public class PdbReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
private java.util.List |
biomolecules |
private java.util.List |
biomts |
private int[] |
chainAtomCounts |
(package private) java.lang.String |
compnd |
private int |
configurationPtr |
private int |
conformationIndex |
private java.util.Hashtable |
currentCompnd |
private java.lang.String |
currentGroup3 |
private java.lang.String |
currentKey |
private int |
currentResno |
private boolean |
haveMappedSerials |
private java.util.Hashtable |
htElementsInCurrentGroup |
private java.util.Hashtable |
htFormul |
private java.util.Hashtable |
htHetero |
private java.util.Hashtable |
htMolIds |
private java.util.Hashtable |
htSites |
private int |
iAtom |
private boolean |
isMultiModel |
private char |
lastAltLoc |
private java.lang.String |
lastAtomData |
private int |
lastAtomIndex |
private int |
lastGroup |
private char |
lastInsertion |
private int |
lineLength |
private static java.lang.String |
lineOptions |
private int |
maxSerial |
private int |
nRes |
private int |
nUNK |
private java.lang.StringBuffer |
pdbHeader |
private boolean |
resetKey |
private java.lang.StringBuffer |
sbConect |
(package private) java.lang.StringBuffer |
sbIgnored |
(package private) java.lang.StringBuffer |
sbSelected |
private int |
serial |
private java.util.List |
vCompnds |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
Constructor and Description |
---|
PdbReader() |
Modifier and Type | Method and Description |
---|---|
private void |
anisou() |
void |
applySymmetryAndSetTrajectory() |
private void |
atom(int serial) |
protected boolean |
checkLine() |
private void |
checkNotPDB() |
private void |
compndOld() |
private void |
compndSource(boolean isSource) |
private void |
conect() |
private void |
cryst1() |
private java.lang.String |
deduceElementSymbol(boolean isHetero) |
private void |
expdta() |
protected boolean |
filterAtom(Atom atom,
int iAtom) |
protected void |
finalizeReader() |
private void |
formul() |
private float |
getFloat(int ich,
int cch) |
private int |
getModelNumber() |
private void |
header() |
private void |
het() |
private void |
hetnam() |
protected void |
initializeReader() |
private void |
model(int modelNumber) |
protected float |
readBFactor() |
protected int |
readOccupancy() |
protected float |
readPartialCharge() |
protected float |
readRadius() |
private void |
remark290() |
private void |
remark350() |
private void |
scale(int n) |
private void |
setBiomoleculeAtomCounts() |
private void |
site() |
private void |
structure() |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private int lineLength
private final java.util.Hashtable htFormul
private java.util.Hashtable htHetero
private java.util.Hashtable htSites
private java.lang.String currentGroup3
private int currentResno
private java.util.Hashtable htElementsInCurrentGroup
private int maxSerial
private int[] chainAtomCounts
private int nUNK
private int nRes
private boolean isMultiModel
private static final java.lang.String lineOptions
private int serial
private java.lang.StringBuffer pdbHeader
private int configurationPtr
private java.util.List vCompnds
private java.util.Hashtable currentCompnd
private java.lang.String currentKey
private java.util.Hashtable htMolIds
private boolean resetKey
java.lang.String compnd
private java.util.List biomolecules
private java.util.List biomts
private int atomCount
private java.lang.String lastAtomData
private int lastAtomIndex
private int iAtom
private int lastGroup
private char lastInsertion
private char lastAltLoc
private int conformationIndex
java.lang.StringBuffer sbIgnored
java.lang.StringBuffer sbSelected
private java.lang.StringBuffer sbConect
private boolean haveMappedSerials
protected void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeReader() throws java.lang.Exception
finalizeReader
in class AtomSetCollectionReader
java.lang.Exception
public void applySymmetryAndSetTrajectory() throws java.lang.Exception
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
java.lang.Exception
private void header()
private void compndOld()
private void compndSource(boolean isSource)
private void setBiomoleculeAtomCounts()
private void remark350() throws java.lang.Exception
java.lang.Exception
private void remark290() throws java.lang.Exception
java.lang.Exception
private void atom(int serial)
protected boolean filterAtom(Atom atom, int iAtom)
filterAtom
in class AtomSetCollectionReader
protected int readOccupancy()
protected float readBFactor()
protected float readPartialCharge()
protected float readRadius()
private java.lang.String deduceElementSymbol(boolean isHetero)
private void conect()
private void structure()
private int getModelNumber()
private void model(int modelNumber)
private void checkNotPDB()
private void cryst1() throws java.lang.Exception
java.lang.Exception
private float getFloat(int ich, int cch) throws java.lang.Exception
java.lang.Exception
private void scale(int n) throws java.lang.Exception
java.lang.Exception
private void expdta()
private void formul()
private void het()
private void hetnam()
private void anisou()
private void site()