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
int	atomCount
Vector	biomolecules
Vector	biomts
int[]	chainAtomCounts
String	compnd
String	currentGroup3
protected String	fileType
boolean	haveMappedSerials
Hashtable	htElementsInCurrentGroup
Hashtable	htFormul
Hashtable	htHetero
Hashtable	htSites
boolean	isNMRdata
String	lastAtomData
int	lastAtomIndex
int	lineLength
static String	lineOptions
int	maxSerial

Method Summary
void	anisou()
void	applySymmetry()
void	atom()
void	compnd()
void	conect()
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 :-(
String	deduceElementSymbol(boolean isHetero)
void	expdta()
void	formul()
float	getFloat(int ich, int cch)
int	getModelNumber()
void	header()
void	het()
void	hetnam()
void	model(int modelNumber)
AtomSetCollection	readAtomSetCollection(BufferedReader reader)
protected float	readBFactor() read the occupancy from cols 55-60 (1-based) should be in the range 0.00 - 1.00
protected int	readOccupancy()
protected float	readPartialCharge() read the bfactor from cols 61-66 (1-based)
protected float	readRadius()
void	remark350()
void	scale(int n)
void	setBiomoleculeAtomCounts()
void	site()
void	structure()

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 :-(