org.jmol.adapter.readers.cifpdb
Class PdbReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by 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()

Field Summary
(package private)  int atomCount
           
(package private)  java.util.Vector biomolecules
           
(package private)  java.util.Vector biomts
           
(package private)  int[] chainAtomCounts
           
(package private)  java.lang.String compnd
           
(package private)  java.lang.String currentGroup3
           
protected  java.lang.String fileType
           
(package private)  boolean haveMappedSerials
           
(package private)  java.util.Hashtable htElementsInCurrentGroup
           
(package private)  java.util.Hashtable htFormul
           
(package private)  java.util.Hashtable htHetero
           
(package private)  java.util.Hashtable htSites
           
(package private)  boolean isNMRdata
           
(package private)  java.lang.String lastAtomData
           
(package private)  int lastAtomIndex
           
(package private)  int lineLength
           
private static java.lang.String lineOptions
           
(package private)  int maxSerial
           
 
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
 
Constructor Summary
PdbReader()
           
 
Method Summary
(package private)  void anisou()
           
 void applySymmetry()
           
(package private)  void atom()
           
private  void compnd()
           
(package private)  void conect()
           
(package private)  void cryst1()
           
(package private)  java.lang.String deduceElementSymbol(boolean isHetero)
           
(package private)  void expdta()
           
(package private)  void formul()
           
(package private)  float getFloat(int ich, int cch)
           
private  int getModelNumber()
           
private  void header()
           
(package private)  void het()
           
(package private)  void hetnam()
           
(package private)  void model(int modelNumber)
           
 AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
           
protected  float readBFactor()
           
protected  int readOccupancy()
           
protected  float readPartialCharge()
           
protected  float readRadius()
           
private  void remark350()
           
(package private)  void scale(int n)
           
private  void setBiomoleculeAtomCounts()
           
private  void site()
           
(package private)  void structure()
           
 
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
 

Field Detail

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
Constructor Detail

PdbReader

public PdbReader()
Method Detail

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