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 String |
dimension |
private boolean |
haveAtomSerials |
private int |
iatom0 |
private boolean |
optimize2D |
private V3000Rdr |
vr |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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MolReader() |
Modifier and Type | Method and Description |
---|---|
void |
addMolAtom(int iAtom,
int isotope,
String elementSymbol,
int charge,
float x,
float y,
float z) |
void |
addMolBond(String iAtom1,
String iAtom2,
int order,
int stereo) |
protected boolean |
checkLine() |
protected void |
finalizeReaderMR() |
void |
finalizeSubclassReader()
optional reader-specific method run first.
|
int |
fixOrder(int order,
int stereo) |
void |
initializeReader() |
private void |
processCtab(boolean isMDL) |
private void |
processMolSdHeader() |
private void |
readAtomsAndBonds(int ac,
int bc) |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
private boolean optimize2D
private boolean haveAtomSerials
protected String dimension
protected boolean allow2D
private int iatom0
private V3000Rdr vr
public void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
public void finalizeSubclassReader() throws Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
Exception
public void addMolAtom(int iAtom, int isotope, String elementSymbol, int charge, float x, float y, float z)
public int fixOrder(int order, int stereo)