CavityBall.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/packstat/CavityBall.cc
///
/// @brief
/// @author will sheffler


// Unit header or inline function header
#include <core/scoring/packstat/CavityBall.hh>

// AUTO-REMOVED #include <ObjexxFCL/string.functions.hh>

#include <iostream>
#include <sstream>

#include <ObjexxFCL/format.hh>





namespace core {
namespace scoring {
namespace packstat {


using namespace std;
using namespace utility;
using namespace numeric;
using namespace ObjexxFCL;
using namespace ObjexxFCL::fmt;

CavityBall::CavityBall( int const id, int const sphere,
    numeric::xyzVector<PackstatReal> const xyz, PackstatReal const r ) :
  id_(id),
  sphere_(sphere),
  cluster_(id),
  xyz_(xyz),
  radius_(r),
  area(0.0),
  vol(0.0),
  exposed_radius(0.0f),
  anb(-12345)
  // sasa_(-1234.0f)//,
  // surrounding_sasa_(N_CAVBALL_DISBINS,30,0.0f),
  //surrounding_sasa_5A_(30,0.0f),
  // heavyatom_(false),
  // num_other_balls_overlap_(-1234),
  // num_buried_other_balls_overlap_(-1234),
  // num_big_other_balls_overlap_(-1234),
  // num_big_buried_other_balls_overlap_(-1234),
  // cluster_id_(-1234),
  // cluster_(NULL)
{

  // hole_sasa_     .clear();
  // hole_sasa_     .resize(N_PR_BIN,0);
  // neighbor_count_.clear();
  // avg_bfactor_   .clear();
  // avg_occupancy_ .clear();
  // absolute_shell_rms_.clear();
  // relative_shell_rms_.clear();
  // neighbor_count_.resize(N_CAVBALL_DISBINS,-1234);
  // avg_bfactor_   .resize(N_CAVBALL_DISBINS,-1234);
  // avg_occupancy_ .resize(N_CAVBALL_DISBINS,-1234);
  // absolute_shell_rms_.resize(N_CAVBALL_DISBINS,-1234);
  // relative_shell_rms_.resize(N_CAVBALL_DISBINS,-1234);

}

// bool CavityBall::cmp( CavityBall * a, CavityBall * b ) {
//  return a->radius() > b->radius();
// }
//
// bool CavityBall::overlaps( CavityBall const *b ) const {
//  return distto(b) < -0.5;
// }

string const CavityBall::str() const {
  ostringstream oss;
  oss << "CavityBall "
    << id_ << " "
    << sphere_ << " "
    << radius_ << " "
    // << sasa_ << " "
    // << I(5, num_other_balls_overlap_ )
    // << I(5, num_buried_other_balls_overlap_ )
    // << I(5, num_big_other_balls_overlap_ )
    // << I(5, num_big_buried_other_balls_overlap_ )
    << ' ' << xyz_.x() << ',' << xyz_.y() << ',' << xyz_.z()
    << ' ';
  // for (int ii=1; ii <= (int)big_buried_neighboring_cavity_balls_.size(); ii++) {
  //  oss<< big_buried_neighboring_cavity_balls_[ii]->id_ << ' ';
  // }
  return oss.str();
}

// new convention is to use rosetta atom# for atom# line
// and 500 + rosetta res# for res number
// before, atom# was 10 x radius and res# was
// hole index in proteinSasa's cavity_balls_ array
string const CavityBall::hetero_atom_line( int const hetresnum, int const /*chain*/, core::Real radsub ) const
{
  // string CAV = ObjexxFCL::string_of(cluster_);
  // if( CAV.size() == 1 ) {
  //  CAV = "C0"+CAV;
  // } else if( CAV.size() == 2 ) {
  //  CAV = "C"+CAV;
  // } else {
  //  CAV = CAV.substr(0,3);
  // }
  std::string alpha = "ZYXWVUTSRQPONMLKJIHGFEDCBA";
  for(int i = 1; i <= 6; ++i) alpha += alpha; // 64 x
  return "HETATM" + I( 5, ( min( 9999, id_) ) ) + "  V   CAV "+alpha[cluster_-1]
    + I( 4, hetresnum ) + "    "
    + F( 8, 3, xyz_.x() ) + F( 8, 3, xyz_.y() ) + F( 8, 3, xyz_.z() )
    + F( 6, 2, exposed_radius ) + ' ' + F( 5, 2, max(0.1,radius_-radsub) );
    //+ F( 6, 2, evdw ) + ' ' + F( 5, 2, max(0.1,radius_-radsub) );
}


// int CavityBall::recursive_mark_hole_neighbors( vector1<CavityBall> & holes, int const cluster ) {
//  if ( cluster_id_ != -1234 ) {
//    return 0;
//  }
//  cluster_id_ = cluster;
//  int count = 1;
//  for ( int ii=1; ii<=(int)big_buried_neighboring_cavity_balls_.size(); ii++) {
//    /*cerr << "PACKING: add hole "
//         << big_buried_neighboring_cavity_balls_[ii]->id_
//         << " to cluster "
//         << cluster
//         << " base atom "
//         << id_
//         << endl; */
//    count += big_buried_neighboring_cavity_balls_[ii]->recursive_mark_hole_neighbors( holes, cluster );
//  }
//  return count;
// }



} // namespace packstat
} // namespace scoring
} // namespace core