Package org.jmol.adapter.readers.xtal

Class CgdReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.CgdReader

All Implemented Interfaces:

javajs.api.GenericLineReader

public class CgdReader
extends AtomSetCollectionReader

A reader for TOPOS systre file Crystal Graph Data format. http://www.topos.samsu.ru/manuals.html http://gavrog.org/Systre-Help.html#file_formats H-M aliases from gavrov distribution geometry/sgtable.data

Field Summary

Fields

Modifier and Type	Field	Description
private javajs.util.Lst<String>	edgeData
private Map<Atom,javajs.util.V3[]>	htEdges
private String	lastName
private boolean	noBondSym
private static String	SG_ALIASES
private String[]	tokens
private static javajs.util.V3[]	vecs

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
CgdReader()

Method Summary

Modifier and Type	Method	Description
private void	atom()
protected boolean	checkLine()
private void	finalizeEdges()	Now that we have all the edge data we can add edges to atoms
private void	finalizeNet()	Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges
void	finalizeSubclassReader()	optional reader-specific method run first.
private Atom	findAtom(javajs.util.P3 pt)
private javajs.util.P3	getCoord(int i)
private String	getName(String name)
private String	group(String name)
void	initializeReader()

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

noBondSym

private boolean noBondSym

tokens

private String[] tokens

htEdges

private Map<Atom,javajs.util.V3[]> htEdges

lastName

private String lastName

edgeData

private javajs.util.Lst<String> edgeData

SG_ALIASES

private static final String SG_ALIASES

See Also:

Constant Field Values

vecs

private static final javajs.util.V3[] vecs

Constructor Detail

CgdReader

public CgdReader()

Method Detail

initializeReader

public void initializeReader()

Overrides:

initializeReader in class AtomSetCollectionReader

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

group

private String group(String name)

atom

private void atom()

getName

private String getName(String name)

finalizeSubclassReader

public void finalizeSubclassReader()
                            throws Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

Exception

finalizeEdges

private void finalizeEdges()

Now that we have all the edge data we can add edges to atoms

getCoord

private javajs.util.P3 getCoord(int i)

finalizeNet

private void finalizeNet()

Using atom.vib as a proxy indicating rotation, make all the bonds indicated in the atom's htEdges

findAtom

private Atom findAtom(javajs.util.P3 pt)