public class MolReader extends AtomSetCollectionReader
http://www.mdli.com/downloads/public/ctfile/ctfile.jsp
also: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory() simple 2D-->3D conversion using load "xxx.mol" FILTER "2D"
Modifier and Type | Field and Description |
---|---|
protected boolean |
allow2D |
protected java.lang.String |
dimension |
private boolean |
haveAtomSerials |
private int |
iatom0 |
private boolean |
is2D |
private boolean |
isV3000 |
addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, vwr
Constructor and Description |
---|
MolReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
private void |
checkLineContinuation() |
void |
finalizeReader()
optional reader-specific method run first.
|
protected void |
finalizeReaderMR() |
private int |
fixOrder(int order,
int stereo) |
void |
initializeReader() |
private void |
processCtab(boolean isMDL) |
private void |
processMolSdHeader() |
private void |
readAtoms(int ac) |
private void |
readBonds(int bondCount) |
private void |
readUserData(int atom0) |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR
private boolean is2D
private boolean isV3000
private boolean haveAtomSerials
protected java.lang.String dimension
protected boolean allow2D
private int iatom0
public void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void readUserData(int atom0) throws java.lang.Exception
java.lang.Exception
public void finalizeReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeReader
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeReaderMR() throws java.lang.Exception
java.lang.Exception
private void processMolSdHeader() throws java.lang.Exception
java.lang.Exception
private void processCtab(boolean isMDL) throws java.lang.Exception
java.lang.Exception
private void readAtoms(int ac) throws java.lang.Exception
java.lang.Exception
private void checkLineContinuation() throws java.lang.Exception
java.lang.Exception
private void readBonds(int bondCount) throws java.lang.Exception
java.lang.Exception
private int fixOrder(int order, int stereo)