CenHBPotential.cc

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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.

/// @file   core/scoring/methods/CenHBPotential.cc
/// @brief  Smooth, differentiable version of centroid hbond term
/// @author Frank DiMaio


#include <core/scoring/CenHBPotential.hh>

// AUTO-REMOVED #include <core/scoring/Energies.hh>
// AUTO-REMOVED #include <core/scoring/EnergyGraph.hh>

// AUTO-REMOVED #include <core/chemical/AA.hh>
// AUTO-REMOVED #include <core/chemical/VariantType.hh>
// AUTO-REMOVED #include <core/conformation/Residue.hh>
#include <basic/database/open.hh>
// AUTO-REMOVED #include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/pose/datacache/CacheableDataType.hh>
// AUTO-REMOVED #include <basic/datacache/BasicDataCache.hh>
// AUTO-REMOVED #include <basic/prof.hh>
#include <utility/io/izstream.hh>

#include <utility/vector1.hh>
#include <boost/bind.hpp>



namespace core {
namespace scoring {

///////////////////////////////////////////////////////////////////////////////////////////////

Real CenHBPotential::func( Size seqsep, Real d, Real xd, Real xh ) const {
  using numeric::constants::f::pi;

  utility::vector1< Real > const & As       = (seqsep<=4) ? sr_As_ : lr_As_;
  utility::vector1< Vector > const & mus    = (seqsep<=4) ? sr_mus_ : lr_mus_;
  utility::vector1< Vector > const & sigmas = (seqsep<=4) ? sr_sigmas_ : lr_sigmas_;

  Real y = 0;
  for (Size i=1; i<=As.size(); ++i) {
    y += As[i] * exp( -(d-mus[i][0])*(d-mus[i][0]) / (2*sigmas[i][0]*sigmas[i][0]) )
               * ( exp( sigmas[i][1]*cos( pi/180*(xd-mus[i][1]) ) ) + exp( sigmas[i][1]*cos( pi/180*(xd+mus[i][1]) ) ) )
               * ( exp( sigmas[i][2]*cos( pi/180*(xh-mus[i][2]) ) ) + exp( sigmas[i][2]*cos( pi/180*(xh+mus[i][2]) ) ) );
  }
  return y;
}


Vector CenHBPotential::dfunc( Size seqsep, Real d, Real xd, Real xh ) const {
  using numeric::constants::f::pi;

  utility::vector1< Real > const & As       = (seqsep<=4) ? sr_As_ : lr_As_;
  utility::vector1< Vector > const & mus    = (seqsep<=4) ? sr_mus_ : lr_mus_;
  utility::vector1< Vector > const & sigmas = (seqsep<=4) ? sr_sigmas_ : lr_sigmas_;

  Vector dy = Vector(0,0,0);
  for (Size i=1; i<=As.size(); ++i) {
      Real s1 = exp( -(d-mus[i][0])*(d-mus[i][0]) / (2*sigmas[i][0]*sigmas[i][0]) );
      Real s2a = exp( sigmas[i][1]*cos( pi/180*(xd-mus[i][1]) ) );
      Real s2b = exp( sigmas[i][1]*cos( pi/180*(xd+mus[i][1]) ) );
      Real s3a = exp( sigmas[i][2]*cos( pi/180*(xh-mus[i][2]) ) );
      Real s3b = exp( sigmas[i][2]*cos( pi/180*(xh+mus[i][2]) ) );
      Real s2 = s2a+s2b;
      Real s3 = s3a+s3b;

      dy[0] += -As[i] * s1 * s2 * s3 * (d-mus[i][0]) / (sigmas[i][0]*sigmas[i][0]);
      dy[1] += -As[i] * s1 * s3 * pi/180 * sigmas[i][1] * ( sin( pi/180*(xd-mus[i][1])) * s2a + sin( pi/180*(xd+mus[i][1])) * s2b );
      dy[2] += -As[i] * s1 * s2 * pi/180 * sigmas[i][2] * ( sin( pi/180*(xh-mus[i][2])) * s3a + sin( pi/180*(xh+mus[i][2])) * s3b );
  }
  return dy;
}

///////////////////////////////////////////////////////////////////////////////////////////////

CenHBPotential::CenHBPotential() {
  // defaults
  cutoff_sr_ = 6.0;
  cutoff_lr_ = 6.0;

  // load the data
  std::string tag,line;
  utility::io::izstream stream;
  basic::database::open( stream, "scoring/score_functions/centroid_smooth/cen_hb_params.txt");

  while ( getline( stream, line ) ) {
    std::istringstream l(line);
    l >> tag;
    if (tag == "HBOND_BB_LR:") {
      l >> tag;
      if (tag == "CUTOFF") {
        l >> cutoff_lr_;
      } else if (tag == "GAUSSIAN3D") {
        Size ngauss; l >> ngauss;
        Real A;
        numeric::xyzVector<Real> mu, sigma;
        for (Size i=1; i<=ngauss; ++i) {
          l >> A >> mu[0] >> mu[1] >> mu[2] >> sigma[0] >> sigma[1] >> sigma[2];
          add_lr_gaussian(A,mu,sigma);
        }
      }
    } else if (tag == "HBOND_BB_SR:") {
      l >> tag;
      if (tag == "CUTOFF") {
        l >> cutoff_sr_;
      } else if (tag == "GAUSSIAN3D") {
        Size ngauss; l >> ngauss;
        Real A;
        numeric::xyzVector<Real> mu, sigma;
        for (Size i=1; i<=ngauss; ++i) {
          l >> A >> mu[0] >> mu[1] >> mu[2] >> sigma[0] >> sigma[1] >> sigma[2];
          add_sr_gaussian(A,mu,sigma);
        }
      }
    } else if (tag != "#") {
      utility_exit_with_message("bad format for cen_smooth_params.txt");
    }

    if ( l.fail() ) utility_exit_with_message("bad format for cen_smooth_params.txt");
  }
}



}
}