org.jmol.adapter.readers.cifpdb
Class PdbReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.cifpdb.PdbReader
- Direct Known Subclasses:
- PqrReader
public class PdbReader
- extends AtomSetCollectionReader
PDB file reader.
http://www.rcsb.org
- Author:
- Miguel, Egon, and Bob (hansonr@stolaf.edu)
symmetry added by Bob Hanson:
setFractionalCoordinates()
setSpaceGroupName()
setUnitCell()
initializeCartesianToFractional();
setUnitCellItem()
setAtomCoord()
applySymmetry()
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
lineLength
int lineLength
isNMRdata
boolean isNMRdata
htFormul
final java.util.Hashtable htFormul
htHetero
java.util.Hashtable htHetero
htSites
java.util.Hashtable htSites
fileType
protected java.lang.String fileType
currentGroup3
java.lang.String currentGroup3
compnd
java.lang.String compnd
htElementsInCurrentGroup
java.util.Hashtable htElementsInCurrentGroup
maxSerial
int maxSerial
chainAtomCounts
int[] chainAtomCounts
lineOptions
private static final java.lang.String lineOptions
- See Also:
- Constant Field Values
biomolecules
java.util.Vector biomolecules
biomts
java.util.Vector biomts
atomCount
int atomCount
lastAtomData
java.lang.String lastAtomData
lastAtomIndex
int lastAtomIndex
haveMappedSerials
boolean haveMappedSerials
PdbReader
public PdbReader()
readAtomSetCollection
public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class AtomSetCollectionReader
header
private void header()
compnd
private void compnd()
setBiomoleculeAtomCounts
private void setBiomoleculeAtomCounts()
remark350
private void remark350()
throws java.lang.Exception
- Throws:
java.lang.Exception
atom
void atom()
readOccupancy
protected int readOccupancy()
readBFactor
protected float readBFactor()
readPartialCharge
protected float readPartialCharge()
readRadius
protected float readRadius()
deduceElementSymbol
java.lang.String deduceElementSymbol(boolean isHetero)
conect
void conect()
structure
void structure()
getModelNumber
private int getModelNumber()
model
void model(int modelNumber)
cryst1
void cryst1()
throws java.lang.Exception
- Throws:
java.lang.Exception
getFloat
float getFloat(int ich,
int cch)
throws java.lang.Exception
- Throws:
java.lang.Exception
scale
void scale(int n)
throws java.lang.Exception
- Throws:
java.lang.Exception
expdta
void expdta()
formul
void formul()
het
void het()
hetnam
void hetnam()
anisou
void anisou()
site
private void site()
applySymmetry
public void applySymmetry()
throws java.lang.Exception
- Overrides:
applySymmetry
in class AtomSetCollectionReader
- Throws:
java.lang.Exception