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

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

MMTFReader
```
public class MMCifReader
extends CifReader
```
mmCIF files are recognized prior to class creation. Required fields include one of: _entry.id _database_PDB_ _pdbx_ _chem_comp.pdbx_type _audit_author.name _atom_site.

Author:

Bob Hanson (hansonr@stolaf.edu)

Nested Class Summary
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.cif.CifReader
  CifReader.Parser

Field Summary

Fields
Modifier and Type	Field	Description
`private static byte`	`ASSEM_ID`
`private static byte`	`ASSEM_LIST`
`private static byte`	`ASSEM_OPERS`
`private static String[]`	`assemblyFields`
`private Map<String,javajs.util.BS>`	`assemblyIdAtoms`
`private static byte`	`BEG_ASYM_ID`
`private static byte`	`BEG_INS_CODE`
`private static byte`	`BEG_SEQ_ID`
`private boolean`	`byChain`
`private boolean`	`bySymop`
`private int[]`	`chainAtomCount`
`private Map<String,int[]>`	`chainAtomCounts`
`private Map<String,javajs.util.P3>`	`chainAtomMap`
`private javajs.util.P3`	`chainSum`
`private static byte`	`CHEM_COMP_BOND_AROMATIC_FLAG`
`private static byte`	`CHEM_COMP_BOND_ATOM_ID_1`
`private static byte`	`CHEM_COMP_BOND_ATOM_ID_2`
`private static byte`	`CHEM_COMP_BOND_ID`
`private static byte`	`CHEM_COMP_BOND_VALUE_ORDER`
`private static byte`	`CHEM_COMP_ID`
`private static byte`	`CHEM_COMP_NAME`
`private static String[]`	`chemCompBondFields`
`private static String[]`	`chemCompFields`
`private static byte`	`CONF_TYPE_ID`
`protected boolean`	`done`
`private boolean`	`doSetBonds`
`private static byte`	`END_ASYM_ID`
`private static byte`	`END_INS_CODE`
`private static byte`	`END_SEQ_ID`
`private static String`	`FAMILY_ASSEM_CAT`
`private static String`	`FAMILY_CHEMCOMP_CAT`
`private static String`	`FAMILY_COMPBOND`
`private static String`	`FAMILY_COMPBOND_CAT`
`private static String`	`FAMILY_NCS`
`private static String`	`FAMILY_NCS_CAT`
`private static String`	`FAMILY_OPER`
`private static String`	`FAMILY_OPER_CAT`
`private static String`	`FAMILY_SEQUENCEDIF_CAT`
`private static String`	`FAMILY_SHEET`
`private static String`	`FAMILY_SHEET_CAT`
`private static String`	`FAMILY_STRUCSITE`
`private static String`	`FAMILY_STRUCSITE_CAT`
`private static String`	`FAMILY_STRUCTCONF`
`private static String`	`FAMILY_STRUCTCONF_CAT`
`private static String`	`FAMILY_STRUCTCONN`
`private static String`	`FAMILY_STRUCTCONN_CAT`
`private static byte`	`HELIX_CLASS`
`private Map<String,javajs.util.M4>`	`htBiomts`
`private Map<String,javajs.util.Lst<Object[]>>`	`htBondMap`
`protected Map<String,String>`	`htHetero`
`protected Map<String,Map<String,Object>>`	`htSites`
`protected boolean`	`isBiomolecule`
`private boolean`	`isLigandBondBug`
`(package private) javajs.util.M4`	`mident`
`private int`	`modelIndex`
`private String`	`modelStrings`
`private static String[]`	`ncsoperFields`
`private static byte`	`OPER_ID`
`private static byte`	`OPER_XYZ`
`private static String[]`	`operFields`
`private boolean`	`requiresSorting`
`private static byte`	`SERIAL_NO`
`private static byte`	`SHEET_ID`
`private static byte`	`SITE_ASYM_ID`
`private static byte`	`SITE_COMP_ID`
`private static byte`	`SITE_ID`
`private static byte`	`SITE_INS_CODE`
`private static byte`	`SITE_SEQ_ID`
`private static byte`	`STRAND_ID`
`private static byte`	`STRUCT_CONN_ALT1`
`private static byte`	`STRUCT_CONN_ALT2`
`private static byte`	`STRUCT_CONN_ASYM1`
`private static byte`	`STRUCT_CONN_ASYM2`
`private static byte`	`STRUCT_CONN_ATOM1`
`private static byte`	`STRUCT_CONN_ATOM2`
`private static byte`	`STRUCT_CONN_COMP1`
`private static byte`	`STRUCT_CONN_COMP2`
`private static byte`	`STRUCT_CONN_ORDER`
`private static byte`	`STRUCT_CONN_SEQ1`
`private static byte`	`STRUCT_CONN_SEQ2`
`private static byte`	`STRUCT_CONN_SYMM1`
`private static byte`	`STRUCT_CONN_SYMM2`
`private static byte`	`STRUCT_CONN_TYPE`
`private static byte`	`STRUCT_ID`
`private static byte`	`STRUCT_REF_G1`
`private static byte`	`STRUCT_REF_G3`
`private static String[]`	`structConfFields`
`private static String[]`	`structConnFields`
`private String`	`structConnList`
`private javajs.util.Lst<Object[]>`	`structConnMap`
`private static String[]`	`structRefFields`
`private static String[]`	`structSheetRangeFields`
`private static String[]`	`structSiteFields`
`private int`	`thisChain`
`protected javajs.util.Lst<Map<String,Object>>`	`vBiomolecules`

