Package org.jmol.adapter.readers.molxyz

Class MolReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.molxyz.MolReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

JcampdxReader, Mol3DReader

public class MolReader
extends AtomSetCollectionReader

A reader for MDLI mol and sdf files.

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)

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	allow2D
private int	atomCount
private String[]	atomData
private boolean	haveAtomSerials
private int	iatom0
private boolean	is2D
private boolean	optimize2D
private V3000Rdr	vr

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addedData, addedDataKey, addVibrations, allow_a_len_1, 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, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor	Description
MolReader()

Method Summary

Modifier and Type	Method	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.
(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(Map<String,Object> molData, javajs.util.Lst<String> _keyList)	Read the SDF data with name in lower case
private void	set2D(boolean b)

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

optimize2D

private boolean optimize2D

haveAtomSerials

private boolean haveAtomSerials

allow2D

protected boolean allow2D

iatom0

private int iatom0

vr

private V3000Rdr vr

atomCount

private int atomCount

atomData

private String[] atomData

is2D

private boolean is2D

Constructor Detail

MolReader

public MolReader()

Method Detail

initializeReader

public void initializeReader()
                      throws Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

Exception

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

finalizeSubclassReader

public void finalizeSubclassReader()
                            throws Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

Exception

finalizeReaderMR

protected void finalizeReaderMR()
                         throws Exception

Throws:

Exception

processMolSdHeader

private void processMolSdHeader()
                         throws Exception

Throws:

Exception

processCtab

private void processCtab(boolean isMDL)
                  throws Exception

Throws:

Exception

readAtomsAndBonds

private void readAtomsAndBonds(int ac,
                               int bc)
                        throws Exception

Throws:

Exception

set2D

private void set2D(boolean b)

readAtomValues

private void readAtomValues()
                     throws Exception

Read all V nnn lines as string data; user can adapt as needed.

Throws:

Exception

readIsotopes

private void readIsotopes()
                   throws Exception

Read all M ISO lines. These are absolute isotope numbers.

Throws:

Exception

readMolData

private void readMolData(Map<String,Object> molData,
                         javajs.util.Lst<String> _keyList)
                  throws Exception

Read the SDF data with name in lower case

Parameters:

molData -

_keyList -

Throws:

Exception

addMolAtom

public void addMolAtom(int iAtom,
                       int isotope,
                       String elementSymbol,
                       int charge,
                       float x,
                       float y,
                       float z)

fixOrder

int fixOrder(int order,
             int stereo)

addMolBond

public void addMolBond(String iAtom1,
                       String iAtom2,
                       int order,
                       int stereo)