Package org.jmol.adapter.readers.cif
Class MMCifReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.cif.CifReader
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- org.jmol.adapter.readers.cif.MMCifReader
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- 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)
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Nested Class Summary
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.cif.CifReader
CifReader.Parser
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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 java.lang.String[]
assemblyFields
private java.util.Map<java.lang.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 java.util.Map<java.lang.String,int[]>
chainAtomCounts
private java.util.Map<java.lang.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 java.lang.String[]
chemCompBondFields
private static java.lang.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 java.lang.String
FAMILY_ASSEM_CAT
private static java.lang.String
FAMILY_CHEMCOMP_CAT
private static java.lang.String
FAMILY_COMPBOND
private static java.lang.String
FAMILY_COMPBOND_CAT
private static java.lang.String
FAMILY_NCS
private static java.lang.String
FAMILY_NCS_CAT
private static java.lang.String
FAMILY_OPER
private static java.lang.String
FAMILY_OPER_CAT
private static java.lang.String
FAMILY_SEQUENCEDIF_CAT
private static java.lang.String
FAMILY_SHEET
private static java.lang.String
FAMILY_SHEET_CAT
private static java.lang.String
FAMILY_STRUCSITE
private static java.lang.String
FAMILY_STRUCSITE_CAT
private static java.lang.String
FAMILY_STRUCTCONF
private static java.lang.String
FAMILY_STRUCTCONF_CAT
private static java.lang.String
FAMILY_STRUCTCONN
private static java.lang.String
FAMILY_STRUCTCONN_CAT
private static byte
HELIX_CLASS
private java.util.Map<java.lang.String,javajs.util.M4>
htBiomts
private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object[]>>
htBondMap
protected java.util.Map<java.lang.String,java.lang.String>
htHetero
protected java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>>
htSites
protected boolean
isBiomolecule
private boolean
isLigandBondBug
(package private) javajs.util.M4
mident
private int
modelIndex
private java.lang.String
modelStrings
private static java.lang.String[]
ncsoperFields
private static byte
OPER_ID
private static byte
OPER_XYZ
private static java.lang.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 java.lang.String[]
structConfFields
private static java.lang.String[]
structConnFields
private java.lang.String
structConnList
private javajs.util.Lst<java.lang.Object[]>
structConnMap
private static java.lang.String[]
structRefFields
private static java.lang.String[]
structSheetRangeFields
private static java.lang.String[]
structSiteFields
private int
thisChain
protected javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>
vBiomolecules
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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, symops, thisDataSetName, useAuthorChainID
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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
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Constructor Summary
Constructors Constructor Description MMCifReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
addAssembly(java.lang.String[] assem)
protected void
addHetero(java.lang.String groupName, java.lang.String hetName, boolean doCheck, boolean addNote)
protected void
addMatrix(java.lang.String id, javajs.util.M4 m4, boolean isNCS)
private void
addStructure(Structure structure)
protected void
checkFilterAssembly(java.lang.String id, java.util.Map<java.lang.String,java.lang.Object> info)
protected int
checkPDBModelField(int modelField, int currentModelNo)
protected boolean
checkSubclassSymmetry()
private void
createParticle(java.lang.String id)
private java.lang.String
crossBinary(java.lang.String ops1, java.lang.String ops2)
private java.lang.String
decodeAssemblyOperators(java.lang.String ops)
protected boolean
finalizeSubclass()
private javajs.util.M4
getOpMatrix(java.lang.String ops)
protected int
incrementModel(int modelNo)
protected void
initSubclass()
private boolean
processAssemblyGenBlock()
private void
processBonds(javajs.util.Lst<java.lang.Object[]> cmap, java.util.Map<java.lang.Object,java.lang.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 TURNprivate boolean
processStructConnLoopBlock()
private boolean
processStructOperListBlock(boolean isNCS)
private boolean
processStructSheetRangeLoopBlock()
identifies sheet rangesprivate boolean
processStructSiteBlock()
identifies structure sitesboolean
processSubclassAtom(Atom atom, java.lang.String assemblyId, java.lang.String strChain)
protected void
processSubclassEntry()
protected boolean
processSubclassLoopBlock()
private int
setBiomolecule(java.util.Map<java.lang.String,java.lang.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
addCifAtom, addHeader, applySymmetryAndSetTrajectory, checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, getCifDataParser, getField, initializeReader, isNull, newModel, nextAtomSet, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock, processLoopBlock
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Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkAndRemoveFilterKey, 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
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Field Detail
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isBiomolecule
protected boolean isBiomolecule
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byChain
private boolean byChain
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bySymop
private boolean bySymop
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chainAtomMap
private java.util.Map<java.lang.String,javajs.util.P3> chainAtomMap
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chainAtomCounts
private java.util.Map<java.lang.String,int[]> chainAtomCounts
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vBiomolecules
protected javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> vBiomolecules
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htBiomts
private java.util.Map<java.lang.String,javajs.util.M4> htBiomts
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htSites
protected java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>> htSites
