javajs.api.GenericLineReader
MMCifReader
public class CifReader extends AtomSetCollectionReader
http://www.iucr.org/iucr-top/cif/ http://www.iucr.org/iucr-top/cif/standard/cifstd5.html
Modifier and Type | Field | Description |
---|---|---|
protected int |
ac |
|
private static byte |
ADP_TYPE |
|
private boolean |
allowRotations |
|
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 static byte |
ASYM_ID |
|
private static byte |
ATOM_ID |
|
private static byte |
ATOM_TYPE_OXIDATION_NUMBER |
|
private static byte |
ATOM_TYPE_SYMBOL |
|
private static java.lang.String[] |
atomFields |
|
private float[] |
atomRadius |
|
private Atom[] |
atoms |
|
private static java.lang.String[] |
atomTypeFields |
|
private java.lang.String |
auditBlockCode |
|
private static byte |
AUTH_ASYM_ID |
|
private static byte |
AUTH_ATOM |
|
private static byte |
AUTH_SEQ_ID |
|
private static byte |
B_ISO |
|
private javajs.util.Lst<java.lang.Object[]> |
bondTypes |
|
private BS |
bsBondDuplicates |
|
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 |
CC_ATOM_CHARGE |
|
private static byte |
CC_ATOM_ID |
|
private static byte |
CC_ATOM_SYM |
|
private static byte |
CC_ATOM_X |
|
private static byte |
CC_ATOM_X_IDEAL |
|
private static byte |
CC_ATOM_Y |
|
private static byte |
CC_ATOM_Y_IDEAL |
|
private static byte |
CC_ATOM_Z |
|
private static byte |
CC_ATOM_Z_IDEAL |
|
private static byte |
CC_COMP_ID |
|
private static byte |
CCDC_GEOM_BOND_TYPE |
|
private java.lang.String |
chemicalName |
|
private static byte |
CITATION_TITLE |
|
private static java.lang.String[] |
citationFields |
|
(package private) int[] |
col2key |
|
private static byte |
COMP_ID |
|
private int |
configurationPtr |
|
private int |
conformationIndex |
|
(package 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 |
|
protected static java.lang.String |
FAMILY_ATOM |
|
private static java.lang.String |
FAMILY_SGOP |
|
(package private) java.lang.String |
field |
|
private boolean |
filterAssembly |
|
private int |
firstAtom |
|
protected 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 |
|
(package private) boolean |
haveCellWaveVector |
|
(package private) boolean |
haveHAtoms |
|
private java.util.Hashtable<java.lang.String,java.lang.Object> |
htAudit |
|
private java.util.Map<java.lang.String,java.lang.String> |
htCellTypes |
|
protected java.util.Map<java.lang.String,java.lang.String> |
htGroup1 |
|
private java.util.Map<java.lang.String,java.lang.Float> |
htOxStates |
|
protected boolean |
iHaveDesiredModel |
|
private static byte |
INS_CODE |
|
protected boolean |
isCourseGrained |
|
protected boolean |
isLigand |
|
private boolean |
isLoop |
|
(package private) boolean |
isMagCIF |
|
protected boolean |
isMMCIF |
|
(package private) java.lang.String |
key |
|
(package private) java.lang.String |
key0 |
|
(package private) int[] |
key2col |
|
private static byte |
LABEL |
|
private char |
lastAltLoc |
|
protected java.lang.String |
lastDataSetName |
|
private java.lang.String |
lastDisorderAssembly |
|
private java.lang.String |
lastSpaceGroupName |
|
private java.lang.String |
latticeType |
|
private javajs.util.Lst<float[]> |
lattvecs |
|
private javajs.util.Lst<java.lang.String> |
magCenterings |
|
protected int |
maxSerial |
|
private int |
modDim |
|
private static byte |
MODEL_NO |
|
java.util.Map<java.lang.String,java.lang.Integer> |
modelMap |
|
private boolean |
modulated |
|
private java.lang.String |
molecularType |
|
private static byte |
MOMENT_LABEL |
|
private static byte |
MOMENT_PRELIM_X |
|
private static byte |
MOMENT_PRELIM_Y |
|
private static byte |
MOMENT_PRELIM_Z |
|
private static byte |
MOMENT_X |
|
private static byte |
MOMENT_Y |
|
private static byte |
MOMENT_Z |
|
private MSCifRdr |
mr |
|
protected int |
nAtoms |
|
protected int |
