private IAtom setAtom ( IAtom atom , String ID ) throws NoSuchAtomTypeException { IAtomType at = null ; String key = "" ; List < ? > data = null ; Double value = null ; at = getAtomType ( ID ) ; if ( atom . getSymbol ( ) == null ) { atom . setSymbol ( at . getSymbol ( ) ) ; } atom . setAtomTypeName ( at . getAtomTypeName ( ) ) ; atom . setFormalNeighbourCount ( at . getFormalNeighbourCount ( ) ) ; key = "vdw" + ID ; data = ( List ) parameterSet . get ( key ) ; value = ( Double ) data . get ( 0 ) ; key = "charge" + ID ; if ( parameterSet . containsKey ( key ) ) { data = ( List ) parameterSet . get ( key ) ; value = ( Double ) data . get ( 0 ) ; atom . setCharge ( value . doubleValue ( ) ) ; } Object color = at . getProperty ( "org.openscience.cdk.renderer.color" ) ; if ( color != null ) { atom . setProperty ( "org.openscience.cdk.renderer.color" , color ) ; } if ( at . getAtomicNumber ( ) != 0 ) { atom . setAtomicNumber ( at . getAtomicNumber ( ) ) ; } if ( at . getExactMass ( ) > 0.0 ) { atom . setExactMass ( at . getExactMass ( ) ) ; } return atom ; }
Assigns an atom type to an atom