org.jmol.adapter.readers.cifpdb

Class PdbReader

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
intatomCount
Vectorbiomolecules
Vectorbiomts
int[]chainAtomCounts
Stringcompnd
StringcurrentGroup3
protected StringfileType
booleanhaveMappedSerials
HashtablehtElementsInCurrentGroup
HashtablehtFormul
HashtablehtHetero
HashtablehtSites
booleanisNMRdata
StringlastAtomData
intlastAtomIndex
intlineLength
static StringlineOptions
intmaxSerial
Method Summary
voidanisou()
voidapplySymmetry()
voidatom()
voidcompnd()
voidconect()
voidcryst1()
mth 2004 02 28 note that the pdb spec says: COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------- 1 - 6 Record name "MODEL " 11 - 14 Integer serial Model serial number. but I received a file with the serial number right after the word MODEL :-(
StringdeduceElementSymbol(boolean isHetero)
voidexpdta()
voidformul()
floatgetFloat(int ich, int cch)
intgetModelNumber()
voidheader()
voidhet()
voidhetnam()
voidmodel(int modelNumber)
AtomSetCollectionreadAtomSetCollection(BufferedReader reader)
protected floatreadBFactor()
read the occupancy from cols 55-60 (1-based) should be in the range 0.00 - 1.00
protected intreadOccupancy()
protected floatreadPartialCharge()
read the bfactor from cols 61-66 (1-based)
protected floatreadRadius()
voidremark350()
voidscale(int n)
voidsetBiomoleculeAtomCounts()
voidsite()
voidstructure()

Field Detail

atomCount

int atomCount

biomolecules

Vector biomolecules

biomts

Vector biomts

chainAtomCounts

int[] chainAtomCounts

compnd

String compnd

currentGroup3

String currentGroup3

fileType

protected String fileType

haveMappedSerials

boolean haveMappedSerials

htElementsInCurrentGroup

Hashtable htElementsInCurrentGroup

htFormul

final Hashtable htFormul

htHetero

Hashtable htHetero

htSites

Hashtable htSites

isNMRdata

boolean isNMRdata

lastAtomData

String lastAtomData

lastAtomIndex

int lastAtomIndex

lineLength

int lineLength

lineOptions

private static final String lineOptions

maxSerial

int maxSerial

Method Detail

anisou

void anisou()

applySymmetry

public void applySymmetry()

atom

void atom()

compnd

private void compnd()

conect

void conect()

cryst1

void cryst1()
mth 2004 02 28 note that the pdb spec says: COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------- 1 - 6 Record name "MODEL " 11 - 14 Integer serial Model serial number. but I received a file with the serial number right after the word MODEL :-(

deduceElementSymbol

String deduceElementSymbol(boolean isHetero)

expdta

void expdta()

formul

void formul()

getFloat

float getFloat(int ich, int cch)

getModelNumber

private int getModelNumber()

header

private void header()

het

void het()

hetnam

void hetnam()

model

void model(int modelNumber)

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(BufferedReader reader)

readBFactor

protected float readBFactor()
read the occupancy from cols 55-60 (1-based) should be in the range 0.00 - 1.00

readOccupancy

protected int readOccupancy()

readPartialCharge

protected float readPartialCharge()
read the bfactor from cols 61-66 (1-based)

readRadius

protected float readRadius()

remark350

private void remark350()

scale

void scale(int n)

setBiomoleculeAtomCounts

private void setBiomoleculeAtomCounts()

site

private void site()

structure

void structure()