SidechainContactDistCutoff.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.
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// (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   protocols/frag_picker/SidechainContactDistCutoff.cc
/// @brief  Defines sidechain contact distance cutoffs.
/// @author David E. Kim (dekim@u.washington.edu)

// Unit headers
#include <protocols/frag_picker/SidechainContactDistCutoff.hh>


// Package headers

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

#include <basic/database/open.hh>
#include <basic/Tracer.hh>

// Utility headers
#include <utility/exit.hh>
#include <utility/io/izstream.hh>

// C/C++ headers
#include <iostream>
#include <string>


namespace protocols {
namespace frag_picker {

// @brief Auto-generated virtual destructor
SidechainContactDistCutoff::~SidechainContactDistCutoff() {}

using namespace core;

static basic::Tracer TR("protocols.frag_picker.SidechainContactDistCutoff");

SidechainContactDistCutoff::SidechainContactDistCutoff() {
  SidechainContactDistCutoff(1.0);
}

SidechainContactDistCutoff::SidechainContactDistCutoff(Real scale_factor) {
  scale_factor_ = scale_factor;
  initialize();
}

void SidechainContactDistCutoff::initialize() {

  // set aa mapping
  // GLY   ALA   SER   CYS   VAL   THR   ILE   PRO   MET   ASP   ASN   LEU   LYS   GLU   GLN   ARG   HIS   PHE   TYR   TRP
  aa_map_.resize(20);
  aa_map_[1] = 'G';
  aa_map_[2] = 'A';
  aa_map_[3] = 'S';
  aa_map_[4] = 'C';
  aa_map_[5] = 'V';
  aa_map_[6] = 'T';
  aa_map_[7] = 'I';
  aa_map_[8] = 'P';
  aa_map_[9] = 'M';
  aa_map_[10] = 'D';
  aa_map_[11] = 'N';
  aa_map_[12] = 'L';
  aa_map_[13] = 'K';
  aa_map_[14] = 'E';
  aa_map_[15] = 'Q';
  aa_map_[16] = 'R';
  aa_map_[17] = 'H';
  aa_map_[18] = 'F';
  aa_map_[19] = 'Y';
  aa_map_[20] = 'W';

  // set aa to index mapping
  for (Size i=1;i<=aa_map_.size();++i)
    aa_to_index_map_[aa_map_[i]] = i;

  utility::vector1<utility::vector1<Real> >  mean_dist;
  utility::vector1<utility::vector1<Real> >  stddev_dist;

  // read distance tables
  // first table is the mean and the second is the standard deviation
  utility::io::izstream data(basic::database::full_name("sampling/sidechain_contact.txt"));
  TR.Info << "read sidechain contact data from sidechain_contact.txt" << std::endl;
  if (!data)
    utility_exit_with_message("[ERROR] Unable to open file: sidechain_contact.txt");

  std::string line;
  Size tablecnt = 0;
  while (getline(data, line)) {
    if (line.size() > 3 && line.substr(0,3) == "GLY") { // tables start with GLY
      tablecnt++;
      Size rowcnt = 1;
      utility::vector1<Real> col(20);
      std::istringstream line_stream( line );
      std::string col1;
      line_stream >> col1;
      if (core::chemical::oneletter_code_from_aa(core::chemical::aa_from_name(col1)) != aa_map_[rowcnt])
        utility_exit_with_message( "Error in sidechain name mapping in sidechain_contact.txt!" );
      for (Size i=1;i<=col.size();++i) line_stream >> col[i];
      if ( line_stream.fail() )
        utility_exit_with_message( "Error reading in SidechainContactDistCutoff()!" );
      if (tablecnt == 1)
        mean_dist.push_back(col);
      else if (tablecnt == 2)
        stddev_dist.push_back(col);
      for (Size j=1;j<=19;++j) { // read the remaining table rows
        getline(data, line);
        rowcnt++;
        std::istringstream line_stream_next(line);
        line_stream_next >> col1;
        if (core::chemical::oneletter_code_from_aa(core::chemical::aa_from_name(col1)) != aa_map_[rowcnt])
          utility_exit_with_message( "Error in sidechain name mapping in sidechain_contact.txt!" );
        for (Size i=1;i<=col.size();++i) line_stream_next >> col[i];
        if ( line_stream_next.fail() )
          utility_exit_with_message( "Error reading in SidechainContactDistCutoff()!" );
        if (tablecnt == 1)
          mean_dist.push_back(col);
        else if (tablecnt == 2)
          stddev_dist.push_back(col);
      }
    }
  }
  data.close();

  // calculate cutoffs
  // from I-TASSER paper
  cutoff_.resize(20);
  cutoff_squared_.resize(20);
  for (Size i=1;i<=mean_dist.size();++i) {
    for (Size j=1;j<=mean_dist[i].size();++j) {
      cutoff_[i].push_back( scale_factor_*(mean_dist[i][j] + 2.5*stddev_dist[i][j]) );
      cutoff_squared_[i].push_back( cutoff_[i][j]*cutoff_[i][j] );
      TR.Debug << "cutoff_squared: " << i << " " << j << " " << cutoff_squared_[i][j] << std::endl;
    }
  }
}

Real SidechainContactDistCutoff::get_cutoff( char aa_i, char aa_j ) {
  return cutoff_[aa_to_index_map_[aa_i]][aa_to_index_map_[aa_j]];
}

Real SidechainContactDistCutoff::get_cutoff_squared( char aa_i, char aa_j ) {
  return cutoff_squared_[aa_to_index_map_[aa_i]][aa_to_index_map_[aa_j]];
}

Real SidechainContactDistCutoff::scale_factor() {
  return scale_factor_;
}

} // frag_picker
} // protocols