java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.cif.CifReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

MMCifReader
```
public class CifReader
extends AtomSetCollectionReader
```
A true line-free CIF file reader for CIF files. Subclasses of CIF -- mmCIF/PDBx (pre-initialized) and msCIF (initialized here) Note that a file can be a PDB file without being Added nonstandard mCIF (magnetic_ tags) 5/2/2014 note that PRELIM keys can be removed at some later time
http://www.iucr.org/iucr-top/cif/ http://www.iucr.org/iucr-top/cif/standard/cifstd5.html

Author:

Miguel, Egon, and Bob (hansonr@stolaf.edu) symmetry added by Bob Hanson: setSpaceGroupName() setSymmetryOperator() setUnitCellItem() setFractionalCoordinates() setAtomCoord() applySymmetryAndSetTrajectory()

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`ac`
`private static byte`	`ADP_TYPE`
`private boolean`	`allowRotations`
`private static byte`	`ALT_ID`
`private static byte`	`ANISO_B11`
`private static byte`	`ANISO_B12`
`private static byte`	`ANISO_B13`
`private static byte`	`ANISO_B22`
`private static byte`	`ANISO_B23`
`private static byte`	`ANISO_B33`
`private static byte`	`ANISO_BETA_11`
`private static byte`	`ANISO_BETA_12`
`private static byte`	`ANISO_BETA_13`
`private static byte`	`ANISO_BETA_22`
`private static byte`	`ANISO_BETA_23`
`private static byte`	`ANISO_BETA_33`
`private static byte`	`ANISO_LABEL`
`private static byte`	`ANISO_MMCIF_ID`
`private static byte`	`ANISO_MMCIF_U11`
`private static byte`	`ANISO_MMCIF_U12`
`private static byte`	`ANISO_MMCIF_U13`
`private static byte`	`ANISO_MMCIF_U22`
`private static byte`	`ANISO_MMCIF_U23`
`private static byte`	`ANISO_MMCIF_U33`
`private static byte`	`ANISO_U11`
`private static byte`	`ANISO_U12`
`private static byte`	`ANISO_U13`
`private static byte`	`ANISO_U22`
`private static byte`	`ANISO_U23`
`private static byte`	`ANISO_U33`
`private java.lang.String`	`appendedData`
`private static byte`	`ASYM_ID`
`private static byte`	`ATOM_ID`
`private static byte`	`ATOM_TYPE_OXIDATION_NUMBER`
`private static byte`	`ATOM_TYPE_SYMBOL`
`private static java.lang.String[]`	`atomFields`
`private float[]`	`atomRadius`
`private Atom[]`	`atoms`
`private static java.lang.String[]`	`atomTypeFields`
`private java.lang.String`	`auditBlockCode`
`private static byte`	`AUTH_ASYM_ID`
`private static byte`	`AUTH_ATOM`
`private static byte`	`AUTH_SEQ_ID`
`private static byte`	`B_ISO`
`private javajs.util.Lst<java.lang.Object[]>`	`bondTypes`
`private BS`	`bsBondDuplicates`
`private BS[]`	`bsConnected`
`private BS`	`bsExclude`
`private BS`	`bsMolecule`
`private BS[]`	`bsSets`
`private static byte`	`CARTN_X`
`private static byte`	`CARTN_Y`
`private static byte`	`CARTN_Z`
`private static byte`	`CC_ATOM_CHARGE`
`private static byte`	`CC_ATOM_ID`
`private static byte`	`CC_ATOM_SYM`
`private static byte`	`CC_ATOM_X`
`private static byte`	`CC_ATOM_X_IDEAL`
`private static byte`	`CC_ATOM_Y`
`private static byte`	`CC_ATOM_Y_IDEAL`
`private static byte`	`CC_ATOM_Z`
`private static byte`	`CC_ATOM_Z_IDEAL`
`private static byte`	`CC_COMP_ID`
`private static byte`	`CCDC_GEOM_BOND_TYPE`
`private java.lang.String`	`chemicalName`
`private static byte`	`CITATION_TITLE`
`private static java.lang.String[]`	`citationFields`
`(package private) int[]`	`col2key`
`private static byte`	`COMP_ID`
`private int`	`configurationPtr`
`private int`	`conformationIndex`
`(package private) java.lang.String`	`data`
`private static byte`	`DISORDER_ASSEMBLY`
`private static byte`	`DISORDER_GROUP`
`private java.lang.String`	`disorderAssembly`
`private static byte`	`DUMMY_ATOM`