Fields inherited from class org.jmol.adapter.readers.cif.CifReader
ac, cifParser, col2key, data, FAMILY_ATOM, field, firstChar, haveCellWaveVector, haveHAtoms, htGroup1, iHaveDesiredModel, isCourseGrained, isLigand, isMagCIF, isMMCIF, key, key0, key2col, lastDataSetName, maxSerial, modelMap, nAtoms, nAtoms0, NONE, pdbID, skipping, subParser, thisDataSetName, useAuthorChainID

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, 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

MMCifReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`addAssembly(String[] assem)`
`protected void`	`addHetero(String groupName, String hetName, boolean doCheck, boolean addNote)`
`protected void`	`addMatrix(String id, javajs.util.M4 m4, boolean isNCS)`
`private void`	`addStructure(Structure structure)`
`protected void`	`checkFilterAssembly(String id, Map<String,Object> info)`
`protected int`	`checkPDBModelField(int modelField, int currentModelNo)`
`protected boolean`	`checkSubclassSymmetry()`
`private void`	`createParticle(String id)`
`private String`	`crossBinary(String ops1, String ops2)`
`private String`	`decodeAssemblyOperators(String ops)`
`protected boolean`	`finalizeSubclass()`
`private javajs.util.M4`	`getOpMatrix(String ops)`
`protected int`	`incrementModel(int modelNo)`
`protected void`	`initSubclass()`
`private boolean`	`processAssemblyGenBlock()`
`private void`	`processBonds(javajs.util.Lst<Object[]> cmap, Map<Object,Integer> map, boolean isStructConn)`
`private boolean`	`processChemCompLoopBlock()`	a general name definition field.
`private boolean`	`processCompBondLoopBlock()`
`private boolean`	`processSequence()`	get canonical 1-letter DNA/RNA sequence code from 3-letter code.
`private boolean`	`processStructConfLoopBlock()`	identifies ranges for HELIX and TURN
`private boolean`	`processStructConnLoopBlock()`
`private boolean`	`processStructOperListBlock(boolean isNCS)`
`private boolean`	`processStructSheetRangeLoopBlock()`	identifies sheet ranges
`private boolean`	`processStructSiteBlock()`	identifies structure sites
`boolean`	`processSubclassAtom(Atom atom, String assemblyId, String strChain)`
`protected void`	`processSubclassEntry()`
`protected boolean`	`processSubclassLoopBlock()`
`private int`	`setBiomolecule(Map<String,Object> biomolecule, javajs.util.BS bsAll)`
`private void`	`setBiomolecules()`
`private void`	`setBonds()`	Note that setting bonds from _struct_conn is only done if we have updated CIF files, which include _chem_comp_bond.
`private void`	`setHetero()`
`protected void`	`sortAssemblyModels()`	issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ...

