public class MMCifReader extends CifReader
Modifier and Type | Field and 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 |
ac, col2key, data, FAMILY_ATOM, field, firstChar, haveCellWaveVector, haveHAtoms, htGroup1, iHaveDesiredModel, isCourseGrained, isLigand, isMagCIF, isMMCIF, key, key0, key2col, lastDataSetName, maxSerial, modelMap, nAtoms, nAtoms0, NONE, parser, pdbID, skipping, thisDataSetName, useAuthorChainID
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, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
MMCifReader() |
Modifier and Type | Method and 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 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,
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 ...
|
addHeader, applySymmetryAndSetTrajectory, checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassReader, finalizeSubclassSymmetry, getBondOrder, getCifDataParser, getField, initializeReader, isNull, newModel, nextAtomSet, parseLoopParameters, parseLoopParametersFor, processAtomSiteLoopBlock, processLoopBlock
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
protected 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
protected javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> vBiomolecules
private java.util.Map<java.lang.String,javajs.util.M4> htBiomts
protected java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>> htSites
protected java.util.Map<java.lang.String,java.lang.String> htHetero
private java.util.Map<java.lang.String,javajs.util.Lst<java.lang.Object[]>> htBondMap
private java.util.Map<java.lang.String,javajs.util.BS> assemblyIdAtoms
private int thisChain
private int modelIndex
private javajs.util.P3 chainSum
private int[] chainAtomCount
private boolean isLigandBondBug
javajs.util.M4 mident
private boolean requiresSorting
private static final byte OPER_ID
private static final byte OPER_XYZ
private static final java.lang.String FAMILY_NCS_CAT
private static final java.lang.String FAMILY_NCS
private static final java.lang.String[] ncsoperFields
private static final java.lang.String FAMILY_OPER_CAT
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_CAT
private static final java.lang.String[] assemblyFields
private static final java.lang.String FAMILY_SEQUENCEDIF_CAT
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 CHEM_COMP_ID
private static final byte CHEM_COMP_NAME
private static final java.lang.String FAMILY_CHEMCOMP_CAT
private static final java.lang.String[] chemCompFields
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 FAMILY_STRUCTCONF_CAT
private static final java.lang.String FAMILY_STRUCTCONF
private static final java.lang.String[] structConfFields
private static final byte SHEET_ID
private static final byte STRAND_ID
private static final java.lang.String FAMILY_SHEET_CAT
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_CAT
private static final java.lang.String FAMILY_STRUCSITE
private static final java.lang.String[] structSiteFields
private static final byte STRUCT_CONN_ASYM1
private static final byte STRUCT_CONN_SEQ1
private static final byte STRUCT_CONN_COMP1
private static final byte STRUCT_CONN_ATOM1
private static final byte STRUCT_CONN_ALT1
private static final byte STRUCT_CONN_SYMM1
private static final byte STRUCT_CONN_ASYM2
private static final byte STRUCT_CONN_SEQ2
private static final byte STRUCT_CONN_COMP2
private static final byte STRUCT_CONN_ATOM2
private static final byte STRUCT_CONN_ALT2
private static final byte STRUCT_CONN_SYMM2
private static final byte STRUCT_CONN_TYPE
private static final byte STRUCT_CONN_ORDER
private static final java.lang.String FAMILY_STRUCTCONN_CAT
private static final java.lang.String FAMILY_STRUCTCONN
private static final java.lang.String[] structConnFields
private javajs.util.Lst<java.lang.Object[]> structConnMap
private java.lang.String structConnList
private boolean doSetBonds
private static final byte CHEM_COMP_BOND_ID
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_CAT
private static final java.lang.String FAMILY_COMPBOND
private static final java.lang.String[] chemCompBondFields
private java.lang.String modelStrings
protected boolean done
protected void initSubclass()
initSubclass
in class CifReader
protected void processSubclassEntry() throws java.lang.Exception
processSubclassEntry
in class CifReader
java.lang.Exception
protected boolean processSubclassLoopBlock() throws java.lang.Exception
processSubclassLoopBlock
in class CifReader
java.lang.Exception
protected void sortAssemblyModels()
protected boolean finalizeSubclass() throws java.lang.Exception
finalizeSubclass
in class CifReader
java.lang.Exception
protected boolean checkSubclassSymmetry()
checkSubclassSymmetry
in class CifReader
private void setBonds()
private void processBonds(javajs.util.Lst<java.lang.Object[]> cmap, java.util.Map<java.lang.Object,java.lang.Integer> map, boolean isStructConn)
private boolean processSequence() throws java.lang.Exception
java.lang.Exception
private boolean processAssemblyGenBlock() throws java.lang.Exception
java.lang.Exception
protected void addAssembly(java.lang.String[] assem) throws java.lang.Exception
java.lang.Exception
protected void checkFilterAssembly(java.lang.String id, java.util.Map<java.lang.String,java.lang.Object> info)
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(boolean isNCS) throws java.lang.Exception
java.lang.Exception
protected void addMatrix(java.lang.String id, javajs.util.M4 m4, boolean isNCS)
private boolean processChemCompLoopBlock() throws java.lang.Exception
java.lang.Exception
protected void addHetero(java.lang.String groupName, java.lang.String hetName, boolean doCheck, boolean addNote)
private boolean processStructConfLoopBlock() throws java.lang.Exception
java.lang.Exception
private void addStructure(Structure structure)
private boolean processStructSheetRangeLoopBlock() throws java.lang.Exception
java.lang.Exception
private boolean processStructSiteBlock() throws java.lang.Exception
java.lang.Exception
private void setBiomolecules()
private int setBiomolecule(java.util.Map<java.lang.String,java.lang.Object> biomolecule, javajs.util.BS bsAll)
private void createParticle(java.lang.String id)
private javajs.util.M4 getOpMatrix(java.lang.String ops)
private boolean processStructConnLoopBlock() throws java.lang.Exception
java.lang.Exception
private boolean processCompBondLoopBlock() 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 int checkPDBModelField(int modelField, int currentModelNo) throws java.lang.Exception
checkPDBModelField
in class CifReader
java.lang.Exception
protected int incrementModel(int modelNo) throws java.lang.Exception
java.lang.Exception
private void setHetero()