public class CifReader extends AtomSetCollectionReader implements JmolLineReader
http://www.iucr.org/iucr-top/cif/ http://www.iucr.org/iucr-top/cif/standard/cifstd5.html
Modifier and Type | Field and Description |
---|---|
private static byte |
ADP_TYPE |
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 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 |
ASYM_ID |
private static byte |
ATOM_TYPE_OXIDATION_NUMBER |
private static byte |
ATOM_TYPE_SYMBOL |
private int |
atomCount |
private static java.lang.String[] |
atomFields |
private float[] |
atomRadius |
private Atom[] |
atoms |
private static java.lang.String[] |
atomTypeFields |
private java.util.Map<java.lang.String,java.lang.Float> |
atomTypes |
private static byte |
AUTH_ASYM_ID |
private static byte |
AUTH_ATOM |
private static byte |
B_ISO |
private static byte |
BEG_ASYM_ID |
private static byte |
BEG_INS_CODE |
private static byte |
BEG_SEQ_ID |
private JmolList<java.lang.Object[]> |
bondTypes |
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 |
CCDC_GEOM_BOND_TYPE |
private static byte |
CHEM_COMP_AC_CHARGE |
private static byte |
CHEM_COMP_AC_ID |
private static byte |
CHEM_COMP_AC_NAME |
private static byte |
CHEM_COMP_AC_SYM |
private static byte |
CHEM_COMP_AC_X |
private static byte |
CHEM_COMP_AC_X_IDEAL |
private static byte |
CHEM_COMP_AC_Y |
private static byte |
CHEM_COMP_AC_Y_IDEAL |
private static byte |
CHEM_COMP_AC_Z |
private static byte |
CHEM_COMP_AC_Z_IDEAL |
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 java.lang.String |
chemicalName |
private static byte |
COMP_ID |
private static byte |
CONF_TYPE_ID |
private int |
configurationPtr |
private int |
conformationIndex |
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 |
private static byte |
END_ASYM_ID |
private static byte |
END_INS_CODE |
private static byte |
END_SEQ_ID |
(package private) java.lang.String |
field |
private byte[] |
fieldOf |
private boolean |
filterAssembly |
private int |
firstAtom |
private 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 |
private boolean |
haveChainsLC |
private static byte |
HELIX_CLASS |
private java.lang.String[] |
hetatmData
optional nonloop format -- see 1jsa.cif
|
private java.util.Map<java.lang.String,Matrix4f> |
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 |
iHaveDesiredModel |
private boolean |
incommensurate |
private static byte |
INS_CODE |
private boolean |
isMolecular |
private boolean |
isPDB |
protected boolean |
isPDBX |
private java.lang.String |
key |
private static byte |
LABEL |
private char |
lastAltLoc |
private java.lang.String |
lastDisorderAssembly |
private static byte |
MODEL_NO |
private java.lang.String |
molecularType |
private int |
nAtoms |
private int |
nMolecular |
private static byte |
NONE |
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 |
OCCUPANCY |
private static byte |
OPER_ID |
private static byte |
OPER_XYZ |
private static java.lang.String[] |
operFields |
private int |
propertyCount |
private int[] |
propertyOf |
private P3 |
ptOffset |
private static byte |
SEQ_ID |
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 boolean |
skipping |
private static byte |
STRAND_ID |
private static byte |
STRUCT_ID |
private static java.lang.String[] |
structConfFields |
private static java.lang.String[] |
structSheetRangeFields |
private static java.lang.String[] |
structSiteRangeFields |
private static byte |
SYM_EQUIV_XYZ |
private static byte |
SYM_SSG_OP |
private static byte |
SYM_SSG_XYZ |
private static java.lang.String[] |
symmetryOperationsFields |
private static byte |
SYMOP_XYZ |
private java.lang.String |
thisDataSetName |
private java.lang.String |
thisFormula |
private java.lang.String |
thisStructuralFormula |
private CifDataReader |
tokenizer |
private static java.lang.String[] |
TransformFields |
private static byte |
TYPE_SYMBOL |
private static byte |
U_ISO_OR_EQUIV |
private JmolList<java.util.Map<java.lang.String,java.lang.Object>> |
vBiomolecules |
private JmolList<Matrix4f> |
vBiomts |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterAtomTypeStr, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, mustFinalizeModelSet, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
CifReader() |
Modifier and Type | Method and Description |
---|---|
private void |
addAssembly() |
private void |
addHetero(java.lang.String groupName,
java.lang.String hetName) |
private void |
addNewBond(int i,
int j,
int order)
add the bond and mark it for molecular processing
|
void |
applySymmetryAndSetTrajectory() |
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.
|
private int |
fieldProperty(int i) |
protected boolean |
filterCIFAtom(Atom atom,
int iAtom,
char assemblyId) |
protected void |
finalizeReader()
optional reader-specific method run first.