`protected static java.lang.String`	`FAMILY_ATOM`
`private static java.lang.String`	`FAMILY_SGOP`
`(package private) java.lang.String`	`field`
`private boolean`	`filterAssembly`
`private int`	`firstAtom`
`protected char`	`firstChar`
`private static byte`	`FRACT_X`
`private static byte`	`FRACT_Y`
`private static byte`	`FRACT_Z`
`private static byte`	`GEOM_BOND_ATOM_SITE_LABEL_1`
`private static byte`	`GEOM_BOND_ATOM_SITE_LABEL_2`
`private static byte`	`GEOM_BOND_DISTANCE`
`private static java.lang.String[]`	`geomBondFields`
`private static byte`	`GROUP_PDB`
`private boolean`	`haveAromatic`
`(package private) boolean`	`haveCellWaveVector`
`(package private) boolean`	`haveHAtoms`
`private java.util.Hashtable<java.lang.String,java.lang.Object>`	`htAudit`
`private java.util.Map<java.lang.String,java.lang.String>`	`htCellTypes`
`protected java.util.Map<java.lang.String,java.lang.String>`	`htGroup1`
`private java.util.Map<java.lang.String,java.lang.Float>`	`htOxStates`
`protected boolean`	`iHaveDesiredModel`
`private static byte`	`INS_CODE`
`protected boolean`	`isCourseGrained`
`protected boolean`	`isLigand`
`private boolean`	`isLoop`
`(package private) boolean`	`isMagCIF`
`protected boolean`	`isMMCIF`
`(package private) java.lang.String`	`key`
`(package private) java.lang.String`	`key0`
`(package private) int[]`	`key2col`
`private static byte`	`LABEL`
`private char`	`lastAltLoc`
`protected java.lang.String`	`lastDataSetName`
`private java.lang.String`	`lastDisorderAssembly`
`private java.lang.String`	`lastSpaceGroupName`
`private java.lang.String`	`latticeType`
`private javajs.util.Lst<float[]>`	`lattvecs`
`private javajs.util.Lst<java.lang.String>`	`magCenterings`
`protected int`	`maxSerial`
`private int`	`modDim`
`private static byte`	`MODEL_NO`
`java.util.Map<java.lang.String,java.lang.Integer>`	`modelMap`
`private boolean`	`modulated`
`private java.lang.String`	`molecularType`
`private static byte`	`MOMENT_LABEL`
`private static byte`	`MOMENT_PRELIM_X`
`private static byte`	`MOMENT_PRELIM_Y`
`private static byte`	`MOMENT_PRELIM_Z`
`private static byte`	`MOMENT_X`
`private static byte`	`MOMENT_Y`
`private static byte`	`MOMENT_Z`
`private MSCifRdr`	`mr`
`protected int`	`nAtoms`
`protected int`	`nAtoms0`
`private int`	`nMolecular`
`protected static byte`	`NONE`
`private static byte`	`OCCUPANCY`
`(package private) javajs.api.GenericCifDataParser`	`parser`
`private javajs.util.P3`	`ptOffset`
`private boolean`	`readIdeal`
`private static byte`	`SEQ_ID`
`private static java.lang.String`	`singleAtomID`
`private static byte`	`SITE_MULT`
`protected boolean`	`skipping`
`private static byte`	`SUBSYS_ID`
`private static byte`	`SYM_EQ_XYZ`
`private static byte`	`SYM_MAGN_CENTERING`
`private static byte`	`SYM_MAGN_REV`
`private static byte`	`SYM_MAGN_REV_PRELIM`
`private static byte`	`SYM_MAGN_SSG_ALG`
`private static byte`	`SYM_MAGN_SSG_CENT_XYZ`
`private static byte`	`SYM_MAGN_SSG_CENTERING`
`private static byte`	`SYM_MAGN_SSG_REV`
`private static byte`	`SYM_MAGN_XYZ`
`private static byte`	`SYM_SSG_ALG`
`private static byte`	`SYM_SSG_EQ_XYZ`
`private static byte`	`SYM_XYZ`
`private static java.lang.String[]`	`symmetryOperationsFields`
`private javajs.util.Lst<java.lang.String>`	`symops`
`private static byte`	`THERMAL_TYPE`
`protected java.lang.String`	`thisDataSetName`
`private java.lang.String`	`thisFormula`
`private java.lang.String`	`thisStructuralFormula`
`private int`	`titleAtomSet`
`private static java.lang.String`	`titleRecords`
`private static java.lang.String[]`	`TransformFields`
`private static byte`	`TYPE_SYMBOL`
`private static byte`	`U_ISO_OR_EQUIV`
`protected boolean`	`useAuthorChainID`

