public class PdbReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private boolean |
applySymmetry |
private int |
atomCount |
private java.util.List<java.util.Map<java.lang.String,java.lang.Object>> |
biomolecules |
private java.util.List<javax.vecmath.Matrix4f> |
biomts |
private int[] |
chainAtomCounts |
private java.lang.String |
compnd |
private int |
configurationPtr |
private int |
conformationIndex |
private java.util.Map<java.lang.String,java.lang.String> |
currentCompnd |
private java.lang.String |
currentGroup3 |
private java.lang.String |
currentKey |
private int |
currentResno |
private boolean |
haveDoubleBonds |
private boolean |
haveMappedSerials |
private java.util.Map<java.lang.String,java.lang.Boolean> |
htElementsInCurrentGroup |
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Boolean>> |
htFormul |
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.String>> |
htMolIds |
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Object>> |
htSites |
private int |
iAtom |
private boolean |
isConnectStateBug |
private boolean |
isMultiModel |
private char |
lastAltLoc |
private java.lang.String |
lastAtomData |
private int |
lastAtomIndex |
private int |
lastGroup |
private char |
lastInsertion |
private int |
lastSourceSerial |
private int |
lastTargetSerial |
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 |
sb |
private java.lang.StringBuffer |
sbConect |
private java.lang.StringBuffer |
sbIgnored |
private java.lang.StringBuffer |
sbSelected |
private int |
serial |
private java.util.List<java.util.Map<java.lang.String,java.lang.String>> |
vCompnds |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
PdbReader() |
Modifier and Type | Method and Description |
---|---|
private void |
anisou() |
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)
The problem here stems from the fact that developers have not fully
understood the PDB specifications -- and that those have changed.
|
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) |
private void |
remark290() |
private void |
remark350() |
private void |
scale(int n) |
protected void |
setAdditionalAtomParameters(Atom atom)
adaptable via subclassing
|
private void |
setBiomoleculeAtomCounts() |
private void |
site() |
private void |
structure() |
private void |
title() |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, 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, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private int lineLength
private final java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Boolean>> htFormul
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 java.lang.String currentGroup3
private int currentResno
private java.util.Map<java.lang.String,java.lang.Boolean> 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 boolean applySymmetry
private boolean isConnectStateBug
private java.util.List<java.util.Map<java.lang.String,java.lang.String>> vCompnds
private java.util.Map<java.lang.String,java.lang.String> currentCompnd
private java.lang.String currentKey
private java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.String>> htMolIds
private boolean resetKey
private java.lang.String compnd
private java.util.List<java.util.Map<java.lang.String,java.lang.Object>> biomolecules
private java.util.List<javax.vecmath.Matrix4f> 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
private java.lang.StringBuffer sbIgnored
private java.lang.StringBuffer sbSelected
private java.lang.StringBuffer sbConect
private java.lang.StringBuffer sb
private int lastSourceSerial
private int lastTargetSerial
private boolean haveDoubleBonds
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
private void header()
private void title()
private void compndSource(boolean isSource)
private void compndOld()
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 void setAdditionalAtomParameters(Atom atom)
atom
- private java.lang.String deduceElementSymbol(boolean isHetero)
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()