ClassicGrid.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/ClassicGrid.cc
/// @author Sam DeLuca

#include <protocols/qsar/scoring_grid/ClassicGrid.hh>
#include <protocols/qsar/scoring_grid/ClassicGridCreator.hh>

#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>

#include <utility/tools/make_vector.hh>
#include <utility/json_spirit/json_spirit_value.h>
#include <utility/tag/Tag.hh>

namespace protocols {
namespace qsar {
namespace scoring_grid {

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

GridBaseOP ClassicGridCreator::create_grid(utility::tag::TagPtr const tag) const
{
  GridBaseOP classic_grid = new ClassicGrid();
  classic_grid->parse_my_tag(tag);
  return classic_grid;
}

GridBaseOP ClassicGridCreator::create_grid() const
{
  return new ClassicGrid();
}

std::string ClassicGridCreator::grid_name()
{
  return "ClassicGrid";
}

ClassicGrid::ClassicGrid(): SingleGrid("ClassicGrid"), atr_radius_(4.75), rep_radius_(2.25)
{
  //
}

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

  Pair atr("atr",Value(atr_radius_));
  Pair rep("rep",Value(rep_radius_));
  Pair base_data("base_data",SingleGrid::serialize());

  return Value(utility::tools::make_vector(atr,rep,base_data));

}

void ClassicGrid::deserialize(utility::json_spirit::mObject data)
{
  atr_radius_ = data["atr"].get_real();
  rep_radius_ = data["rep"].get_real();
  SingleGrid::deserialize(data["base_data"].get_obj());
}

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

}

void ClassicGrid::refresh(core::pose::Pose const & pose, core::Vector const & )
{
  //set attractive zones
  for(core::Size residue_index = 1; residue_index <=pose.total_residue(); ++residue_index)
  {
    core::conformation::Residue const & residue(pose.residue(residue_index));
    if(!residue.is_protein()) continue;
    for(core::Size atom_index = 1; atom_index <= residue.nheavyatoms(); ++atom_index)
    {
      set_sphere(residue.xyz(atom_index),atr_radius_,-1);
    }
  }

  //set neutral zones
  for(core::Size residue_index = 1; residue_index <= pose.total_residue(); ++residue_index)
  {
    core::conformation::Residue const & residue(pose.residue(residue_index));
    if(!residue.is_protein()) continue;
    for(core::Size atom_index = 1; atom_index <= residue.nheavyatoms(); ++atom_index)
    {
      set_sphere(residue.xyz(atom_index),rep_radius_,0);
    }
  }

  //set repulsive zones
  for(core::Size residue_index = 1; residue_index <= pose.total_residue(); ++residue_index)
  {
    core::conformation::Residue const & residue = pose.residue(residue_index);
    if( !residue.is_protein() ) continue;
    if( residue.has("CB") ) set_sphere(residue.xyz("CB"), rep_radius_, 1);
    if( residue.has("N") ) set_sphere(residue.xyz("N"), rep_radius_, 1);
    if( residue.has("CA") ) set_sphere(residue.xyz("CA"), rep_radius_, 1);
    if( residue.has("C") ) set_sphere(residue.xyz("C"), rep_radius_, 1);
    if( residue.has("O") ) set_sphere(residue.xyz("O"), rep_radius_, 1);
  }
}

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

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



}
}
}