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htHetero
protected java.util.Map<java.lang.String,java.lang.String> htHetero
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htBondMap
private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object[]>> htBondMap
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assemblyIdAtoms
private java.util.Map<java.lang.String,javajs.util.BS> assemblyIdAtoms
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thisChain
private int thisChain
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modelIndex
private int modelIndex
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chainSum
private javajs.util.P3 chainSum
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chainAtomCount
private int[] chainAtomCount
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isLigandBondBug
private boolean isLigandBondBug
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mident
javajs.util.M4 mident
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requiresSorting
private boolean requiresSorting
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OPER_ID
private static final byte OPER_ID
- See Also:
- Constant Field Values
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OPER_XYZ
private static final byte OPER_XYZ
- See Also:
- Constant Field Values
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FAMILY_NCS_CAT
private static final java.lang.String FAMILY_NCS_CAT
- See Also:
- Constant Field Values
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FAMILY_NCS
private static final java.lang.String FAMILY_NCS
- See Also:
- Constant Field Values
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ncsoperFields
private static final java.lang.String[] ncsoperFields
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FAMILY_OPER_CAT
private static final java.lang.String FAMILY_OPER_CAT
- See Also:
- Constant Field Values
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FAMILY_OPER
private static final java.lang.String FAMILY_OPER
- See Also:
- Constant Field Values
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operFields
private static final java.lang.String[] operFields
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ASSEM_ID
private static final byte ASSEM_ID
- See Also:
- Constant Field Values
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ASSEM_OPERS
private static final byte ASSEM_OPERS
- See Also:
- Constant Field Values
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ASSEM_LIST
private static final byte ASSEM_LIST
- See Also:
- Constant Field Values
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FAMILY_ASSEM_CAT
private static final java.lang.String FAMILY_ASSEM_CAT
- See Also:
- Constant Field Values
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assemblyFields
private static final java.lang.String[] assemblyFields
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FAMILY_SEQUENCEDIF_CAT
private static final java.lang.String FAMILY_SEQUENCEDIF_CAT
- See Also:
- Constant Field Values
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STRUCT_REF_G3
private static final byte STRUCT_REF_G3
- See Also:
- Constant Field Values
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STRUCT_REF_G1
private static final byte STRUCT_REF_G1
- See Also:
- Constant Field Values
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structRefFields
private static final java.lang.String[] structRefFields
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CHEM_COMP_ID
private static final byte CHEM_COMP_ID
- See Also:
- Constant Field Values
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CHEM_COMP_NAME
private static final byte CHEM_COMP_NAME
- See Also:
- Constant Field Values
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FAMILY_CHEMCOMP_CAT
private static final java.lang.String FAMILY_CHEMCOMP_CAT
- See Also:
- Constant Field Values
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chemCompFields
private static final java.lang.String[] chemCompFields
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CONF_TYPE_ID
private static final byte CONF_TYPE_ID
- See Also:
- Constant Field Values
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BEG_ASYM_ID
private static final byte BEG_ASYM_ID
- See Also:
- Constant Field Values
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BEG_SEQ_ID
private static final byte BEG_SEQ_ID
- See Also:
- Constant Field Values
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BEG_INS_CODE
private static final byte BEG_INS_CODE
- See Also:
- Constant Field Values
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END_ASYM_ID
private static final byte END_ASYM_ID
- See Also:
- Constant Field Values
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END_SEQ_ID
private static final byte END_SEQ_ID
- See Also:
- Constant Field Values
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END_INS_CODE
private static final byte END_INS_CODE
- See Also:
- Constant Field Values
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STRUCT_ID
private static final byte STRUCT_ID
- See Also:
- Constant Field Values
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SERIAL_NO
private static final byte SERIAL_NO
- See Also:
- Constant Field Values
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HELIX_CLASS
private static final byte HELIX_CLASS
- See Also:
- Constant Field Values
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FAMILY_STRUCTCONF_CAT
private static final java.lang.String FAMILY_STRUCTCONF_CAT
- See Also:
- Constant Field Values
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FAMILY_STRUCTCONF
private static final java.lang.String FAMILY_STRUCTCONF
- See Also:
- Constant Field Values
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structConfFields
private static final java.lang.String[] structConfFields
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SHEET_ID
private static final byte SHEET_ID
- See Also:
- Constant Field Values
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STRAND_ID
private static final byte STRAND_ID
- See Also:
- Constant Field Values
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FAMILY_SHEET_CAT
private static final java.lang.String FAMILY_SHEET_CAT
- See Also:
- Constant Field Values
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FAMILY_SHEET
private static final java.lang.String FAMILY_SHEET
- See Also:
