VallProvider.hh

Go to the documentation of this file.

// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   protocols/frag_picker/VallProvider.hh
/// @brief  reads a vall library and serves the data in chunks
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#ifndef INCLUDED_protocols_frag_picker_VallProvider_hh
#define INCLUDED_protocols_frag_picker_VallProvider_hh

// type headers
#include <core/types.hh>
#include <utility/pointer/ReferenceCount.hh>

// unit headers
#include <protocols/frag_picker/VallProvider.fwd.hh>

// package headers
#include <protocols/frag_picker/VallChunk.hh>

// mini headers
#include <core/sequence/SequenceProfile.hh>
// AUTO-REMOVED #include <utility/vector1.hh>
#include <core/pose/Pose.hh>

// AUTO-REMOVED #include <string>

namespace protocols {
namespace frag_picker {

/// @brief  a vector of vall chunks
class VallProvider: public utility::pointer::ReferenceCount {
public:

  /// @brief
  VallProvider() {
    cached_profile_id_ = "";
    cached_pose_id_ = "";
    largest_chunk_size_ = 0;
  }
  virtual ~VallProvider();

  /// @brief Vall reader
  /// THe defaults should ensure that the file is fully read if startline and endline ar not specified. endline = 0 means read to the end.
  Size vallChunksFromLibrary(std::string const & filename, Size startline = 1, Size endline = 0 );

  Size vallChunksFromLibraries( utility::vector1< std::string > const & fns );

  /// @brief Runs through the Vall and stores number of lines
  Size vallNumLines(std::string const & filename);

  /// @brief says how many chunks do we have
  inline Size size() {
    return chunks_.size();
  }

  /// @brief returns a certain chunk (starts from 1)
  inline VallChunkOP at(Size index) {
    return chunks_.at(index);
  }

  /// @brief adds a new chunk to this provider
  inline void push_back(VallChunkOP what) {
    return chunks_.push_back(what);
  }

  /// @brief says what is the length of the largest chunk known to this
  /// provider
  inline Size get_largest_chunk_size() {
    return largest_chunk_size_;
  }

  /// @brief tries to find a chunk defined by PDB id, chain id and a residue
  /// sequence id @detailed If this VallProvider does not contain a desired
  /// chunk, 0 is returned.
  VallChunkOP find_chunk(std::string, char, Size);

  /// @brief cache a sequence profile for a given chunk
  core::sequence::SequenceProfileOP cache_profile(VallChunkOP source_chunk);

  ///@brief cache a pose for a given chunk
  core::pose::PoseOP cache_pose(VallChunkOP source_chunk);

private:
  utility::vector1<VallChunkOP> chunks_;
  Size largest_chunk_size_;
  std::string cached_profile_id_;
  core::sequence::SequenceProfileOP cached_profile_;
  core::pose::PoseOP cached_pose_;
  std::string cached_pose_id_;
  std::string poly_A_seq_;
};

} // frag_picker
} // protocols


#endif /* INCLUDED_protocols_frag_picker_VallProvider_HH */