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

CifReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`addCellType(java.lang.String type, java.lang.String data, boolean isFrom)`
`protected void`	`addHeader()`
`private void`	`addLatticeVectors()`
`private void`	`addModelTitle(java.lang.String key)`
`private void`	`addMore()`
`private void`	`addNewBond(int i, int j, int order)`	add the bond and mark it for molecular processing
`void`	`applySymmetryAndSetTrajectory()`
`protected boolean`	`checkAllFieldsPresent(java.lang.String[] keys, int lastKey, boolean critical)`
`private boolean`	`checkBondDistance(Atom a, Atom b, float distance, float dx)`
`protected int`	`checkPDBModelField(int modelField, int currentModelNo)`
`protected boolean`	`checkSubclassSymmetry()`
`private boolean`	`createBonds(boolean doInit)`	Use the site bitset to check for atoms that are within +/-dx Angstroms of the specified distances in GEOM_BOND where dx is determined by the uncertainty (dx) in the record.
`private void`	`disableField(int fieldIndex)`	used for turning off fractional or nonfractional coord.
`void`	`doPreSymmetry()`
`protected int`	`fieldProperty(int i)`
`protected boolean`	`filterCIFAtom(Atom atom, java.lang.String componentId)`
`protected boolean`	`finalizeSubclass()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`protected void`	`finalizeSubclassSymmetry(boolean haveSymmetry)`
`private void`	`fixAtomForBonding(javajs.util.P3 pt, int i)`
`int`	`getBondOrder(java.lang.String field)`
`private boolean`	`getData()`
`protected java.lang.String`	`getField(byte type)`
`private MSCifRdr`	`getModulationReader()`
`private MSCifRdr`	`initializeMSCIF()`
`void`	`initializeReader()`
`protected void`	`initSubclass()`
`protected boolean`	`isNull(java.lang.String key)`
`protected void`	`newModel(int modelNo)`
`protected void`	`nextAtomSet()`
`(package private) void`	`parseLoopParameters(java.lang.String[] fields)`	sets up arrays and variables for tokenizer.getData()
`(package private) void`	`parseLoopParametersFor(java.lang.String key, java.lang.String[] fields)`
`(package private) boolean`	`processAtomSiteLoopBlock(boolean isLigand)`	reads atom data in any order
`private void`	`processAtomTypeLoopBlock()`	reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.
`private void`	`processCellParameter()`	unit cell parameters -- two options, so we use MOD 6
`private java.lang.String`	`processChemicalInfo(java.lang.String type)`	reads some of the more interesting info into specific atomSetAuxiliaryInfo elements
`private void`	`processCitationListBlock()`
`private void`	`processDataParameter()`	initialize a new atom set
`private void`	`processGeomBondLoopBlock()`	reads bond data -- N_ijk symmetry business is ignored, so we only indicate bonds within the unit cell to just the original set of atoms.
`protected void`	`processLoopBlock()`	processes loop_ blocks of interest or skips the data
`protected boolean`	`processSubclassAtom(Atom atom, java.lang.String assemblyId, java.lang.String strChain)`
`protected void`	`processSubclassEntry()`
`protected boolean`	`processSubclassLoopBlock()`
`private void`	`processSymmetryOperationsLoopBlock()`	retrieves symmetry operations
`private void`	`processSymmetrySpaceGroupName()`	done by AtomSetCollectionReader
`private void`	`processUnitCellTransform()`
`private void`	`processUnitCellTransformMatrix()`	the PDB transformation matrix cartesian --> fractional
`private boolean`	`readAllData()`
`private void`	`readCifData()`
`private void`	`readSingleAtom()`	No need for anything other than the atom name and symbol; coordinates will be (0 0 0), and no other information is needed.
`private void`	`setBondingAndMolecules()`	(1) If GEOM_BOND records are present, we (a) use them to generate bonds (b) add H atoms to bonds if necessary (c) turn off autoBonding ("hasBonds") (2) If MOLECULAR, then we (a) use {1 1 1} if lattice is not defined (b) use asc.bonds[] to construct a preliminary molecule and connect as we go (c) check symmetry for connections to molecule in any one of the 27 3x3 adjacent cells (d) move those atoms and their connected branch set (e) iterate as necessary to get all atoms desired (f) delete unselected atoms (g) set all coordinates as Cartesians (h) remove all unit cell information
`private void`	`setBs(Atom[] atoms, int iatom, BS[] bsBonds, BS bs)`	iteratively run through connected atoms, adding them to the set

