DesignContrast.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
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// (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
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// (C) 199x-2008 University of Washington
// (C) 199x-2008 University of California Santa Cruz
// (C) 199x-2008 University of California San Francisco
// (C) 199x-2008 Johns Hopkins University
// (C) 199x-2008 University of North Carolina, Chapel Hill
// (C) 199x-2008 Vanderbilt University

/// @file   core/io/sequence_comparation/DesignContrast.cc
///
/// @brief
/// @author Yi Liu


// C++ headers
#include <fstream>
#include <iostream>
#include <cstdlib>

// Unit Headers
// AUTO-REMOVED #include <utility/stream_util.hh>
#include <basic/Tracer.hh>
// AUTO-REMOVED #include <basic/basic.hh>
// AUTO-REMOVED #include <core/init.hh>
#include <core/types.hh>

// Utility Headers
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>


// Project Headers
#include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>
#include <core/io/sequence_comparation/DesignContrast.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <basic/options/option.hh>

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

// ObjexxFCL headers
#include <ObjexxFCL/format.hh>


// option key includes

#include <basic/options/keys/in.OptionKeys.gen.hh>




namespace core {
namespace io {
namespace sequence_comparation {

using namespace core;
using namespace basic;

using namespace core::pose;

using namespace basic::options;
using namespace basic::options::OptionKeys;

using namespace ObjexxFCL::fmt;

using basic::T;
using basic::Error;
using basic::Warning;

using core::Size;

using utility::vector1;

/// Tracer instance for this file
static basic::Tracer TR("core.io.sequence_comparation.DesignContrast");

  DesignContrast::DesignContrast(DesignContrast const & dc) {
    list_file_names_ = dc.getListNames();
    pdb_file_names_ = dc.getPdbNames();
    nneighbs_ = dc.getNeighbors();
    secstructs_ = dc.getSecStruct();
    pdb_codes_ = dc.getPdbCodes();
  }

  /// @details go through residues in the pose, count the number of neighbors of each residue.
  /// currently using tenA neighbor graph to # neighbors within 10 Angstroms
  void DesignContrast::setNeighbors(pose::Pose & pose) {
    pose.update_residue_neighbors();
    nneighbs_.clear();
    int nneighb;
    for ( Size i=1; i<= pose.total_residue(); ++i ) {
      nneighb = pose.energies().tenA_neighbor_graph().get_node(i)->num_neighbors_counting_self();
      nneighbs_.push_back(nneighb);
    }
  }

  vector1<int> & DesignContrast::getNeighbors(){
    return nneighbs_;
  }

  vector1<int> const & DesignContrast::getNeighbors() const {
    return nneighbs_;
  }


  /// @details Set secondary structure for residues in the pose. Have to call
  /// set_ss_from_phipsi to set up the secondary structure infomation for pose.
  void DesignContrast::setSecStruct(pose::Pose & pose){
    secstructs_.clear();
    set_ss_from_phipsi(pose); // This function is defined in pose/util.cc
    std::string secstruct;
    for ( Size i=1; i<= pose.total_residue(); ++i ) {
      secstruct = pose.secstruct(i);
      secstructs_.push_back(secstruct);
    }
  }

  vector1<std::string> & DesignContrast::getSecStruct(){
    return secstructs_;
  }
  vector1<std::string> const & DesignContrast::getSecStruct() const {
    return secstructs_;
  }

  /// @details Copied the major parts of this function from Andrew. Read the lines
  /// of the list files and store the pdb names in pdb_file_names.
  void DesignContrast::setNames () {
    list_file_names_.clear();
    pdb_file_names_.clear();
    if ( option[ in::file::s ].active() )
      pdb_file_names_ = option[ in::file::s ]().vector();
    if ( option[ in::file::l ].active() ) {
      list_file_names_ = option[ in::file::l ]().vector(); // make the copy of list file
    }
    for(vector1< FileName >::iterator i = list_file_names_.begin(), i_end = list_file_names_.end(); i != i_end; ++i) {
      std::string listname( i->name() );
      utility::io::izstream data( listname.c_str() );
      if ( !data.good() ) {
        utility_exit_with_message( "Unable to open file: " + listname + '\n' );
      }
      std::string line;
      while( getline(data, line) ) {
        pdb_file_names_.push_back( line );
      }
      data.close();
    }
  }

  vector1<FileName> & DesignContrast::getPdbNames(){
    return pdb_file_names_;
  }

  vector1<FileName> const & DesignContrast::getPdbNames() const {
    return pdb_file_names_;
  }

  vector1<FileName> & DesignContrast::getListNames() {
    return list_file_names_;
  }

  vector1<FileName> const & DesignContrast::getListNames() const {
    return list_file_names_;
  }

  void DesignContrast::setPdbCodes(){
    std::string code;
    for (Size i=1; i<=pdb_file_names_.size(); ++i){
      code = std::string(pdb_file_names_[i]).substr(std::string(pdb_file_names_[i]).size()-8,4);
      TR << "in DesignContrast check the code: " << code <<std::endl;
      pdb_codes_.push_back(code);
    }
  }

  vector1<std::string> & DesignContrast::getPdbCodes(){
    return pdb_codes_;
  }

  vector1<std::string> const & DesignContrast::getPdbCodes() const {
    return pdb_codes_;
  }

  void DesignContrast::output_sqc_file (
                        pose::Pose & native_pose,
                        pose::Pose & decoy_pose,
                        std::string const & single_code,
                        std::ofstream & sqc
                        ){

    TR << "in the start of output_sqc_file"<< std::endl;
    setNeighbors(native_pose);
    TR << "after setNeighbors "<< std::endl;
    setSecStruct(decoy_pose);
    TR << "after setSecStruct "<< std::endl;

    vector1<std::string> native_res_name;
    vector1<std::string> decoy_res_name;
    vector1<char> chain_ids;
    vector1<int> pdb_res_num;

    // this block is commented out due to deprecation of old PDBInfo interface
    // chain ids
//    chain_ids = decoy_pose.pdb_chains();
//    TR << "after get chains"<< std::endl;
    // sequence position for each residue.
//    pdb_res_num = decoy_pose.pdb_numbering();
//    TR << "after get pdb number "<< std::endl;

    for (Size i=1; i<=native_pose.total_residue(); ++i){
      native_res_name.push_back(native_pose.residue(i).name3());
    }
    for (Size j=1 ; j<=decoy_pose.total_residue(); ++j) {
      decoy_res_name.push_back(decoy_pose.residue(j).name3());
    }
    TR << "total residues: " << decoy_pose.total_residue() << std::endl;
    for (Size n=1; n<=decoy_pose.total_residue(); ++n){
      sqc
        << single_code << "  "
        << decoy_pose.pdb_info()->chain(n) << " "
        << I( 4, decoy_pose.pdb_info()->number(n) ) << ' '
        << A( 3, native_res_name[n] ) << ' '
        << A( 3, decoy_res_name[n] ) << ' '
        << I( 5, nneighbs_[n]) << ' '
        << A( 2, secstructs_[n] ) << ' '
        << '\n';
    }
    TR << "end of sqc output" << std::endl;
  }

  void DesignContrast::clear() {
    list_file_names_.clear();
    pdb_file_names_.clear();
    nneighbs_.clear();
    secstructs_.clear();
    pdb_codes_.clear();
  }

} // namespace sequence_comparation
} // namespace io
} // namespace core