private void setAtomTypes ( IChemObjectBuilder builder ) throws Exception { String name = "" ; String rootType = "" ; int an = 0 ; int rl = 255 ; int gl = 20 ; int bl = 147 ; int maxbond = 0 ; double mass = 0.0 ; st . nextToken ( ) ; String sid = st . nextToken ( ) ; rootType = st . nextToken ( ) ; name = st . nextToken ( ) ; String san = st . nextToken ( ) ; String sam = st . nextToken ( ) ; String smaxbond = st . nextToken ( ) ; try { mass = new Double ( sam ) . doubleValue ( ) ; an = Integer . parseInt ( san ) ; maxbond = Integer . parseInt ( smaxbond ) ; } catch ( NumberFormatException nfe ) { throw new IOException ( "AtomTypeTable.ReadAtypes: " + "Malformed Number" ) ; } IAtomType atomType = builder . newInstance ( IAtomType . class , name , rootType ) ; atomType . setAtomicNumber ( an ) ; atomType . setExactMass ( mass ) ; atomType . setMassNumber ( massNumber ( an , mass ) ) ; atomType . setFormalNeighbourCount ( maxbond ) ; atomType . setSymbol ( rootType ) ; Color co = new Color ( rl , gl , bl ) ; atomType . setProperty ( "org.openscience.cdk.renderer.color" , co ) ; atomType . setAtomTypeName ( sid ) ; atomTypes . add ( atomType ) ; }
Read and stores the atom types in a vector