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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

titleRecords

private static final java.lang.String titleRecords

See Also:: Constant Field Values

mr
```
private MSCifRdr mr
```

parser
```
javajs.api.GenericCifDataParser parser
```

filterAssembly
```
private boolean filterAssembly
```

allowRotations
```
private boolean allowRotations
```

readIdeal
```
private boolean readIdeal
```

configurationPtr
```
private int configurationPtr
```

useAuthorChainID
```
protected boolean useAuthorChainID
```

thisDataSetName

protected java.lang.String thisDataSetName

lastDataSetName

protected java.lang.String lastDataSetName

chemicalName
```
private java.lang.String chemicalName
```

thisStructuralFormula

private java.lang.String thisStructuralFormula

thisFormula
```
private java.lang.String thisFormula
```

iHaveDesiredModel
```
protected boolean iHaveDesiredModel
```

isMMCIF
```
protected boolean isMMCIF
```

isLigand
```
protected boolean isLigand
```

isMagCIF
```
boolean isMagCIF
```

haveHAtoms
```
boolean haveHAtoms
```

molecularType
```
private java.lang.String molecularType
```

lastAltLoc
```
private char lastAltLoc
```

haveAromatic
```
private boolean haveAromatic
```

conformationIndex
```
private int conformationIndex
```

nMolecular
```
private int nMolecular
```

appendedData
```
private java.lang.String appendedData
```

skipping
```
protected boolean skipping
```

nAtoms
```
protected int nAtoms
```

ac
```
protected int ac
```

auditBlockCode

private java.lang.String auditBlockCode

lastSpaceGroupName

private java.lang.String lastSpaceGroupName

modulated
```
private boolean modulated
```

isCourseGrained
```
protected boolean isCourseGrained
```

haveCellWaveVector
```
boolean haveCellWaveVector
```

latticeType
```
private java.lang.String latticeType
```

modDim
```
private int modDim
```

htGroup1

protected java.util.Map<java.lang.String,java.lang.String> htGroup1

nAtoms0
```
protected int nAtoms0
```

titleAtomSet
```
private int titleAtomSet
```

htCellTypes

private java.util.Map<java.lang.String,java.lang.String> htCellTypes

modelMap

public java.util.Map<java.lang.String,java.lang.Integer> modelMap

htAudit

private java.util.Hashtable<java.lang.String,java.lang.Object> htAudit

symops

private javajs.util.Lst<java.lang.String> symops

TransformFields

private static final java.lang.String[] TransformFields

key
```
java.lang.String key
```

key0
```
java.lang.String key0
```

data
```
java.lang.String data
```

isLoop
```
private boolean isLoop
```

col2key
```
int[] col2key
```

key2col
```
int[] key2col
```

field
```
java.lang.String field
```

firstChar
```
protected char firstChar
```

htOxStates

private java.util.Map<java.lang.String,java.lang.Float> htOxStates

bondTypes

private javajs.util.Lst<java.lang.Object[]> bondTypes

disorderAssembly

private java.lang.String disorderAssembly

lastDisorderAssembly

private java.lang.String lastDisorderAssembly

lattvecs

private javajs.util.Lst<float[]> lattvecs

magCenterings

private javajs.util.Lst<java.lang.String> magCenterings

maxSerial
```
protected int maxSerial
```

ATOM_TYPE_SYMBOL
```
private static final byte ATOM_TYPE_SYMBOL
```
See Also:

Constant Field Values

ATOM_TYPE_OXIDATION_NUMBER
```
private static final byte ATOM_TYPE_OXIDATION_NUMBER
```
See Also:

Constant Field Values

atomTypeFields

private static final java.lang.String[] atomTypeFields

NONE
```
protected static final byte NONE
```
See Also:

Constant Field Values

TYPE_SYMBOL
```
private static final byte TYPE_SYMBOL
```
See Also:

Constant Field Values

LABEL
```
private static final byte LABEL
```
See Also:

Constant Field Values

AUTH_ATOM
```
private static final byte AUTH_ATOM
```
See Also:

Constant Field Values

FRACT_X
```
private static final byte FRACT_X
```
See Also:

Constant Field Values

FRACT_Y
```
private static final byte FRACT_Y
```
See Also:

Constant Field Values

FRACT_Z
```
private static final byte FRACT_Z
```
See Also:

Constant Field Values

CARTN_X
```
private static final byte CARTN_X
```
See Also:

Constant Field Values

CARTN_Y
```
private static final byte CARTN_Y
```
See Also:

Constant Field Values

CARTN_Z
```
private static final byte CARTN_Z
```
See Also:

Constant Field Values

OCCUPANCY
```
private static final byte OCCUPANCY
```
See Also:

Constant Field Values

B_ISO
```
private static final byte B_ISO
```
See Also:

Constant Field Values

COMP_ID
```
private static final byte COMP_ID
```
See Also:

Constant Field Values

AUTH_ASYM_ID
```
private static final byte AUTH_ASYM_ID
```
See Also:

Constant Field Values

AUTH_SEQ_ID
```
private static final byte AUTH_SEQ_ID
```
See Also:

Constant Field Values

INS_CODE
```
private static final byte INS_CODE
```
See Also:

