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, setupASCR
private 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 AtomSetCollectionReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
public void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
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 readAtomsAndBonds(int ac, int bc) throws java.lang.Exception
java.lang.Exception
private void set2D(boolean b)
private void readAtomValues() throws java.lang.Exception
java.lang.Exception
private void readIsotopes() throws java.lang.Exception
java.lang.Exception
private 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.Exception
public 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)