Methods inherited from class org.jmol.adapter.readers.cif.CifReader
addHeader, applySymmetryAndSetTrajectory, checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, getCifDataParser, getField, initializeReader, isNull, newModel, nextAtomSet, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock, processLoopBlock

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, fill3x3, 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

isBiomolecule
```
protected boolean isBiomolecule
```

byChain
```
private boolean byChain
```

bySymop
```
private boolean bySymop
```

chainAtomMap

private Map<String,javajs.util.P3> chainAtomMap

chainAtomCounts

private Map<String,int[]> chainAtomCounts

vBiomolecules

protected javajs.util.Lst<Map<String,Object>> vBiomolecules

htBiomts

private Map<String,javajs.util.M4> htBiomts

htSites

protected Map<String,Map<String,Object>> htSites

htHetero

protected Map<String,String> htHetero

htBondMap

private Map<String,javajs.util.Lst<Object[]>> htBondMap

assemblyIdAtoms

private Map<String,javajs.util.BS> assemblyIdAtoms

thisChain
```
private int thisChain
```

modelIndex
```
private int modelIndex
```

chainSum
```
private javajs.util.P3 chainSum
```

chainAtomCount
```
private int[] chainAtomCount
```

isLigandBondBug
```
private boolean isLigandBondBug
```

mident
```
javajs.util.M4 mident
```

requiresSorting
```
private boolean requiresSorting
```

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

Constant Field Values

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

Constant Field Values

FAMILY_NCS_CAT

private static final String FAMILY_NCS_CAT

See Also:: Constant Field Values

FAMILY_NCS
```
private static final String FAMILY_NCS
```
See Also:

Constant Field Values

ncsoperFields

private static final String[] ncsoperFields

FAMILY_OPER_CAT

private static final String FAMILY_OPER_CAT

See Also:: Constant Field Values

FAMILY_OPER

private static final String FAMILY_OPER

See Also:: Constant Field Values

operFields

private static final String[] operFields

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

FAMILY_ASSEM_CAT

private static final String FAMILY_ASSEM_CAT

See Also:: Constant Field Values

assemblyFields

private static final String[] assemblyFields

FAMILY_SEQUENCEDIF_CAT

private static final String FAMILY_SEQUENCEDIF_CAT

See Also:: Constant Field Values

STRUCT_REF_G3
```
private static final byte STRUCT_REF_G3
```
See Also:

Constant Field Values

STRUCT_REF_G1
```
private static final byte STRUCT_REF_G1
```
See Also:

Constant Field Values

structRefFields

private static final String[] structRefFields

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

Constant Field Values

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

Constant Field Values

FAMILY_CHEMCOMP_CAT

private static final String FAMILY_CHEMCOMP_CAT

See Also:: Constant Field Values

chemCompFields

private static final String[] chemCompFields

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

FAMILY_STRUCTCONF_CAT

private static final String FAMILY_STRUCTCONF_CAT

See Also:: Constant Field Values

FAMILY_STRUCTCONF

private static final String FAMILY_STRUCTCONF

See Also:: Constant Field Values

structConfFields

private static final String[] structConfFields

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

Constant Field Values

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

Constant Field Values

FAMILY_SHEET_CAT

private static final String FAMILY_SHEET_CAT

See Also:: Constant Field Values

FAMILY_SHEET

private static final String FAMILY_SHEET

See Also:: Constant Field Values

structSheetRangeFields

private static final String[] structSheetRangeFields

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

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

Constant Field Values

FAMILY_STRUCSITE_CAT

private static final String FAMILY_STRUCSITE_CAT

See Also:: Constant Field Values

FAMILY_STRUCSITE

private static final String FAMILY_STRUCSITE

See Also:: Constant Field Values

structSiteFields

private static final String[] structSiteFields

STRUCT_CONN_ASYM1
```
private static final byte STRUCT_CONN_ASYM1
```
See Also:

Constant Field Values

STRUCT_CONN_SEQ1
```
private static final byte STRUCT_CONN_SEQ1
```
See Also:

Constant Field Values

STRUCT_CONN_COMP1
```
private static final byte STRUCT_CONN_COMP1
```
See Also:

Constant Field Values

STRUCT_CONN_ATOM1
```
private static final byte STRUCT_CONN_ATOM1
```
See Also:

Constant Field Values

STRUCT_CONN_ALT1
```
private static final byte STRUCT_CONN_ALT1
```
See Also:

