org.jmol.adapter.readers.more
public class Mol2Reader extends AtomSetCollectionReader
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 | |
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int | atomCount |
char | chainID |
boolean | isPDB |
int | lastSequenceNumber |
int | nAtoms |
Method Summary | |
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static String | deduceElementSymbol(boolean isHetero, String XX, String group3) |
void | processMolecule() |
void | readAtoms(int atomCount, boolean iHaveCharges) |
AtomSetCollection | readAtomSetCollection(BufferedReader reader) |
void | readBonds(int bondCount) |
void | readCrystalInfo() |
void | readResInfo(int resCount) |