PcsDataLanthanide.hh

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// -*- 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.
 //////////////////////////////////////////////
 /// @begin
 ///
 /// @file protocols/scoring/methods/pcs2/PcsDataLanthanide.hh
 ///
 /// @brief
 ///
 /// @detailed
 ///
 /// @param
 ///
 /// @return
 ///
 /// @remarks
 ///
 /// @references
 ///
 /// @authorsv Christophe Schmitz
 ///
 /// @last_modified February 2010
 ////////////////////////////////////////////////

#ifndef INCLUDED_protocols_scoring_methods_pcs2_PcsDataLanthanide_hh
#define INCLUDED_protocols_scoring_methods_pcs2_PcsDataLanthanide_hh


// Package headers
#include <protocols/scoring/methods/pcs2/PcsTensor.fwd.hh>
#include <protocols/scoring/methods/pcs2/PcsInputLine.fwd.hh>

// Project headers
#include <core/types.hh>

// Utility headers
#include <utility/vector1.hh>

// Basic headers
#include <basic/svd/SVD_Solver.hh>

// ObjexxFCL headers
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray1D.hh>

// c++ headers

//#define LOGPCS

namespace protocols{
namespace scoring{
namespace methods{
namespace pcs2{

class PcsDataLanthanide{
private:
  std::string const filename_;
  core::Real const weight_;

  core::Size n_pcs_;
  utility::vector1<core::Size> A_index_; //index on the giant matrix A to build all the smalls matrix A_
  ////  ObjexxFCL::FArray2D< core::Real > fstyle_A_; //We are going to SVD Ax = b
  ////  ObjexxFCL::FArray1D< core::Real > fstyle_b_; //I should make this one const
  utility::vector1< utility::vector1<core::Real> > cstyle_A_;
  utility::vector1<core::Real> cstyle_b_;
  utility::vector1<core::Real> cstyle_b_individual_scale_;
  basic::svd::SVD_Solver svd_s_;
  core::Real normalization_1_; // SQRT(SUMi( PCS(calc,i)^2 ) )
  core::Real normalization_2_; // Standard deviation
  core::Real normalization_3_; // SQRT(SUMi( PCS(calc,i)^2 )/N )
  core::Real normalization_factor_;
  core::Real normalization_factor_inversed_;
  core::Real individual_scale_;

public:


  void
  update_my_A_matrix_for_cstyle(utility::vector1< utility::vector1<core::Real> > & A_all);

  PcsDataLanthanide(); //construct

  ~PcsDataLanthanide(); //destruct

  PcsDataLanthanide(PcsDataLanthanide const &other); //copy

  PcsDataLanthanide &
  operator=( PcsDataLanthanide const & other ); //=

  PcsDataLanthanide(std::string, core::Real const weight, utility::vector1< PcsInputLine > & pcs_i_l, core::Size start, core::Size end, core::Real individual_scale);

  /// @brief Set a value of the A_index_ vector
  void
  set_A_index(core::Size j, core::Size n_pcs_spin_);

  /// @brief update the A matrix given A_all matrix.
  /// Dimensions of A_all >= dimension of A.
  /// A_all is common to all the lanthanide sharing the same center
  void
  update_my_A_matrix_for_svd(utility::vector1< utility::vector1<core::Real> > & A_all);

  /// @brief give me the weight associated with this PCS data
  core::Real
  get_weight() const;

  core::Real
  get_individual_scale() const;


  /// @brief give me the normalization factor associated with this PCS data
  core::Real
  get_normalization_factor() const;

  /// @brief give me the normalization factor associated with this PCS data
  core::Real
  get_normalization_factor_inversed() const;


  /// @brief give me the filename associated with this PCS data
  std::string
  get_filename() const;

  /// @brief give me the number of PCS data
  core::Size
  get_n_pcs() const;

  /// @brief Give me the A_index_ vector
  utility::vector1<core::Size> const &
  get_A_index() const;

  /// @brief return the b vector in FArray1D format
  /*
  ObjexxFCL::FArray1D< core::Real > const &
  get_fstyle_b() const;

  ObjexxFCL::FArray2D< core::Real > const &
  get_fstyle_A() const;
  */

  const utility::vector1< utility::vector1<core::Real> > &
  get_cstyle_A() const;

  const utility::vector1<core::Real> &
  get_cstyle_b() const;

  const utility::vector1<core::Real> &
  get_cstyle_b_individual_scale() const;

  /// @Print me
  friend
  std::ostream &
  operator << ( std::ostream& out, const PcsDataLanthanide &me );

  /// @This return the score and populate the PcsTensor with svd.
  core::Real
  calculate_tensor_and_cost_with_svd(PcsTensor &pcs_t);

  core::Real
  calculate_cost_only_with_svd();


  /// @This populate the PcsTensor with svd.
  void
  calculate_tensor_only_with_svd(PcsTensor &pcs_t);

  void
  retrieve_tensor_from_svd(PcsTensor &pcs_t);


  /*
  core::Real
  calculate_tensor_and_cost_with_svd_precalc(PcsTensor &pcs_t);
  */
};

bool
do_I_skip(PcsInputLine & pcs_i_l, core::Size start, core::Size end);


}//namespace pcs2
}//namespace methods
}//namespace scoring
}//namespace protocols
#endif