nAtoms0 |
|
private int |
nMolecular |
|
protected static byte |
NONE |
|
private static byte |
OCCUPANCY |
|
(package private) javajs.api.GenericCifDataParser |
parser |
|
private javajs.util.P3 |
ptOffset |
|
private boolean |
readIdeal |
|
private static byte |
SEQ_ID |
|
private static java.lang.String |
singleAtomID |
|
private static byte |
SITE_MULT |
|
protected boolean |
skipping |
|
private static byte |
SUBSYS_ID |
|
private static byte |
SYM_EQ_XYZ |
|
private static byte |
SYM_MAGN_CENTERING |
|
private static byte |
SYM_MAGN_REV |
|
private static byte |
SYM_MAGN_REV_PRELIM |
|
private static byte |
SYM_MAGN_SSG_ALG |
|
private static byte |
SYM_MAGN_SSG_CENT_XYZ |
|
private static byte |
SYM_MAGN_SSG_CENTERING |
|
private static byte |
SYM_MAGN_SSG_REV |
|
private static byte |
SYM_MAGN_XYZ |
|
private static byte |
SYM_SSG_ALG |
|
private static byte |
SYM_SSG_EQ_XYZ |
|
private static byte |
SYM_XYZ |
|
private static java.lang.String[] |
symmetryOperationsFields |
|
private javajs.util.Lst<java.lang.String> |
symops |
|
private static byte |
THERMAL_TYPE |
|
protected java.lang.String |
thisDataSetName |
|
private java.lang.String |
thisFormula |
|
private java.lang.String |
thisStructuralFormula |
|
private int |
titleAtomSet |
|
private static java.lang.String |
titleRecords |
|
private static java.lang.String[] |
TransformFields |
|
private static byte |
TYPE_SYMBOL |
|
private static byte |
U_ISO_OR_EQUIV |
|
protected boolean |
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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor | Description |
---|---|
CifReader() |
Modifier and Type | Method | Description |
---|---|---|
private void |
addCellType(java.lang.String type,
java.lang.String data,
boolean isFrom) |
|
protected void |
addHeader() |
|
private void |
addLatticeVectors() |
|
private void |
addModelTitle(java.lang.String key) |
|
private void |
addMore() |
|
private void |
addNewBond(int i,
int j,
int order) |
add the bond and mark it for molecular processing
|
void |
applySymmetryAndSetTrajectory() |
|
protected boolean |
checkAllFieldsPresent(java.lang.String[] keys,
int lastKey,
boolean critical) |
|
private boolean |
checkBondDistance(Atom a,
Atom b,
float distance,
float dx) |
|
protected int |
checkPDBModelField(int modelField,
int currentModelNo) |
|
protected boolean |
checkSubclassSymmetry() |
|
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.
|
void |
doPreSymmetry() |
|
protected int |
fieldProperty(int i) |
|
protected boolean |
filterCIFAtom(Atom atom,
java.lang.String componentId) |
|
protected boolean |
finalizeSubclass() |
|
protected void |
finalizeSubclassReader() |
optional reader-specific method run first.
|
protected void |
finalizeSubclassSymmetry(boolean haveSymmetry) |
|
private void |
fixAtomForBonding(javajs.util.P3 pt,
int i) |
|
int |
getBondOrder(java.lang.String field) |
|
private boolean |
getData() |
|
protected java.lang.String |
getField(byte type) |
|
private MSCifRdr |
getModulationReader() |
|
private MSCifRdr |
initializeMSCIF() |
|
void |
initializeReader() |
|
protected void |
initSubclass() |
|
protected boolean |
isNull(java.lang.String key) |
|
protected void |
newModel(int modelNo) |
|
protected void |
nextAtomSet() |
|
(package private) void |
parseLoopParameters(java.lang.String[] fields) |
sets up arrays and variables for tokenizer.getData()
|
(package private) void |
parseLoopParametersFor(java.lang.String key,
java.lang.String[] fields) |
|
(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 java.lang.String |
processChemicalInfo(java.lang.String type) |
reads some of the more interesting info into specific atomSetAuxiliaryInfo
elements
|
private void |
processCitationListBlock() |
|
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.
