public static void calculateDsspSecondaryStructure ( Structure bioJavaStruct ) { SecStrucCalc ssp = new SecStrucCalc ( ) ; try { ssp . calculate ( bioJavaStruct , true ) ; } catch ( StructureException e ) { LOGGER . warn ( "Could not calculate secondary structure (error {}). Will try to get a DSSP file from the RCSB web server instead." , e . getMessage ( ) ) ; try { DSSPParser . fetch ( bioJavaStruct . getPDBCode ( ) , bioJavaStruct , true ) ; //download from PDB the DSSP result } catch ( Exception bige ) { LOGGER . warn ( "Could not get a DSSP file from RCSB web server. There will not be secondary structure assignment for this structure ({}). Error: {}" , bioJavaStruct . getPDBCode ( ) , bige . getMessage ( ) ) ; } } }
Generate the secondary structure for a Biojava structure object .