Constant Field Values

ALT_ID
```
private static final byte ALT_ID
```
See Also:

Constant Field Values

GROUP_PDB
```
private static final byte GROUP_PDB
```
See Also:

Constant Field Values

MODEL_NO
```
private static final byte MODEL_NO
```
See Also:

Constant Field Values

DUMMY_ATOM
```
private static final byte DUMMY_ATOM
```
See Also:

Constant Field Values

DISORDER_GROUP
```
private static final byte DISORDER_GROUP
```
See Also:

Constant Field Values

ANISO_LABEL
```
private static final byte ANISO_LABEL
```
See Also:

Constant Field Values

ANISO_MMCIF_ID
```
private static final byte ANISO_MMCIF_ID
```
See Also:

Constant Field Values

ANISO_U11
```
private static final byte ANISO_U11
```
See Also:

Constant Field Values

ANISO_U22
```
private static final byte ANISO_U22
```
See Also:

Constant Field Values

ANISO_U33
```
private static final byte ANISO_U33
```
See Also:

Constant Field Values

ANISO_U12
```
private static final byte ANISO_U12
```
See Also:

Constant Field Values

ANISO_U13
```
private static final byte ANISO_U13
```
See Also:

Constant Field Values

ANISO_U23
```
private static final byte ANISO_U23
```
See Also:

Constant Field Values

ANISO_MMCIF_U11
```
private static final byte ANISO_MMCIF_U11
```
See Also:

Constant Field Values

ANISO_MMCIF_U22
```
private static final byte ANISO_MMCIF_U22
```
See Also:

Constant Field Values

ANISO_MMCIF_U33
```
private static final byte ANISO_MMCIF_U33
```
See Also:

Constant Field Values

ANISO_MMCIF_U12
```
private static final byte ANISO_MMCIF_U12
```
See Also:

Constant Field Values

ANISO_MMCIF_U13
```
private static final byte ANISO_MMCIF_U13
```
See Also:

Constant Field Values

ANISO_MMCIF_U23
```
private static final byte ANISO_MMCIF_U23
```
See Also:

Constant Field Values

U_ISO_OR_EQUIV
```
private static final byte U_ISO_OR_EQUIV
```
See Also:

Constant Field Values

ANISO_B11
```
private static final byte ANISO_B11
```
See Also:

Constant Field Values

ANISO_B22
```
private static final byte ANISO_B22
```
See Also:

Constant Field Values

ANISO_B33
```
private static final byte ANISO_B33
```
See Also:

Constant Field Values

ANISO_B12
```
private static final byte ANISO_B12
```
See Also:

Constant Field Values

ANISO_B13
```
private static final byte ANISO_B13
```
See Also:

Constant Field Values

ANISO_B23
```
private static final byte ANISO_B23
```
See Also:

Constant Field Values

ANISO_BETA_11
```
private static final byte ANISO_BETA_11
```
See Also:

Constant Field Values

ANISO_BETA_22
```
private static final byte ANISO_BETA_22
```
See Also:

Constant Field Values

ANISO_BETA_33
```
private static final byte ANISO_BETA_33
```
See Also:

Constant Field Values

ANISO_BETA_12
```
private static final byte ANISO_BETA_12
```
See Also:

Constant Field Values

ANISO_BETA_13
```
private static final byte ANISO_BETA_13
```
See Also:

Constant Field Values

ANISO_BETA_23
```
private static final byte ANISO_BETA_23
```
See Also:

Constant Field Values

ADP_TYPE
```
private static final byte ADP_TYPE
```
See Also:

Constant Field Values

CC_COMP_ID
```
private static final byte CC_COMP_ID
```
See Also:

Constant Field Values

CC_ATOM_ID
```
private static final byte CC_ATOM_ID
```
See Also:

Constant Field Values

CC_ATOM_SYM
```
private static final byte CC_ATOM_SYM
```
See Also:

Constant Field Values

CC_ATOM_CHARGE
```
private static final byte CC_ATOM_CHARGE
```
See Also:

Constant Field Values

CC_ATOM_X
```
private static final byte CC_ATOM_X
```
See Also:

Constant Field Values

CC_ATOM_Y
```
private static final byte CC_ATOM_Y
```
See Also:

Constant Field Values

CC_ATOM_Z
```
private static final byte CC_ATOM_Z
```
See Also:

Constant Field Values

CC_ATOM_X_IDEAL
```
private static final byte CC_ATOM_X_IDEAL
```
See Also:

Constant Field Values

CC_ATOM_Y_IDEAL
```
private static final byte CC_ATOM_Y_IDEAL
```
See Also:

Constant Field Values

CC_ATOM_Z_IDEAL
```
private static final byte CC_ATOM_Z_IDEAL
```
See Also:

