VdwGrid.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   src/protocols/qsar/scoring_grid/VdwGrid.cc
/// @author Sam DeLuca

#include <protocols/qsar/scoring_grid/VdwGrid.hh>
#include <protocols/qsar/scoring_grid/VdwGridCreator.hh>


#include <core/id/AtomID.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomType.hh>
#include <core/pose/util.hh>
#include <core/pose/Pose.hh>

#include <basic/database/open.hh>

#include <numeric/interpolation/util.hh>
#include <numeric/interpolation/spline/SimpleInterpolator.hh>

#include <utility/tag/Tag.hh>
#include <utility/tools/make_vector.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace qsar {
namespace scoring_grid {

std::string VdwGridCreator::keyname() const
{
  return VdwGridCreator::grid_name();
}

GridBaseOP VdwGridCreator::create_grid(utility::tag::TagPtr const tag) const
{
  GridBaseOP vdw_grid= new VdwGrid();

  vdw_grid->parse_my_tag(tag);

  return vdw_grid;
}

GridBaseOP VdwGridCreator::create_grid() const
{
  return new VdwGrid();
}


std::string VdwGridCreator::grid_name()
{
  return "VdwGrid";
}

VdwGrid::VdwGrid() : SingleGrid("VdwGrid"), cutoff_(10.0)
{
  std::string lj_file(basic::database::full_name("scoring/qsar/lj_table.txt"));
  lj_spline_ = numeric::interpolation::spline_from_file(lj_file,0.01).get_interpolator();
}

void
VdwGrid::parse_my_tag(utility::tag::TagPtr const /*tag*/){

}


void VdwGrid::refresh(core::pose::Pose const & pose, core::Vector const &  )
{
  // loop through all the atoms in the pose
  // get the VDW radius of the atom
  // for each square within cutoff of the atom, update the score
  // continue

  core::Size chain_id = core::pose::get_chain_id_from_chain(get_chain(),pose);
  //core::Size chain_begin = pose.conformation().chain_begin(chain_id);
  //core::Size chain_end = pose.conformation().chain_end(chain_id);

  this->fill_with_value(cutoff_);


  for(core::Size residue_index = 1; residue_index <= pose.n_residue(); ++residue_index)
  {
    core::conformation::Residue residue = pose.residue(residue_index);
    if(residue.chain() == chain_id)
    {
      continue;
    }
    for(core::Size atom_index = 1; atom_index <= residue.natoms();++atom_index)
    {
      core::id::AtomID atom_id(atom_index,residue_index);
      core::Vector xyz(pose.xyz(atom_id));
      core::Real const & radius(residue.atom_type(atom_index).lj_radius());
      this->set_distance_sphere_for_atom(radius,xyz,cutoff_);
    }
  }
}

void VdwGrid::refresh(core::pose::Pose const & pose, core::Vector const & center, core::Size const & )
{
  refresh(pose,center);
}

void VdwGrid::refresh(core::pose::Pose const & pose, core::Vector const & center, utility::vector1<core::Size> )
{
  refresh(pose,center);
}

VdwGrid::~VdwGrid()
{

}

core::Real VdwGrid::score(core::conformation::Residue const & residue, core::Real const max_score, qsarMapOP )
{
  core::Real score = 0.0;

  for(core::Size atom_index = 1; atom_index <= residue.natoms() && score < max_score; ++atom_index )
  {
    core::Vector const & atom_coord(residue.xyz(atom_index));
    core::Real const & radius(residue.atom_type(atom_index).lj_radius());
    if(this->get_grid().is_in_grid(atom_coord.x(),atom_coord.y(),atom_coord.z()))
    {
      core::Real max_radius = this->get_point(atom_coord.x(),atom_coord.y(),atom_coord.z());
      core::Real spline_score = 0.0;
      core::Real spline_score_deriv = 0.0;

      lj_spline_->interpolate(max_radius-radius,spline_score,spline_score_deriv);

      score += spline_score;
    }
  }
  return score;
}

core::Real VdwGrid::atom_score(core::conformation::Residue const & residue, core::Size atomno, qsarMapOP /*qsar_map*/)
{
  core::Vector const & atom_coord(residue.xyz(atomno));
  core::Real const & radius(residue.atom_type(atomno).lj_radius());
  if(this->get_grid().is_in_grid(atom_coord.x(),atom_coord.y(),atom_coord.z()))
  {
    core::Real max_radius = this->get_point(atom_coord.x(),atom_coord.y(),atom_coord.z());
    core::Real spline_score = 0.0;
    core::Real spline_score_deriv = 0.0;

    lj_spline_->interpolate(max_radius-radius,spline_score,spline_score_deriv);

    return spline_score;
  }
  return 0;
}

utility::json_spirit::Value VdwGrid::serialize()
{
  using utility::json_spirit::Value;
  using utility::json_spirit::Pair;

  Pair cutoff_data("cutoff",Value(cutoff_));
  Pair spline_data("spline",lj_spline_->serialize());
  Pair base_data("base_data",SingleGrid::serialize());
  #ifdef PYROSETTA
    Value _;  return _;
  #endif
  return Value(utility::tools::make_vector(cutoff_data,spline_data,base_data));
}

void VdwGrid::deserialize(utility::json_spirit::mObject data)
{
  cutoff_ = data["cutoff"].get_real();
  numeric::interpolation::spline::InterpolatorOP interp = new numeric::interpolation::spline::SimpleInterpolator;
  interp->deserialize(data["spline"].get_obj());
  lj_spline_ = interp;
  SingleGrid::deserialize(data["base_data"].get_obj());
}

}
}
}