|
protected void |
processLoopBlock() |
processes loop_ blocks of interest or skips the data
|
protected boolean |
processSubclassAtom(Atom atom,
java.lang.String assemblyId,
java.lang.String strChain) |
|
protected void |
processSubclassEntry() |
|
protected boolean |
processSubclassLoopBlock() |
|
private void |
processSymmetryOperationsLoopBlock() |
retrieves symmetry operations
|
private void |
processSymmetrySpaceGroupName() |
done by AtomSetCollectionReader
|
private void |
processUnitCellTransform() |
|
private void |
processUnitCellTransformMatrix() |
the PDB transformation matrix cartesian --> fractional
|
private boolean |
readAllData() |
|
private void |
readCifData() |
|
private void |
readSingleAtom() |
No need for anything other than the atom name and symbol; coordinates will
be (0 0 0), and no other information is needed.
|
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
asc.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
|
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, 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
private static final java.lang.String titleRecords
private MSCifRdr mr
javajs.api.GenericCifDataParser parser
private boolean filterAssembly
private boolean allowRotations
private boolean readIdeal
private int configurationPtr
protected boolean useAuthorChainID
protected java.lang.String thisDataSetName
protected java.lang.String lastDataSetName
private java.lang.String chemicalName
private java.lang.String thisStructuralFormula
private java.lang.String thisFormula
protected boolean iHaveDesiredModel
protected boolean isMMCIF
protected boolean isLigand
boolean isMagCIF
boolean haveHAtoms
private java.lang.String molecularType
private char lastAltLoc
private boolean haveAromatic
private int conformationIndex
private int nMolecular
private java.lang.String appendedData
protected boolean skipping
protected int nAtoms
protected int ac
private java.lang.String auditBlockCode
private java.lang.String lastSpaceGroupName
private boolean modulated
protected boolean isCourseGrained
boolean haveCellWaveVector
private java.lang.String latticeType
private int modDim
protected java.util.Map<java.lang.String,java.lang.String> htGroup1
protected int nAtoms0
private int titleAtomSet
private java.util.Map<java.lang.String,java.lang.String> htCellTypes
public java.util.Map<java.lang.String,java.lang.Integer> modelMap
private java.util.Hashtable<java.lang.String,java.lang.Object> htAudit
private javajs.util.Lst<java.lang.String> symops
private static final java.lang.String[] TransformFields
java.lang.String key
java.lang.String key0
java.lang.String data
private boolean isLoop
int[] col2key
int[] key2col
java.lang.String field
protected char firstChar
private java.util.Map<java.lang.String,java.lang.Float> htOxStates
private javajs.util.Lst<java.lang.Object[]> bondTypes
private java.lang.String disorderAssembly
private java.lang.String lastDisorderAssembly
private javajs.util.Lst<float[]> lattvecs
private javajs.util.Lst<java.lang.String> magCenterings
protected int maxSerial
private static final byte ATOM_TYPE_SYMBOL
private static final byte ATOM_TYPE_OXIDATION_NUMBER
private static final java.lang.String[] atomTypeFields
protected 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 AUTH_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 CC_COMP_ID
private static final byte CC_ATOM_ID
private static final byte CC_ATOM_SYM
private static final byte CC_ATOM_CHARGE
private static final byte CC_ATOM_X
private static final byte CC_ATOM_Y
private static final byte CC_ATOM_Z
private static final byte CC_ATOM_X_IDEAL
private static final byte CC_ATOM_Y_IDEAL
private static final byte CC_ATOM_Z_IDEAL
private static final byte DISORDER_ASSEMBLY
private static final byte ASYM_ID
private static final byte SUBSYS_ID
private static final byte SITE_MULT
private static final byte THERMAL_TYPE
private static final byte MOMENT_LABEL
private static final byte MOMENT_PRELIM_X
private static final byte MOMENT_PRELIM_Y
private static final byte MOMENT_PRELIM_Z
private static final byte MOMENT_X
private static final byte MOMENT_Y
private static final byte MOMENT_Z
private static final byte ATOM_ID
private static final byte SEQ_ID
protected static final java.lang.String FAMILY_ATOM
private static final java.lang.String[] atomFields
private static final java.lang.String singleAtomID
private static final byte CITATION_TITLE
