org.jmol.adapter.readers.cifpdb
public class PdbReader extends AtomSetCollectionReader
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 | |
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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
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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() |