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" Jmol 14.8.2 adds bond type 15 (quintuple) and 16 (sextuple)
| Modifier and Type | Field and Description |
|---|---|
protected boolean |
allow2D |
private int |
atomCount |
private java.lang.String[] |
atomData |
private boolean |
haveAtomSerials |
private int |
iatom0 |
private boolean |
is2D |
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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr| Constructor and Description |
|---|
MolReader() |
| Modifier and Type | Method and Description |
|---|---|
void |
addMolAtom(int iAtom,
int isotope,
java.lang.String elementSymbol,
int charge,
float x,
float y,
float z) |
void |
addMolBond(java.lang.String iAtom1,
java.lang.String iAtom2,
int order,
int stereo) |
protected boolean |
checkLine() |
protected void |
finalizeReaderMR() |
void |
finalizeSubclassReader()
optional reader-specific method run first.
|
(package private) int |
fixOrder(int order,
int stereo) |
void |
initializeReader() |
private void |
processCtab(boolean isMDL) |
private void |
processMolSdHeader() |
private void |
readAtomsAndBonds(int ac,
int bc) |
private void |
readAtomValues()
Read all V nnn lines as string data; user can adapt as needed.
|
private void |
readIsotopes()
Read all M ISO lines.
|
private void |
readMolData(java.util.Map<java.lang.String,java.lang.Object> molData,
javajs.util.Lst<java.lang.String> _keyList)
Read the SDF data with name in lower case
|
private void |
set2D(boolean b) |
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, 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, setupASCRprivate boolean optimize2D
private boolean haveAtomSerials
protected boolean allow2D
private int iatom0
private V3000Rdr vr
private int atomCount
private java.lang.String[] atomData
private boolean is2D
public void initializeReader()
throws java.lang.Exception
initializeReader in class AtomSetCollectionReaderjava.lang.Exceptionprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionpublic void finalizeSubclassReader()
throws java.lang.Exception
AtomSetCollectionReaderfinalizeSubclassReader in class AtomSetCollectionReaderjava.lang.Exceptionprotected void finalizeReaderMR()
throws java.lang.Exception
java.lang.Exceptionprivate void processMolSdHeader()
throws java.lang.Exception
java.lang.Exceptionprivate void processCtab(boolean isMDL)
throws java.lang.Exception
java.lang.Exceptionprivate void readAtomsAndBonds(int ac,
int bc)
throws java.lang.Exception
java.lang.Exceptionprivate void set2D(boolean b)
private void readAtomValues()
throws java.lang.Exception
java.lang.Exceptionprivate void readIsotopes()
throws java.lang.Exception
java.lang.Exceptionprivate void readMolData(java.util.Map<java.lang.String,java.lang.Object> molData,
javajs.util.Lst<java.lang.String> _keyList)
throws java.lang.Exception
molData - _keyList - java.lang.Exceptionpublic void addMolAtom(int iAtom,
int isotope,
java.lang.String elementSymbol,
int charge,
float x,
float y,
float z)
int fixOrder(int order,
int stereo)
public void addMolBond(java.lang.String iAtom1,
java.lang.String iAtom2,
int order,
int stereo)