private static final java.lang.String[] citationFields
private static final byte SYM_XYZ
private static final byte SYM_MAGN_XYZ
private static final byte SYM_SSG_ALG
private static final byte SYM_MAGN_SSG_ALG
private static final byte SYM_EQ_XYZ
private static final byte SYM_SSG_EQ_XYZ
private static final byte SYM_MAGN_REV
private static final byte SYM_MAGN_SSG_REV
private static final byte SYM_MAGN_REV_PRELIM
private static final byte SYM_MAGN_CENTERING
private static final byte SYM_MAGN_SSG_CENTERING
private static final byte SYM_MAGN_SSG_CENT_XYZ
private static final java.lang.String FAMILY_SGOP
private static final java.lang.String[] symmetryOperationsFields
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 float[] atomRadius
private BS[] bsConnected
private BS[] bsSets
private final javajs.util.P3 ptOffset
private BS bsMolecule
private BS bsExclude
private int firstAtom
private Atom[] atoms
private BS bsBondDuplicates
public void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected void initSubclass()
private void readCifData() throws java.lang.Exception
java.lang.Exception
private boolean readAllData() throws java.lang.Exception
java.lang.Exception
private void addModelTitle(java.lang.String key)
protected void processSubclassEntry() throws java.lang.Exception
java.lang.Exception
private void processUnitCellTransform()
private void addCellType(java.lang.String type, java.lang.String data, boolean isFrom)
private void readSingleAtom()
private MSCifRdr getModulationReader() throws java.lang.Exception
java.lang.Exception
private MSCifRdr initializeMSCIF() throws java.lang.Exception
java.lang.Exception
protected void newModel(int modelNo) throws java.lang.Exception
java.lang.Exception
protected void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
protected void addHeader()
protected boolean finalizeSubclass() throws java.lang.Exception
java.lang.Exception
public void doPreSymmetry() throws java.lang.Exception
doPreSymmetry
in class AtomSetCollectionReader
java.lang.Exception
public void applySymmetryAndSetTrajectory() throws java.lang.Exception
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeSubclassSymmetry(boolean haveSymmetry) throws java.lang.Exception
finalizeSubclassSymmetry
in class AtomSetCollectionReader
java.lang.Exception
private void processDataParameter()
protected 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 addLatticeVectors()
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
protected void processLoopBlock() throws java.lang.Exception
java.lang.Exception
protected boolean processSubclassLoopBlock() throws java.lang.Exception
java.lang.Exception
private void addMore()
protected int fieldProperty(int i)
void parseLoopParameters(java.lang.String[] fields) throws java.lang.Exception
fields
- java.lang.Exception
void parseLoopParametersFor(java.lang.String key, java.lang.String[] fields) throws java.lang.Exception
java.lang.Exception
private void disableField(int fieldIndex)
fieldIndex
- private void processAtomTypeLoopBlock() throws java.lang.Exception
java.lang.Exception
boolean processAtomSiteLoopBlock(boolean isLigand) throws java.lang.Exception
isLigand
- java.lang.Exception
protected int checkPDBModelField(int modelField, int currentModelNo) throws java.lang.Exception
modelField
- currentModelNo
- java.lang.Exception
protected boolean processSubclassAtom(Atom atom, java.lang.String assemblyId, java.lang.String strChain)
atom
- assemblyId
- strChain
- protected boolean filterCIFAtom(Atom atom, java.lang.String componentId)
private void processCitationListBlock() throws java.lang.Exception
java.lang.Exception
private void processSymmetryOperationsLoopBlock() throws java.lang.Exception
java.lang.Exception
public int getBondOrder(java.lang.String field)
private void processGeomBondLoopBlock() throws java.lang.Exception
java.lang.Exception
private void setBondingAndMolecules()
private void fixAtomForBonding(javajs.util.P3 pt, int i)
private boolean createBonds(boolean doInit)
doInit
- private void addNewBond(int i, int j, int order)
i
- j
- order
- private void setBs(Atom[] atoms, int iatom, BS[] bsBonds, BS bs)
atoms
- iatom
- bsBonds
- bs
- protected boolean checkSubclassSymmetry()
protected boolean checkAllFieldsPresent(java.lang.String[] keys, int lastKey, boolean critical)
protected java.lang.String getField(byte type)
protected boolean isNull(java.lang.String key)