Constant Field Values

STRUCT_CONN_SYMM1
```
private static final byte STRUCT_CONN_SYMM1
```
See Also:

Constant Field Values

STRUCT_CONN_ASYM2
```
private static final byte STRUCT_CONN_ASYM2
```
See Also:

Constant Field Values

STRUCT_CONN_SEQ2
```
private static final byte STRUCT_CONN_SEQ2
```
See Also:

Constant Field Values

STRUCT_CONN_COMP2
```
private static final byte STRUCT_CONN_COMP2
```
See Also:

Constant Field Values

STRUCT_CONN_ATOM2
```
private static final byte STRUCT_CONN_ATOM2
```
See Also:

Constant Field Values

STRUCT_CONN_ALT2
```
private static final byte STRUCT_CONN_ALT2
```
See Also:

Constant Field Values

STRUCT_CONN_SYMM2
```
private static final byte STRUCT_CONN_SYMM2
```
See Also:

Constant Field Values

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

Constant Field Values

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

Constant Field Values

FAMILY_STRUCTCONN_CAT

private static final String FAMILY_STRUCTCONN_CAT

See Also:: Constant Field Values

FAMILY_STRUCTCONN

private static final String FAMILY_STRUCTCONN

See Also:: Constant Field Values

structConnFields

private static final String[] structConnFields

structConnMap

private javajs.util.Lst<Object[]> structConnMap

structConnList
```
private String structConnList
```

doSetBonds
```
private boolean doSetBonds
```

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

Constant Field Values

CHEM_COMP_BOND_ATOM_ID_1
```
private static final byte CHEM_COMP_BOND_ATOM_ID_1
```
See Also:

Constant Field Values

CHEM_COMP_BOND_ATOM_ID_2
```
private static final byte CHEM_COMP_BOND_ATOM_ID_2
```
See Also:

Constant Field Values

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

Constant Field Values

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

Constant Field Values

FAMILY_COMPBOND_CAT

private static final String FAMILY_COMPBOND_CAT

See Also:: Constant Field Values

FAMILY_COMPBOND

private static final String FAMILY_COMPBOND

See Also:: Constant Field Values

chemCompBondFields

private static final String[] chemCompBondFields

modelStrings
```
private String modelStrings
```

done
```
protected boolean done
```

Constructor Detail
- MMCifReader
```
public MMCifReader()
```

Method Detail

initSubclass
```
protected void initSubclass()
```
Overrides:

initSubclass in class CifReader

processSubclassEntry

protected void processSubclassEntry()
                             throws Exception

Overrides:: processSubclassEntry in class CifReader
Throws:: Exception

processSubclassLoopBlock

protected boolean processSubclassLoopBlock()
                                    throws Exception

Overrides:: processSubclassLoopBlock in class CifReader
Throws:: Exception

sortAssemblyModels
```
protected void sortAssemblyModels()
```
issue here is that mmCIF assembly atoms can be in different blocks by chain: Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ... and so assigned to too many atom sets.

finalizeSubclass

protected boolean finalizeSubclass()
                            throws Exception

Overrides:: finalizeSubclass in class CifReader
Throws:: Exception

checkSubclassSymmetry
```
protected boolean checkSubclassSymmetry()
```
Overrides:

checkSubclassSymmetry in class CifReader

setBonds
```
private void setBonds()
```
Note that setting bonds from _struct_conn is only done if we have updated CIF files, which include _chem_comp_bond.

processBonds

private void processBonds(javajs.util.Lst<Object[]> cmap,
                          Map<Object,Integer> map,
                          boolean isStructConn)

processSequence
```
private boolean processSequence()
                         throws Exception
```
get canonical 1-letter DNA/RNA sequence code from 3-letter code. For example, "2MG" → "G"

Returns:

true

Throws:

Exception

processAssemblyGenBlock

private boolean processAssemblyGenBlock()
                                 throws Exception

Throws:: Exception

addAssembly

protected void addAssembly(String[] assem)
                    throws Exception

Throws:: Exception

checkFilterAssembly

protected void checkFilterAssembly(String id,
                                   Map<String,Object> info)

decodeAssemblyOperators

private String decodeAssemblyOperators(String ops)

crossBinary

private String crossBinary(String ops1,
                           String ops2)

processStructOperListBlock

private boolean processStructOperListBlock(boolean isNCS)
                                    throws Exception