Constant Field Values

DISORDER_ASSEMBLY
```
private static final byte DISORDER_ASSEMBLY
```
See Also:

Constant Field Values

ASYM_ID
```
private static final byte ASYM_ID
```
See Also:

Constant Field Values

SUBSYS_ID
```
private static final byte SUBSYS_ID
```
See Also:

Constant Field Values

SITE_MULT
```
private static final byte SITE_MULT
```
See Also:

Constant Field Values

THERMAL_TYPE
```
private static final byte THERMAL_TYPE
```
See Also:

Constant Field Values

MOMENT_LABEL
```
private static final byte MOMENT_LABEL
```
See Also:

Constant Field Values

MOMENT_PRELIM_X
```
private static final byte MOMENT_PRELIM_X
```
See Also:

Constant Field Values

MOMENT_PRELIM_Y
```
private static final byte MOMENT_PRELIM_Y
```
See Also:

Constant Field Values

MOMENT_PRELIM_Z
```
private static final byte MOMENT_PRELIM_Z
```
See Also:

Constant Field Values

MOMENT_X
```
private static final byte MOMENT_X
```
See Also:

Constant Field Values

MOMENT_Y
```
private static final byte MOMENT_Y
```
See Also:

Constant Field Values

MOMENT_Z
```
private static final byte MOMENT_Z
```
See Also:

Constant Field Values

ATOM_ID
```
private static final byte ATOM_ID
```
See Also:

Constant Field Values

SEQ_ID
```
private static final byte SEQ_ID
```
See Also:

Constant Field Values

FAMILY_ATOM

protected static final java.lang.String FAMILY_ATOM

See Also:: Constant Field Values

atomFields

private static final java.lang.String[] atomFields

singleAtomID

private static final java.lang.String singleAtomID

CITATION_TITLE
```
private static final byte CITATION_TITLE
```
See Also:

Constant Field Values

citationFields

private static final java.lang.String[] citationFields

SYM_XYZ
```
private static final byte SYM_XYZ
```
See Also:

Constant Field Values

SYM_MAGN_XYZ
```
private static final byte SYM_MAGN_XYZ
```
See Also:

Constant Field Values

SYM_SSG_ALG
```
private static final byte SYM_SSG_ALG
```
See Also:

Constant Field Values

SYM_MAGN_SSG_ALG
```
private static final byte SYM_MAGN_SSG_ALG
```
See Also:

Constant Field Values

SYM_EQ_XYZ
```
private static final byte SYM_EQ_XYZ
```
See Also:

Constant Field Values

SYM_SSG_EQ_XYZ
```
private static final byte SYM_SSG_EQ_XYZ
```
See Also:

Constant Field Values

SYM_MAGN_REV
```
private static final byte SYM_MAGN_REV
```
See Also:

Constant Field Values

SYM_MAGN_SSG_REV
```
private static final byte SYM_MAGN_SSG_REV
```
See Also:

Constant Field Values

SYM_MAGN_REV_PRELIM
```
private static final byte SYM_MAGN_REV_PRELIM
```
See Also:

Constant Field Values

SYM_MAGN_CENTERING
```
private static final byte SYM_MAGN_CENTERING
```
See Also:

Constant Field Values

SYM_MAGN_SSG_CENTERING
```
private static final byte SYM_MAGN_SSG_CENTERING
```
See Also:

Constant Field Values

SYM_MAGN_SSG_CENT_XYZ
```
private static final byte SYM_MAGN_SSG_CENT_XYZ
```
See Also:

Constant Field Values

FAMILY_SGOP

private static final java.lang.String FAMILY_SGOP

See Also:: Constant Field Values

symmetryOperationsFields

private static final java.lang.String[] symmetryOperationsFields

GEOM_BOND_ATOM_SITE_LABEL_1
```
private static final byte GEOM_BOND_ATOM_SITE_LABEL_1
```
See Also:

Constant Field Values

GEOM_BOND_ATOM_SITE_LABEL_2
```
private static final byte GEOM_BOND_ATOM_SITE_LABEL_2
```
See Also:

Constant Field Values

GEOM_BOND_DISTANCE
```
private static final byte GEOM_BOND_DISTANCE
```
See Also:

Constant Field Values

CCDC_GEOM_BOND_TYPE
```
private static final byte CCDC_GEOM_BOND_TYPE
```
See Also:

