public class MMCifReader extends CifReader
Modifier and Type | Field and Description |
---|---|
private java.lang.String[] |
assem |
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,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_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 |
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 |
private static java.lang.String |
FAMILY_COMPBOND |
private static java.lang.String |
FAMILY_OPER |
private static java.lang.String |
FAMILY_SHEET |
private static java.lang.String |
FAMILY_STRUCSITE |
private static java.lang.String |
FAMILY_STRUCTCONF |
private static byte |
HELIX_CLASS |
private java.lang.String[] |
hetatmData
optional nonloop format -- see 1jsa.cif
|
private java.util.Map<java.lang.String,javajs.util.M4> |
htBiomts |
private java.util.Map<java.lang.String,java.lang.String> |
htHetero |
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>> |
htSites |
private boolean |
isBiomolecule |
private boolean |
isLigandBondBug |
private static byte |
NONPOLY_COMP_ID |
private static byte |
NONPOLY_ENTITY_ID |
private static byte |
NONPOLY_NAME |
private static java.lang.String[] |
nonpolyFields |
private static byte |
OPER_ID |
private static byte |
OPER_XYZ |
private static java.lang.String[] |
operFields |
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_ID |
private static byte |
STRUCT_REF_G1 |
private static byte |
STRUCT_REF_G3 |
private static java.lang.String[] |
structConfFields |
private static java.lang.String[] |
structRefFields |
private static java.lang.String[] |
structSheetRangeFields |
private static java.lang.String[] |
structSiteFields |
private java.util.Map<java.lang.String,java.lang.Object> |
thisBiomolecule |
private int |
thisChain |
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> |
vBiomolecules |
ac, data, FAMILY_ATOM, field, fieldOf, firstChar, haveCellWaveVector, htGroup1, isCourseGrained, isMagCIF, isMMCIF, key, modelMap, nAtoms, NONE, parser, propertyCount, propertyOf
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
MMCifReader() |
Modifier and Type | Method and Description |
---|---|
private void |
addAssembly() |
private void |
addHetero(java.lang.String groupName,
java.lang.String hetName) |
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 void |
finalizeSubclass() |
private javajs.util.M4 |
getOpMatrix(java.lang.String ops) |
protected void |
initSubclass() |
private void |
processAddedData() |
private boolean |
processAssemblyGenBlock() |
private boolean |
processChemCompLoopBlock()
a general name definition field.
|
private void |
processDataAssemblyGen() |
private void |
processDataNonpoly() |
private boolean |
processLigandBondLoopBlock() |
private boolean |
processNonpolyLoopBlock()
a HETERO name definition field.
|
private boolean |
processSequence() |
private boolean |
processStructConfLoopBlock()
identifies ranges for HELIX and TURN
|
private boolean |
processStructOperListBlock() |
private boolean |
processStructSheetRangeLoopBlock()
identifies sheet ranges
|
private boolean |
processStructSiteBlock()
identifies structure sites
|
boolean |
processSubclassAtom(Atom atom,
java.lang.String assemblyId,
java.lang.String strChain) |
protected void |
processSubclassEntry() |
protected boolean |
processSubclassLoopBlock() |
private void |
setBiomolecules(java.util.Map<java.lang.String,java.lang.Object> biomolecule) |
applySymmetryAndSetTrajectory, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, initializeReader, newModel, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, forceSymmetry, 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, processDSSR, 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
private boolean isBiomolecule
private boolean byChain
private boolean bySymop
private java.util.Map<java.lang.String,javajs.util.P3> chainAtomMap
private java.util.Map<java.lang.String,int[]> chainAtomCounts
private javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> vBiomolecules
private java.util.Map<java.lang.String,java.lang.Object> thisBiomolecule
private java.util.Map<java.lang.String,javajs.util.M4> htBiomts
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>> htSites
private java.util.Map<java.lang.String,BS> assemblyIdAtoms
private int thisChain
private javajs.util.P3 chainSum
private int[] chainAtomCount
private boolean isLigandBondBug
