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 |
---|---|
(package private) boolean |
allow2D |
protected java.lang.String |
dimension |
(package private) boolean |
is2D |
private boolean |
isV3000 |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterAtomTypeStr, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, mustFinalizeModelSet, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
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() |
void |
initializeReader() |
(package private) void |
processCtab(boolean isMDL) |
(package private) void |
processMolSdHeader() |
(package private) void |
readAtoms(int atomCount) |
(package private) void |
readBonds(int atom0,
int bondCount) |
private void |
readUserData(int atom0) |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setLoadNote, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
boolean is2D
private boolean isV3000
protected java.lang.String dimension
boolean allow2D
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
void processMolSdHeader() throws java.lang.Exception
java.lang.Exception
void processCtab(boolean isMDL) throws java.lang.Exception
java.lang.Exception
void readAtoms(int atomCount) throws java.lang.Exception
java.lang.Exception
private void checkLineContinuation() throws java.lang.Exception
java.lang.Exception
void readBonds(int atom0, int bondCount) throws java.lang.Exception
java.lang.Exception