|
private int |
getBondOrder(java.lang.String field) |
private boolean |
getData() |
void |
initializeReader() |
protected void |
initializeReaderCif() |
private static boolean |
isMatch(java.lang.String str1,
java.lang.String str2) |
protected void |
newModel(int modelNo) |
private void |
nextAtomSet() |
private void |
parseLoopParameters(java.lang.String[] fields)
sets up arrays and variables for tokenizer.getData()
|
private void |
processAssemblyGen() |
private void |
processAssemblyGenBlock() |
(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 void |
processChemCompLoopBlock()
a general name definition field.
|
private java.lang.String |
processChemicalInfo(java.lang.String type)
reads some of the more interesting info into specific atomSetAuxiliaryInfo
elements
|
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.
|
private void |
processLigandBondLoopBlock() |
private void |
processLoopBlock()
processes loop_ blocks of interest or skips the data
|
private void |
processNonpolyData() |
private void |
processNonpolyLoopBlock()
a HETERO name definition field.
|
private void |
processStructConfLoopBlock()
identifies ranges for HELIX and TURN
|
private void |
processStructOperListBlock() |
private void |
processStructSheetRangeLoopBlock()
identifies sheet ranges
|
private void |
processStructSiteBlock()
identifies structure sites
|
private void |
processSymmetryOperationsLoopBlock()
retrieves symmetry operations
|
private void |
processSymmetrySpaceGroupName()
done by AtomSetCollectionReader
|
private void |
processUnitCellTransformMatrix()
the PDB transformation matrix cartesian --> fractional
|
private boolean |
readAllData() |
java.lang.String |
readNextLine() |
private void |
setBiomolecules() |
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
atomSetCollection.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
|
private void |
skipLoop()
skips all associated loop data
|
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setLoadNote, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
protected boolean isPDBX
private CifDataReader tokenizer
private java.lang.String thisDataSetName
private java.lang.String chemicalName
private java.lang.String thisStructuralFormula
private java.lang.String thisFormula
private boolean iHaveDesiredModel
private boolean isPDB
private java.util.Map<java.lang.String,java.lang.String> htHetero
private boolean isMolecular
private java.lang.String molecularType
private char lastAltLoc
private int configurationPtr
private int conformationIndex
private boolean filterAssembly
private boolean haveAromatic
private JmolList<java.util.Map<java.lang.String,java.lang.Object>> vBiomolecules
private java.util.Map<java.lang.String,Matrix4f> htBiomts
private java.util.Map<java.lang.String,BS> assemblyIdAtoms
private java.lang.String appendedData
private boolean skipping
private boolean haveChainsLC
private int nAtoms
private int nMolecular
private boolean incommensurate
private static final java.lang.String[] TransformFields
private java.lang.String key
private java.lang.String data
private java.util.Map<java.lang.String,java.lang.Float> atomTypes
private JmolList<java.lang.Object[]> bondTypes
private java.lang.String disorderAssembly
private java.lang.String lastDisorderAssembly
private static final byte ATOM_TYPE_SYMBOL
private static final byte ATOM_TYPE_OXIDATION_NUMBER
private static final java.lang.String[] atomTypeFields
private static final byte NONE
private static final byte TYPE_SYMBOL
private static final byte LABEL
private static final byte AUTH_ATOM
private static final byte FRACT_X
private static final byte FRACT_Y
private static final byte FRACT_Z
private static final byte CARTN_X
private static final byte CARTN_Y
private static final byte CARTN_Z
private static final byte OCCUPANCY
private static final byte B_ISO
private static final byte COMP_ID
private static final byte AUTH_ASYM_ID
private static final byte SEQ_ID
private static final byte INS_CODE
private static final byte ALT_ID
private static final byte GROUP_PDB
private static final byte MODEL_NO
private static final byte DUMMY_ATOM
private static final byte DISORDER_GROUP
private static final byte ANISO_LABEL
private static final byte ANISO_MMCIF_ID
private static final byte ANISO_U11
private static final byte ANISO_U22
private static final byte ANISO_U33
private static final byte ANISO_U12
private static final byte ANISO_U13
private static final byte ANISO_U23
private static final byte ANISO_MMCIF_U11
private static final byte ANISO_MMCIF_U22
private static final byte ANISO_MMCIF_U33
private static final byte ANISO_MMCIF_U12
private static final byte ANISO_MMCIF_U13
private static final byte ANISO_MMCIF_U23
private static final byte U_ISO_OR_EQUIV
private static final byte ANISO_B11
private static final byte ANISO_B22
private static final byte ANISO_B33
private static final byte ANISO_B12
private static final byte ANISO_B13
private static final byte ANISO_B23
private static final byte ANISO_Beta_11
private static final byte ANISO_Beta_22
private static final byte ANISO_Beta_33
private static final byte ANISO_Beta_12
private static final byte ANISO_Beta_13
private static final byte ANISO_Beta_23
private static final byte ADP_TYPE
