org.jmol.adapter.readers.more

Class Mol2Reader

public class Mol2Reader extends AtomSetCollectionReader

A minimal multi-file reader for TRIPOS SYBYL mol2 files.

http://www.tripos.com/data/support/mol2.pdf PDB note: Note that mol2 format of PDB files is quite minimal. All we get is the PDB atom name, coordinates, residue number, and residue name No chain terminator, not chain designator, no element symbol. Chains based on numbering reset just labeled A B C D .... Z a b c d .... z Element symbols based on reasoned guess and properties of hetero groups So this is just a hack -- trying to guess at all of these.

Field Summary
intatomCount
charchainID
booleanisPDB
intlastSequenceNumber
intnAtoms
Method Summary
static StringdeduceElementSymbol(boolean isHetero, String XX, String group3)
voidprocessMolecule()
voidreadAtoms(int atomCount, boolean iHaveCharges)
AtomSetCollectionreadAtomSetCollection(BufferedReader reader)
voidreadBonds(int bondCount)
voidreadCrystalInfo()
voidreadResInfo(int resCount)

Field Detail

atomCount

private int atomCount

chainID

private char chainID

isPDB

private boolean isPDB

lastSequenceNumber

private int lastSequenceNumber

nAtoms

private int nAtoms

Method Detail

deduceElementSymbol

private static String deduceElementSymbol(boolean isHetero, String XX, String group3)

processMolecule

private void processMolecule()

readAtoms

private void readAtoms(int atomCount, boolean iHaveCharges)

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(BufferedReader reader)

readBonds

private void readBonds(int bondCount)

readCrystalInfo

private void readCrystalInfo()

readResInfo

private void readResInfo(int resCount)