Constant Field Values

geomBondFields

private static final java.lang.String[] geomBondFields

atomRadius
```
private float[] atomRadius
```

bsConnected
```
private BS[] bsConnected
```

bsSets
```
private BS[] bsSets
```

ptOffset
```
private final javajs.util.P3 ptOffset
```

bsMolecule
```
private BS bsMolecule
```

bsExclude
```
private BS bsExclude
```

firstAtom
```
private int firstAtom
```

atoms
```
private Atom[] atoms
```

bsBondDuplicates
```
private BS bsBondDuplicates
```

Constructor Detail
- CifReader
```
public CifReader()
```

Method Detail

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

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

initSubclass
```
protected void initSubclass()
```

readCifData

private void readCifData()
                  throws java.lang.Exception

Throws:: java.lang.Exception

readAllData

private boolean readAllData()
                     throws java.lang.Exception

Throws:: java.lang.Exception

addModelTitle

private void addModelTitle(java.lang.String key)

processSubclassEntry

protected void processSubclassEntry()
                             throws java.lang.Exception

Throws:: java.lang.Exception

processUnitCellTransform

private void processUnitCellTransform()

addCellType

private void addCellType(java.lang.String type,
                         java.lang.String data,
                         boolean isFrom)

readSingleAtom
```
private void readSingleAtom()
```
No need for anything other than the atom name and symbol; coordinates will be (0 0 0), and no other information is needed.

getModulationReader

private MSCifRdr getModulationReader()
                              throws java.lang.Exception

Throws:: java.lang.Exception

initializeMSCIF

private MSCifRdr initializeMSCIF()
                          throws java.lang.Exception

