org.jmol.adapter.readers.more
Class CsfReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.more.MopacDataReader
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
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 |
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 |
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
CsfReader
public CsfReader()
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)