public static final List < String > getPDBresnum ( int aligPos , AFPChain afpChain , Atom [ ] ca ) { List < String > lst = new ArrayList < String > ( ) ; if ( aligPos > 1 ) { System . err . println ( "multiple alignments not supported yet!" ) ; return lst ; } int blockNum = afpChain . getBlockNum ( ) ; int [ ] optLen = afpChain . getOptLen ( ) ; int [ ] [ ] [ ] optAln = afpChain . getOptAln ( ) ; if ( optLen == null ) return lst ; for ( int bk = 0 ; bk < blockNum ; bk ++ ) { for ( int i = 0 ; i < optLen [ bk ] ; i ++ ) { int pos = optAln [ bk ] [ aligPos ] [ i ] ; if ( pos < ca . length ) { String pdbInfo = JmolTools . getPdbInfo ( ca [ pos ] ) ; //lst.add(ca1[pos].getParent().getPDBCode()); lst . add ( pdbInfo ) ; } } } return lst ; }
Return a list of pdb Strings corresponding to the aligned positions of the molecule . Only supports a pairwise alignment with the AFPChain DS .