SpliceSegment.hh

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//
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file protocols/protein_interface_design/movers/SpliceSegment.hh
/// @author Sarel Fleishman

#ifndef INCLUDED_protocols_protein_interface_design_movers_SpliceSegment_hh
#define INCLUDED_protocols_protein_interface_design_movers_SpliceSegment_hh
#include <protocols/protein_interface_design/movers/SpliceSegment.fwd.hh>
#include <core/sequence/SequenceProfile.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>
#include <map>

namespace protocols {
namespace protein_interface_design {
namespace movers {

/* A SpliceSegment is one stretch of residues, which is associated with one or more sequence profiles. SpliceSegment is a class that helps manage these profiles

Two types of input files per splice segment are expected:
pdb-profile match: This file should be formatted as pdb, profile_name:
1y32 L1.1
1y33 L1.1
1ya3 L1.2
.
.
.

Each splice_segment is additionally associated with the sequence profiles mentioned in the pdb-profile match file. These should be
formatted as Rosetta-readable PSSM files*/

///@brief utility class and functions for dealing with sequence profiles for varying segments in Splice
class SpliceSegment : public utility::pointer::ReferenceCount
{
  public:
    SpliceSegment();
    virtual ~SpliceSegment();
    void read_profile( std::string const file_name, std::string const segment_name ); /// read pssm
    void read_pdb_profile( std::string const file_name ); /// read the pdb-profile match from a disk file
    core::sequence::SequenceProfileOP get_profile( std::string const segment_name ); // return the requested sequence profile
    void add_pdb_profile_pair( std::string const pdb, std::string const profile_name ); /// add a sequence profile
    core::sequence::SequenceProfileOP pdb_profile( std::string const pdb_name ); // return a sequence profile according to a pdb file name
    core::sequence::SequenceProfileOP sequence_profile( std::string const profile_name ); // return a sequence profile according to a profile name
  private:
    std::map< std::string/*L1.1*/, core::sequence::SequenceProfileOP > sequence_profile_;
    std::map< std::string/*1y32*/, std::string/*L1.1*/ > pdb_to_profile_map_;
};

/* pose comments
segment_L1 1y32
segment_FR2 1x9q
segment_L2 1jxw
*/

core::sequence::SequenceProfileOP concatenate_profiles( utility::vector1< core::sequence::SequenceProfileOP > const profiles ); // utility function to generate a single concatenated profile from a vector of profiles

} // movers
} // protein_interface_design
} // protocols


#endif /*INCLUDED_protocols_protein_interface_design_movers_Splice_HH*/