private static final byte OPER_ID
private static final byte OPER_XYZ
private static final java.lang.String FAMILY_OPER
private static final java.lang.String[] operFields
private static final byte ASSEM_ID
private static final byte ASSEM_OPERS
private static final byte ASSEM_LIST
private static final java.lang.String FAMILY_ASSEM
private static final java.lang.String[] assemblyFields
private java.lang.String[] assem
private static final byte STRUCT_REF_G3
private static final byte STRUCT_REF_G1
private static final java.lang.String[] structRefFields
private static final byte NONPOLY_ENTITY_ID
private static final byte NONPOLY_NAME
private static final byte NONPOLY_COMP_ID
private static final java.lang.String[] nonpolyFields
private java.lang.String[] hetatmData
private static final byte CHEM_COMP_ID
private static final byte CHEM_COMP_NAME
private static final java.lang.String[] chemCompFields
private java.util.Map<java.lang.String,java.lang.String> htHetero
private static final byte CONF_TYPE_ID
private static final byte BEG_ASYM_ID
private static final byte BEG_SEQ_ID
private static final byte BEG_INS_CODE
private static final byte END_ASYM_ID
private static final byte END_SEQ_ID
private static final byte END_INS_CODE
private static final byte STRUCT_ID
private static final byte SERIAL_NO
private static final byte HELIX_CLASS
private static final java.lang.String[] structConfFields
private static final java.lang.String FAMILY_STRUCTCONF
private static final byte SHEET_ID
private static final byte STRAND_ID
private static final java.lang.String FAMILY_SHEET
private static final java.lang.String[] structSheetRangeFields
private static final byte SITE_ID
private static final byte SITE_COMP_ID
private static final byte SITE_ASYM_ID
private static final byte SITE_SEQ_ID
private static final byte SITE_INS_CODE
private static final java.lang.String FAMILY_STRUCSITE
private static final java.lang.String[] structSiteFields
private static final byte CHEM_COMP_BOND_ATOM_ID_1
private static final byte CHEM_COMP_BOND_ATOM_ID_2
private static final byte CHEM_COMP_BOND_VALUE_ORDER
private static final byte CHEM_COMP_BOND_AROMATIC_FLAG
private static final java.lang.String FAMILY_COMPBOND
private static final java.lang.String[] chemCompBondFields
protected void initSubclass()
initSubclass
in class CifReader
protected void finalizeSubclass() throws java.lang.Exception
finalizeSubclass
in class CifReader
java.lang.Exception
protected void processSubclassEntry() throws java.lang.Exception
processSubclassEntry
in class CifReader
java.lang.Exception
private void processAddedData()
private boolean processSequence() throws java.lang.Exception
java.lang.Exception
private void processDataNonpoly() throws java.lang.Exception
java.lang.Exception
private void processDataAssemblyGen() throws java.lang.Exception
java.lang.Exception
private boolean processAssemblyGenBlock() throws java.lang.Exception
java.lang.Exception
private void addAssembly() throws java.lang.Exception
java.lang.Exception
private java.lang.String decodeAssemblyOperators(java.lang.String ops)
private java.lang.String crossBinary(java.lang.String ops1, java.lang.String ops2)
private boolean processStructOperListBlock() throws java.lang.Exception
java.lang.Exception
private boolean processChemCompLoopBlock() throws java.lang.Exception
java.lang.Exception
private boolean processNonpolyLoopBlock() throws java.lang.Exception
java.lang.Exception
private void addHetero(java.lang.String groupName, java.lang.String hetName)
private boolean processStructConfLoopBlock() throws java.lang.Exception
java.lang.Exception
private boolean processStructSheetRangeLoopBlock() throws java.lang.Exception
java.lang.Exception
private boolean processStructSiteBlock() throws java.lang.Exception
java.lang.Exception
private void setBiomolecules(java.util.Map<java.lang.String,java.lang.Object> biomolecule)
private void createParticle(java.lang.String id)
private javajs.util.M4 getOpMatrix(java.lang.String ops)
private boolean processLigandBondLoopBlock() throws java.lang.Exception
java.lang.Exception
public boolean processSubclassAtom(Atom atom, java.lang.String assemblyId, java.lang.String strChain)
processSubclassAtom
in class CifReader
protected boolean processSubclassLoopBlock() throws java.lang.Exception
processSubclassLoopBlock
in class CifReader
java.lang.Exception