

private void setBond(Bond bond,
                     int[] connect)

processAtomObject

void processAtomObject()
                 throws java.lang.Exception
Throws:
java.lang.Exception

processBondObject

void processBondObject()
                 throws java.lang.Exception
Throws:
java.lang.Exception

processVibrationObject

void processVibrationObject()
                      throws java.lang.Exception
Throws:
java.lang.Exception

processMolecularOrbitalObject

void processMolecularOrbitalObject()
                             throws java.lang.Exception
Throws:
java.lang.Exception

processBasisObject

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

createSlaterByType

void createSlaterByType(int iAtom,
                        int atomicNumber,
                        java.lang.String type,
                        float zeta,
                        float coef)