private static final byte CHEM_COMP_AC_ID
private static final byte CHEM_COMP_AC_NAME
private static final byte CHEM_COMP_AC_SYM
private static final byte CHEM_COMP_AC_CHARGE
private static final byte CHEM_COMP_AC_X
private static final byte CHEM_COMP_AC_Y
private static final byte CHEM_COMP_AC_Z
private static final byte CHEM_COMP_AC_X_IDEAL
private static final byte CHEM_COMP_AC_Y_IDEAL
private static final byte CHEM_COMP_AC_Z_IDEAL
private static final byte DISORDER_ASSEMBLY
private static final byte ASYM_ID
private static final java.lang.String[] atomFields
private static final byte OPER_ID
private static final byte OPER_XYZ
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[] assemblyFields
private java.lang.String[] assem
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[] chemCompBondFields
private static final byte GEOM_BOND_ATOM_SITE_LABEL_1
private static final byte GEOM_BOND_ATOM_SITE_LABEL_2
private static final byte GEOM_BOND_DISTANCE
private static final byte CCDC_GEOM_BOND_TYPE
private static final java.lang.String[] geomBondFields
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 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 byte SHEET_ID
private static final byte STRAND_ID
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[] structSiteRangeFields
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>> htSites
private static final byte SYMOP_XYZ
private static final byte SYM_EQUIV_XYZ
private static final byte SYM_SSG_XYZ
private static final byte SYM_SSG_OP
private static final java.lang.String[] symmetryOperationsFields
java.lang.String field
private char firstChar
private int[] propertyOf
private byte[] fieldOf
private int propertyCount
private float[] atomRadius
private BS[] bsConnected
private BS[] bsSets
private final P3 ptOffset
private BS bsMolecule
private BS bsExclude
private int firstAtom
private int atomCount
private Atom[] atoms
public void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected void initializeReaderCif() throws java.lang.Exception
java.lang.Exception
public java.lang.String readNextLine() throws java.lang.Exception
readNextLine
in interface JmolLineReader
java.lang.Exception
private boolean readAllData() throws java.lang.Exception
java.lang.Exception
protected void newModel(int modelNo) throws java.lang.Exception
java.lang.Exception
protected void finalizeReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeReader
in class AtomSetCollectionReader
java.lang.Exception
private void setBiomolecules()
public void applySymmetryAndSetTrajectory() throws java.lang.Exception
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
java.lang.Exception
private void processDataParameter()
private void nextAtomSet()
private java.lang.String processChemicalInfo(java.lang.String type) throws java.lang.Exception
type
- "name" "formula" etc.java.lang.Exception
private void processSymmetrySpaceGroupName() throws java.lang.Exception
java.lang.Exception
private void processCellParameter() throws java.lang.Exception
java.lang.Exception
private void processUnitCellTransformMatrix() throws java.lang.Exception
java.lang.Exception
private boolean getData() throws java.lang.Exception
java.lang.Exception
private void processLoopBlock() throws java.lang.Exception
java.lang.Exception
private void processAtomTypeLoopBlock() throws java.lang.Exception
java.lang.Exception
boolean processAtomSiteLoopBlock(boolean isLigand) throws java.lang.Exception
isLigand
- java.lang.Exception
protected boolean filterCIFAtom(Atom atom, int iAtom, char assemblyId)
private void processAssemblyGen() throws java.lang.Exception
java.lang.Exception
private void processAssemblyGenBlock() throws java.lang.Exception
java.lang.Exception
private void addAssembly() throws java.lang.Exception
java.lang.Exception
private void processStructOperListBlock() throws java.lang.Exception
java.lang.Exception
private void processLigandBondLoopBlock() throws java.lang.Exception
java.lang.Exception
private int getBondOrder(java.lang.String field)
private void processGeomBondLoopBlock() throws java.lang.Exception
java.lang.Exception
private void processNonpolyData()
private void processChemCompLoopBlock() throws java.lang.Exception
java.lang.Exception
private void processNonpolyLoopBlock() throws java.lang.Exception
java.lang.Exception
private void addHetero(java.lang.String groupName, java.lang.String hetName)
private void processStructConfLoopBlock() throws java.lang.Exception
java.lang.Exception
private void processStructSheetRangeLoopBlock() throws java.lang.Exception
java.lang.Exception
private void processStructSiteBlock() throws java.lang.Exception
java.lang.Exception
private void processSymmetryOperationsLoopBlock() throws java.lang.Exception
java.lang.Exception
private int fieldProperty(int i)
private void parseLoopParameters(java.lang.String[] fields) throws java.lang.Exception
fields
- java.lang.Exception
private void disableField(int fieldIndex)
fieldIndex
- private void skipLoop() throws java.lang.Exception
java.lang.Exception
private static boolean isMatch(java.lang.String str1, java.lang.String str2)
str1
- str2
- private void setBondingAndMolecules()
private boolean createBonds(boolean doInit)
doInit
- private void addNewBond(int i, int j, int order)
i
- j
- order
-