org.jmol.adapter.readers.cifpdb
public class PdbReader extends AtomSetCollectionReader
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 |
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PdbReader() |
Modifier and Type | Method and Description |
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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 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 String currentGroup3
private int currentResno
private int maxSerial
private int[] chainAtomCounts
private int nUNK
private int nRes
private boolean isMultiModel
private static final String lineOptions
private int serial
private StringBuffer pdbHeader
private int configurationPtr
private boolean applySymmetry
private boolean isConnectStateBug
private String currentKey
private boolean resetKey
private String compnd
private int atomCount
private String lastAtomData
private int lastAtomIndex
private int iAtom
private int lastGroup
private char lastInsertion
private char lastAltLoc
private int conformationIndex
private StringBuffer sbIgnored
private StringBuffer sbSelected
private StringBuffer sbConect
private StringBuffer sb
private int lastSourceSerial
private int lastTargetSerial
private boolean haveDoubleBonds
private boolean haveMappedSerials
protected void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
protected void finalizeReader() throws Exception
finalizeReader
in class AtomSetCollectionReader
Exception
private void header()
private void title()
private void compndSource(boolean isSource)
private void compndOld()
private void setBiomoleculeAtomCounts()
private void atom(int serial)
protected boolean filterAtom(Atom atom, int iAtom)
filterAtom
in class AtomSetCollectionReader
protected void setAdditionalAtomParameters(Atom atom)
atom
- private String deduceElementSymbol(boolean isHetero)
isHetero
- private void conect()
private void structure()
private int getModelNumber()
private void model(int modelNumber)
private void checkNotPDB()
private void expdta()
private void formul()
private void het()
private void hetnam()
private void anisou()
private void site()