org.jmol.adapter.readers.simple
public class GhemicalMMReader extends AtomSetCollectionReader
!Header mm1gp 100
!Info 1
!Atoms 6
0 6
1 6
2 1
3 1
4 1
5 1
!Bonds 5
1 0 D
2 0 S
3 0 S
4 1 S
5 1 S
!Coord
0 0.06677 -0.00197151 4.968e-07
1 -0.0667699 0.00197154 -5.19252e-07
2 0.118917 -0.097636 2.03406e-06
3 0.124471 0.0904495 -4.84021e-07
4 -0.118917 0.0976359 -2.04017e-06
5 -0.124471 -0.0904493 5.12591e-07
!Charges
0 -0.2
1 -0.2
2 0.1
3 0.1
4 0.1
5 0.1
!End
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
Constructor and Description |
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GhemicalMMReader() |
Modifier and Type | Method and Description |
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protected boolean |
checkLine() |
(package private) void |
processAtoms() |
(package private) void |
processBonds() |
(package private) void |
processCharges() |
(package private) void |
processCoord() |
(package private) void |
processHeader() |
(package private) void |
processInfo() |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
void processHeader()
void processInfo()