Throws:: java.lang.Exception

newModel

protected void newModel(int modelNo)
                 throws java.lang.Exception

Throws:: java.lang.Exception

finalizeSubclassReader
```
protected 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

addHeader
```
protected void addHeader()
```

finalizeSubclass

protected boolean finalizeSubclass()
                            throws java.lang.Exception

Throws:: java.lang.Exception

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

doPreSymmetry in class AtomSetCollectionReader

Throws:

java.lang.Exception

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

applySymmetryAndSetTrajectory in class AtomSetCollectionReader

Throws:

java.lang.Exception

finalizeSubclassSymmetry

protected void finalizeSubclassSymmetry(boolean haveSymmetry)
                                 throws java.lang.Exception

Overrides:: finalizeSubclassSymmetry in class AtomSetCollectionReader
Throws:: java.lang.Exception

processDataParameter
```
private void processDataParameter()
```
initialize a new atom set

nextAtomSet
```
protected void nextAtomSet()
```

processChemicalInfo
```
private java.lang.String processChemicalInfo(java.lang.String type)
                                      throws java.lang.Exception
```
reads some of the more interesting info into specific atomSetAuxiliaryInfo elements

Parameters:

type - "name" "formula" etc.

Returns:

data

Throws:

java.lang.Exception

processSymmetrySpaceGroupName

private void processSymmetrySpaceGroupName()
                                    throws java.lang.Exception

done by AtomSetCollectionReader

Throws:: java.lang.Exception

addLatticeVectors
```
private void addLatticeVectors()
```

processCellParameter
```
private void processCellParameter()
                           throws java.lang.Exception
```
unit cell parameters -- two options, so we use MOD 6

Throws:

java.lang.Exception

processUnitCellTransformMatrix

private void processUnitCellTransformMatrix()
                                     throws java.lang.Exception

the PDB transformation matrix cartesian --> fractional

Throws:: java.lang.Exception

getData
```
private boolean getData()
                 throws java.lang.Exception
```
Returns:

TRUE if data, even if ''; FALSE if '.' or '?' or eof.

Throws:

java.lang.Exception

processLoopBlock
```
protected void processLoopBlock()
                         throws java.lang.Exception
```
processes loop_ blocks of interest or skips the data

Throws:

java.lang.Exception

processSubclassLoopBlock

protected boolean processSubclassLoopBlock()
                                    throws java.lang.Exception

Throws:: java.lang.Exception

addMore
```
private void addMore()
```

fieldProperty

protected int fieldProperty(int i)

parseLoopParameters
```
void parseLoopParameters(java.lang.String[] fields)
                  throws java.lang.Exception
```
sets up arrays and variables for tokenizer.getData()

Parameters:

fields -

Throws:

java.lang.Exception

parseLoopParametersFor

void parseLoopParametersFor(java.lang.String key,
                            java.lang.String[] fields)
                     throws java.lang.Exception

Throws:: java.lang.Exception

disableField
```
private void disableField(int fieldIndex)
```
used for turning off fractional or nonfractional coord.

Parameters:

fieldIndex -

processAtomTypeLoopBlock
```
private void processAtomTypeLoopBlock()
                               throws java.lang.Exception
```
reads the oxidation number and associates it with an atom name, which can then later be associated with the right atom indirectly.

Throws:

java.lang.Exception

processAtomSiteLoopBlock
```
boolean processAtomSiteLoopBlock(boolean isLigand)
                          throws java.lang.Exception
```
reads atom data in any order

Parameters:

isLigand -

Returns:

TRUE if successful; FALS if EOF encountered

Throws:

java.lang.Exception

checkPDBModelField

protected int checkPDBModelField(int modelField,
                                 int currentModelNo)
                          throws java.lang.Exception

Parameters:: modelField -; currentModelNo -
Returns:: new currentModelNo
Throws:: java.lang.Exception

processSubclassAtom

protected boolean processSubclassAtom(Atom atom,
                                      java.lang.String assemblyId,
                                      java.lang.String strChain)

Parameters:: atom -; assemblyId -; strChain -
Returns:: true if valid atom

filterCIFAtom

protected boolean filterCIFAtom(Atom atom,
                                java.lang.String componentId)

processCitationListBlock

private void processCitationListBlock()
                               throws java.lang.Exception

Throws:: java.lang.Exception

processSymmetryOperationsLoopBlock

private void processSymmetryOperationsLoopBlock()
                                         throws java.lang.Exception

retrieves symmetry operations

Throws:: java.lang.Exception

getBondOrder

public int getBondOrder(java.lang.String field)

processGeomBondLoopBlock
```
private void processGeomBondLoopBlock()
                               throws java.lang.Exception
```
reads bond data -- N_ijk symmetry business is ignored, so we only indicate bonds within the unit cell to just the original set of atoms. "connect" script or "set forceAutoBond" will override these values, but see below.

Throws:

java.lang.Exception

setBondingAndMolecules
```
private void setBondingAndMolecules()
```
(1) If GEOM_BOND records are present, we (a) use them to generate bonds (b) add H atoms to bonds if necessary (c) turn off autoBonding ("hasBonds") (2) If MOLECULAR, then we (a) use {1 1 1} if lattice is not defined (b) use asc.bonds[] to construct a preliminary molecule and connect as we go (c) check symmetry for connections to molecule in any one of the 27 3x3 adjacent cells (d) move those atoms and their connected branch set (e) iterate as necessary to get all atoms desired (f) delete unselected atoms (g) set all coordinates as Cartesians (h) remove all unit cell information

fixAtomForBonding

private void fixAtomForBonding(javajs.util.P3 pt,
                               int i)

createBonds
```
private boolean createBonds(boolean doInit)
```
Use the site bitset to check for atoms that are within +/-dx Angstroms of the specified distances in GEOM_BOND where dx is determined by the uncertainty (dx) in the record. Note that this also "connects" the atoms that might have been moved in a previous iteration. Also connect H atoms based on a distance <= 1.1 Angstrom from a nearby atom. Then create molecules.

Parameters:

doInit -

Returns:

TRUE if need to continue

checkBondDistance

private boolean checkBondDistance(Atom a,
                                  Atom b,
                                  float distance,
                                  float dx)

addNewBond

private void addNewBond(int i,
                        int j,
                        int order)

add the bond and mark it for molecular processing

Parameters:: i -; j -; order -

setBs

private void setBs(Atom[] atoms,
                   int iatom,
                   BS[] bsBonds,
                   BS bs)

iteratively run through connected atoms, adding them to the set

Parameters:: atoms -; iatom -; bsBonds -; bs -

checkSubclassSymmetry

protected boolean checkSubclassSymmetry()

checkAllFieldsPresent

protected boolean checkAllFieldsPresent(java.lang.String[] keys,
                                        int lastKey,
                                        boolean critical)

getField

protected java.lang.String getField(byte type)

isNull

protected boolean isNull(java.lang.String key)

Class CifReader

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

titleRecords

mr

parser

filterAssembly

allowRotations

readIdeal

configurationPtr

useAuthorChainID

thisDataSetName

lastDataSetName

chemicalName

thisStructuralFormula

thisFormula

iHaveDesiredModel

isMMCIF

isLigand

isMagCIF

haveHAtoms

molecularType

lastAltLoc

haveAromatic

conformationIndex

nMolecular

appendedData

skipping

nAtoms

ac

auditBlockCode

lastSpaceGroupName

modulated

isCourseGrained

haveCellWaveVector

latticeType

modDim

htGroup1

nAtoms0

titleAtomSet

htCellTypes

modelMap

htAudit

symops

TransformFields

key

key0

data

isLoop

col2key

key2col

field

firstChar

htOxStates

bondTypes

disorderAssembly

lastDisorderAssembly

lattvecs

magCenterings

maxSerial

ATOM_TYPE_SYMBOL

ATOM_TYPE_OXIDATION_NUMBER

atomTypeFields

NONE

TYPE_SYMBOL

LABEL

AUTH_ATOM

FRACT_X

FRACT_Y

FRACT_Z

CARTN_X

CARTN_Y

CARTN_Z

OCCUPANCY

B_ISO