Throws:: Exception

addMatrix

protected void addMatrix(String id,
                         javajs.util.M4 m4,
                         boolean isNCS)

processChemCompLoopBlock
```
private boolean processChemCompLoopBlock()
                                  throws Exception
```
a general name definition field. Not all hetero

Returns:

true if successful; false to skip

Throws:

Exception

addHetero

protected void addHetero(String groupName,
                         String hetName,
                         boolean doCheck,
                         boolean addNote)

processStructConfLoopBlock
```
private boolean processStructConfLoopBlock()
                                    throws Exception
```
identifies ranges for HELIX and TURN

Returns:

true if successful; false to skip

Throws:

Exception

addStructure

private void addStructure(Structure structure)

processStructSheetRangeLoopBlock

private boolean processStructSheetRangeLoopBlock()
                                          throws Exception

identifies sheet ranges

Returns:: true if successful; false to skip
Throws:: Exception

processStructSiteBlock
```
private boolean processStructSiteBlock()
                                throws Exception
```
identifies structure sites

Returns:

true if successful; false to skip

Throws:

Exception

setBiomolecules
```
private void setBiomolecules()
```

setBiomolecule

private int setBiomolecule(Map<String,Object> biomolecule,
                           javajs.util.BS bsAll)

createParticle

private void createParticle(String id)

getOpMatrix

private javajs.util.M4 getOpMatrix(String ops)

processStructConnLoopBlock

private boolean processStructConnLoopBlock()
                                    throws Exception

Throws:: Exception

processCompBondLoopBlock

private boolean processCompBondLoopBlock()
                                  throws Exception

Throws:: Exception

processSubclassAtom

public boolean processSubclassAtom(Atom atom,
                                   String assemblyId,
                                   String strChain)

Overrides:: processSubclassAtom in class CifReader
Returns:: true if valid atom

checkPDBModelField

protected int checkPDBModelField(int modelField,
                                 int currentModelNo)
                          throws Exception

Overrides:: checkPDBModelField in class CifReader
Returns:: new currentModelNo
Throws:: Exception

incrementModel

protected int incrementModel(int modelNo)
                      throws Exception

Throws:: Exception

setHetero
```
private void setHetero()
```

Class MMCifReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.cif.CifReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.cif.CifReader

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

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.cif.CifReader

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

Methods inherited from class java.lang.Object

Field Detail

isBiomolecule

byChain

bySymop

chainAtomMap

chainAtomCounts

vBiomolecules

htBiomts

htSites

htHetero

htBondMap

assemblyIdAtoms

thisChain

modelIndex

chainSum

chainAtomCount

isLigandBondBug

mident

requiresSorting

OPER_ID

OPER_XYZ

FAMILY_NCS_CAT

FAMILY_NCS

ncsoperFields

FAMILY_OPER_CAT

FAMILY_OPER

operFields

ASSEM_ID

ASSEM_OPERS

ASSEM_LIST

FAMILY_ASSEM_CAT

assemblyFields

FAMILY_SEQUENCEDIF_CAT

STRUCT_REF_G3

STRUCT_REF_G1

structRefFields

CHEM_COMP_ID

CHEM_COMP_NAME

FAMILY_CHEMCOMP_CAT

chemCompFields

CONF_TYPE_ID

BEG_ASYM_ID

BEG_SEQ_ID

BEG_INS_CODE

END_ASYM_ID

END_SEQ_ID

END_INS_CODE

STRUCT_ID

SERIAL_NO

HELIX_CLASS

FAMILY_STRUCTCONF_CAT

FAMILY_STRUCTCONF

structConfFields

SHEET_ID

STRAND_ID

FAMILY_SHEET_CAT

FAMILY_SHEET

structSheetRangeFields

SITE_ID

SITE_COMP_ID

SITE_ASYM_ID

SITE_SEQ_ID

SITE_INS_CODE

FAMILY_STRUCSITE_CAT

FAMILY_STRUCSITE

structSiteFields

STRUCT_CONN_ASYM1

STRUCT_CONN_SEQ1

STRUCT_CONN_COMP1