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 java.lang.String[]`	`atomData`
`private boolean`	`haveAtomSerials`
`private int`	`iatom0`
`(package private) boolean`	`is2D`
`(package 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, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, paramsCentroid, paramsLattice, 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, 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
```
boolean optimize2D
```

haveAtomSerials
```
private boolean haveAtomSerials
```

allow2D
```
protected boolean allow2D
```

iatom0
```
private int iatom0
```

vr
```
private V3000Rdr vr
```

atomCount
```
private int atomCount
```

atomData
```
private java.lang.String[] atomData
```

is2D
```
boolean is2D
```

Constructor Detail
- MolReader
```
public MolReader()
```

Method Detail

initializeReader
```
public void initializeReader()
                      throws java.lang.Exception
```
Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

finalizeSubclassReader
```
public void finalizeSubclassReader()
                            throws java.lang.Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

finalizeReaderMR

protected void finalizeReaderMR()
                         throws java.lang.Exception

Throws:: java.lang.Exception

processMolSdHeader

private void processMolSdHeader()
                         throws java.lang.Exception

Throws:: java.lang.Exception

processCtab

private void processCtab(boolean isMDL)
                  throws java.lang.Exception

Throws:: java.lang.Exception

readAtomsAndBonds

private void readAtomsAndBonds(int ac,
                               int bc)
                        throws java.lang.Exception

Throws:: java.lang.Exception

readAtomValues
```
private void readAtomValues()
                     throws java.lang.Exception
```
Read all V nnn lines as string data; user can adapt as needed.

Throws:

java.lang.Exception

readIsotopes
```
private void readIsotopes()
                   throws java.lang.Exception
```
Read all M ISO lines. These are absolute isotope numbers.

Throws:

java.lang.Exception

readMolData

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

Read the SDF data with name in lower case

Parameters:: molData -; _keyList -
Throws:: java.lang.Exception

addMolAtom

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

fixOrder

int fixOrder(int order,
             int stereo)

addMolBond

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

Class MolReader

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

optimize2D

haveAtomSerials

allow2D

iatom0

vr

atomCount

atomData

is2D

Constructor Detail

MolReader

Method Detail

initializeReader

checkLine

finalizeSubclassReader

finalizeReaderMR

processMolSdHeader

processCtab

readAtomsAndBonds

readAtomValues

readIsotopes

readMolData

addMolAtom

fixOrder

addMolBond