- Constant Field Values
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structSheetRangeFields
private static final java.lang.String[] structSheetRangeFields
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SITE_ID
private static final byte SITE_ID
- See Also:
- Constant Field Values
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SITE_COMP_ID
private static final byte SITE_COMP_ID
- See Also:
- Constant Field Values
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SITE_ASYM_ID
private static final byte SITE_ASYM_ID
- See Also:
- Constant Field Values
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SITE_SEQ_ID
private static final byte SITE_SEQ_ID
- See Also:
- Constant Field Values
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SITE_INS_CODE
private static final byte SITE_INS_CODE
- See Also:
- Constant Field Values
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FAMILY_STRUCSITE_CAT
private static final java.lang.String FAMILY_STRUCSITE_CAT
- See Also:
- Constant Field Values
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FAMILY_STRUCSITE
private static final java.lang.String FAMILY_STRUCSITE
- See Also:
- Constant Field Values
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structSiteFields
private static final java.lang.String[] structSiteFields
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STRUCT_CONN_ASYM1
private static final byte STRUCT_CONN_ASYM1
- See Also:
- Constant Field Values
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STRUCT_CONN_SEQ1
private static final byte STRUCT_CONN_SEQ1
- See Also:
- Constant Field Values
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STRUCT_CONN_COMP1
private static final byte STRUCT_CONN_COMP1
- See Also:
- Constant Field Values
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STRUCT_CONN_ATOM1
private static final byte STRUCT_CONN_ATOM1
- See Also:
- Constant Field Values
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STRUCT_CONN_ALT1
private static final byte STRUCT_CONN_ALT1
- See Also:
- Constant Field Values
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STRUCT_CONN_SYMM1
private static final byte STRUCT_CONN_SYMM1
- See Also:
- Constant Field Values
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STRUCT_CONN_ASYM2
private static final byte STRUCT_CONN_ASYM2
- See Also:
- Constant Field Values
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STRUCT_CONN_SEQ2
private static final byte STRUCT_CONN_SEQ2
- See Also:
- Constant Field Values
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STRUCT_CONN_COMP2
private static final byte STRUCT_CONN_COMP2
- See Also:
- Constant Field Values
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STRUCT_CONN_ATOM2
private static final byte STRUCT_CONN_ATOM2
- See Also:
- Constant Field Values
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STRUCT_CONN_ALT2
private static final byte STRUCT_CONN_ALT2
- See Also:
- Constant Field Values
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STRUCT_CONN_SYMM2
private static final byte STRUCT_CONN_SYMM2
- See Also:
- Constant Field Values
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STRUCT_CONN_TYPE
private static final byte STRUCT_CONN_TYPE
- See Also:
- Constant Field Values
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STRUCT_CONN_ORDER
private static final byte STRUCT_CONN_ORDER
- See Also:
- Constant Field Values
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FAMILY_STRUCTCONN_CAT
private static final java.lang.String FAMILY_STRUCTCONN_CAT
- See Also:
- Constant Field Values
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FAMILY_STRUCTCONN
private static final java.lang.String FAMILY_STRUCTCONN
- See Also:
- Constant Field Values
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structConnFields
private static final java.lang.String[] structConnFields
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structConnMap
private javajs.util.Lst<java.lang.Object[]> structConnMap
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structConnList
private java.lang.String structConnList
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doSetBonds
private boolean doSetBonds
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CHEM_COMP_BOND_ID
private static final byte CHEM_COMP_BOND_ID
- See Also:
- Constant Field Values
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CHEM_COMP_BOND_ATOM_ID_1
private static final byte CHEM_COMP_BOND_ATOM_ID_1
- See Also:
- Constant Field Values
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CHEM_COMP_BOND_ATOM_ID_2
private static final byte CHEM_COMP_BOND_ATOM_ID_2
- See Also:
- Constant Field Values
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CHEM_COMP_BOND_VALUE_ORDER
private static final byte CHEM_COMP_BOND_VALUE_ORDER
- See Also:
- Constant Field Values
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CHEM_COMP_BOND_AROMATIC_FLAG
private static final byte CHEM_COMP_BOND_AROMATIC_FLAG
- See Also:
- Constant Field Values
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FAMILY_COMPBOND_CAT
private static final java.lang.String FAMILY_COMPBOND_CAT
- See Also:
- Constant Field Values
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FAMILY_COMPBOND
private static final java.lang.String FAMILY_COMPBOND
- See Also:
- Constant Field Values
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chemCompBondFields
private static final java.lang.String[] chemCompBondFields
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modelStrings
private java.lang.String modelStrings
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done
protected boolean done
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Method Detail
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initSubclass
protected void initSubclass()
- Overrides:
initSubclass
in classCifReader
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processSubclassEntry
protected void processSubclassEntry() throws java.lang.Exception
- Overrides:
processSubclassEntry
in classCifReader
- Throws:
java.lang.Exception
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processSubclassLoopBlock
protected boolean processSubclassLoopBlock() throws java.lang.Exception
- Overrides:
processSubclassLoopBlock
in classCifReader
- Throws:
java.lang.Exception
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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.
