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SpliceSegment.hh File Reference
#include <protocols/splice/SpliceSegment.fwd.hh>
#include <protocols/splice/Splice.fwd.hh>
#include <core/sequence/SequenceProfile.fwd.hh>
#include <utility/VirtualBase.hh>
#include <utility/vector1.hh>
#include <map>
#include <core/types.hh>


class  protocols::splice::SpliceSegment
 utility class and functions for dealing with sequence profiles for varying segments in Splice More...


 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.


core::sequence::SequenceProfileOP protocols::splice::concatenate_profiles (utility::vector1< core::sequence::SequenceProfileOP > const &profiles, utility::vector1< std::string > segment_names_ordered, std::string H3_seq)
 generate one long sequence profile out of several sequence-profile segments. More...
std::map< std::string,
std::string > 
protocols::splice::read_H3_seq (std::string const &Protein_family_path)
 Reads from given file the H3 sequences from all PDBs in the db. More...
std::map< std::string,
std::string > 
protocols::splice::read_pdb_seq (std::string const &Protein_family_path)
 in cases where we have only one sequence per pdb we store the sequences in a seperate map we can later use them to create pssms using blosum More...

Detailed Description

Sarel Fleishman