public static StructureAlignmentJmol display ( AFPChain afpChain , Atom [ ] ca1 , Atom [ ] ca2 ) throws StructureException { if ( ca1 . length < 1 || ca2 . length < 1 ) { throw new StructureException ( "length of atoms arrays is too short! " + ca1 . length + "," + ca2 . length ) ; } Group [ ] twistedGroups = AlignmentTools . prepareGroupsForDisplay ( afpChain , ca1 , ca2 ) ; List < Group > hetatms = StructureTools . getUnalignedGroups ( ca1 ) ; List < Group > hetatms2 = StructureTools . getUnalignedGroups ( ca2 ) ; return DisplayAFP . display ( afpChain , twistedGroups , ca1 , ca2 , hetatms , hetatms2 ) ; }
Display an AFPChain alignment