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finalizeSubclass
protected boolean finalizeSubclass() throws java.lang.Exception
- Overrides:
finalizeSubclass
in classCifReader
- Throws:
java.lang.Exception
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checkSubclassSymmetry
protected boolean checkSubclassSymmetry()
- Overrides:
checkSubclassSymmetry
in classCifReader
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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.
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processBonds
private void processBonds(javajs.util.Lst<java.lang.Object[]> cmap, java.util.Map<java.lang.Object,java.lang.Integer> map, boolean isStructConn)
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processSequence
private boolean processSequence() throws java.lang.Exception
get canonical 1-letter DNA/RNA sequence code from 3-letter code. For example, "2MG" --> "G"- Returns:
- true
- Throws:
java.lang.Exception
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processAssemblyGenBlock
private boolean processAssemblyGenBlock() throws java.lang.Exception
- Throws:
java.lang.Exception
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addAssembly
protected void addAssembly(java.lang.String[] assem) throws java.lang.Exception
- Throws:
java.lang.Exception
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checkFilterAssembly
protected void checkFilterAssembly(java.lang.String id, java.util.Map<java.lang.String,java.lang.Object> info)
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decodeAssemblyOperators
private java.lang.String decodeAssemblyOperators(java.lang.String ops)
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crossBinary
private java.lang.String crossBinary(java.lang.String ops1, java.lang.String ops2)
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processStructOperListBlock
private boolean processStructOperListBlock(boolean isNCS) throws java.lang.Exception
- Throws:
java.lang.Exception
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addMatrix
protected void addMatrix(java.lang.String id, javajs.util.M4 m4, boolean isNCS)
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processChemCompLoopBlock
private boolean processChemCompLoopBlock() throws java.lang.Exception
a general name definition field. Not all hetero- Returns:
- true if successful; false to skip
- Throws:
java.lang.Exception
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addHetero
protected void addHetero(java.lang.String groupName, java.lang.String hetName, boolean doCheck, boolean addNote)
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processStructConfLoopBlock
private boolean processStructConfLoopBlock() throws java.lang.Exception
identifies ranges for HELIX and TURN- Returns:
- true if successful; false to skip
- Throws:
java.lang.Exception
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addStructure
private void addStructure(Structure structure)
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processStructSheetRangeLoopBlock
private boolean processStructSheetRangeLoopBlock() throws java.lang.Exception
identifies sheet ranges- Returns:
- true if successful; false to skip
- Throws:
java.lang.Exception
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processStructSiteBlock
private boolean processStructSiteBlock() throws java.lang.Exception
identifies structure sites- Returns:
- true if successful; false to skip
- Throws:
java.lang.Exception
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setBiomolecules
private void setBiomolecules()
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setBiomolecule
private int setBiomolecule(java.util.Map<java.lang.String,java.lang.Object> biomolecule, javajs.util.BS bsAll)
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createParticle
private void createParticle(java.lang.String id)
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getOpMatrix
private javajs.util.M4 getOpMatrix(java.lang.String ops)
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processStructConnLoopBlock
private boolean processStructConnLoopBlock() throws java.lang.Exception
- Throws:
java.lang.Exception
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processCompBondLoopBlock
private boolean processCompBondLoopBlock() throws java.lang.Exception
- Throws:
java.lang.Exception
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processSubclassAtom
public boolean processSubclassAtom(Atom atom, java.lang.String assemblyId, java.lang.String strChain)
- Overrides:
processSubclassAtom
in classCifReader
- Returns:
- true if valid atom
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checkPDBModelField
protected int checkPDBModelField(int modelField, int currentModelNo) throws java.lang.Exception
- Overrides:
checkPDBModelField
in classCifReader
- Returns:
- new currentModelNo
- Throws:
java.lang.Exception
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incrementModel
protected int incrementModel(int modelNo) throws java.lang.Exception
- Throws:
java.lang.Exception
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setHetero
private void setHetero()
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