java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.simple.MopacReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class MopacReader
extends AtomSetCollectionReader
```
Reads Mopac 93, 6, 7, 2002, or 2009 output files

Author:

Egon Willighagen

Field Summary

Fields
Modifier and Type Field Description

private boolean chargesFound

private boolean haveHeader

private int mopacVersion
- Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
  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 Summary

Constructors
Constructor Description

MopacReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`protected void`	`initializeReader()`
`(package private) void`	`processAtomicCharges()`	Reads the section in MOPAC files with atomic charges.
`(package private) void`	`processCoordinates()`	Reads the section in MOPAC files with cartesian coordinates.
`(package private) void`	`processTotalEnergy()`
`private void`	`readFrequencies()`	Interprets the Harmonic frequencies section.

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

chargesFound
```
private boolean chargesFound
```

haveHeader
```
private boolean haveHeader
```

mopacVersion
```
private int mopacVersion
```

Constructor Detail
- MopacReader
```
public MopacReader()
```

Method Detail

initializeReader
```
protected 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

processTotalEnergy
```
void processTotalEnergy()
```

processAtomicCharges

void processAtomicCharges()
                   throws java.lang.Exception

Reads the section in MOPAC files with atomic charges. These sections look like:

               NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
 
          ATOM NO.   TYPE          CHARGE        ATOM  ELECTRON DENSITY
            1          C          -0.077432        4.0774
            2          C          -0.111917        4.1119
            3          C           0.092081        3.9079

They are expected to be found in the file before the cartesian coordinate section.

Throws:: java.lang.Exception

processCoordinates

void processCoordinates()
                 throws java.lang.Exception

Reads the section in MOPAC files with cartesian coordinates. These sections look like:

           CARTESIAN COORDINATES
 
     NO.       ATOM         X         Y         Z
 
      1         C        0.0000    0.0000    0.0000
      2         C        1.3952    0.0000    0.0000
      3         C        2.0927    1.2078    0.0000

In a MOPAC2002 file the columns are different:

          CARTESIAN COORDINATES
 
 NO.       ATOM           X             Y             Z
 
  1         H        0.00000000    0.00000000    0.00000000
  2         O        0.95094500    0.00000000    0.00000000
  3         H        1.23995160    0.90598439    0.00000000

Throws:: java.lang.Exception

readFrequencies

private void readFrequencies()
                      throws java.lang.Exception

Interprets the Harmonic frequencies section.

     THE LAST 6 VIBRATIONS ARE THE TRANSLATION AND ROTATION MODES
    THE FIRST THREE OF THESE BEING TRANSLATIONS IN X, Y, AND Z, RESPECTIVELY
              NORMAL COORDINATE ANALYSIS
   
       ROOT NO.    1           2           3           4           5           6
   
              370.51248   370.82204   618.03031   647.68700   647.74806   744.32662
     
            1   0.00002     0.00001    -0.00002    -0.05890     0.07204    -0.00002
            2   0.00001    -0.00006    -0.00001     0.01860     0.13517     0.00000
            3   0.00421    -0.11112     0.06838    -0.00002    -0.00003    -0.02449
   
            4   0.00002     0.00001    -0.00002    -0.04779     0.07977    -0.00001
            5  -0.00002     0.00002     0.00001     0.13405    -0.02908     0.00004
            6  -0.10448     0.05212    -0.06842    -0.00005    -0.00002    -0.02447

The vectors are added to a clone of the last read AtomSet. Only the Frequencies are set as properties for each of the frequency type AtomSet generated.

Throws:: java.lang.Exception - If an I/O error occurs

Modifier and Type	Field	Description
`private boolean`	`chargesFound`
`private boolean`	`haveHeader`
`private int`	`mopacVersion`

Class MopacReader

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

chargesFound

haveHeader

mopacVersion

Constructor Detail

MopacReader

Method Detail

initializeReader

checkLine

processTotalEnergy

processAtomicCharges

processCoordinates

readFrequencies