MMAtomTypeSet.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/chemical/MMAtomTypeSet.cc
/// @brief
/// @author P. Douglas Renfrew (renfrew@unc.edu)

// Unit headers
#include <core/chemical/MMAtomTypeSet.hh>

// Project headers
#include <basic/Tracer.hh>

#include <core/chemical/MMAtomType.hh>

// C++ headers
#include <fstream>
#include <iostream>
#include <utility/io/izstream.hh>

#include <utility/vector1.hh>


namespace core {
namespace chemical {

static basic::Tracer tr("core.chemical");


MMAtomTypeSet::MMAtomTypeSet():
  atom_type_index_(),
  atoms_()
{
}


MMAtomTypeSet::~MMAtomTypeSet() {}


/// @details Initialize an MMAtomTypeSet from an external file "filename",
/// and set parameters and properties for each MMAtomType.
/// Refer to minirosetta_database_stock/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt
/// for file format
///
void
MMAtomTypeSet::read_file( std::string const & filename )
{
  utility::io::izstream data( filename.c_str() ); 

  if ( !data.good() ) utility_exit_with_message( "Unable to open MM atom type set file: "+filename );

  // parse the header line
  utility::vector1< std::string > tags;
  { // scope
    std::string line, tag;
    getline( data, line );
    std::istringstream l( line );
    l >> tag;
    if ( tag != "NAME" ) {
      utility_exit_with_message("MMAtomTypeSet::read_file: bad first line: "+ line );
    }
    l >> tag;
    while ( !l.fail() ) {
      tags.push_back( tag );
      l >> tag;
    }
  }

  // now parse the rest of the file
  int const ntags( tags.size() );
  {
    using namespace basic;

    std::string line, tag, name_wo_whitespace;
    while ( getline( data,line ) ) {
      std::istringstream l( line );
      l >> name_wo_whitespace;
      if ( name_wo_whitespace.find("#",0) == 0 ) continue; // skip comment lines
      if ( l.fail() ) {
        utility_exit_with_message("bad line: "+line);
      }

      MMAtomType* mm_atom_type_ptr( new MMAtomType( name_wo_whitespace ) );

      // now parse the parameters
      for ( int i=1; i<= ntags; ++i ) {
        Real setting;
        l >> setting;
        mm_atom_type_ptr->set_parameter( tags[i], setting );
      }
      if ( l.fail() ) {
        utility_exit_with_message("bad line: "+line);
      }

      // add this to the list
      atoms_.push_back( mm_atom_type_ptr );
      if ( atom_type_index_.count( name_wo_whitespace ) ) {
        utility_exit_with_message("MMAtomTypeSet:: duplicate atom name "+name_wo_whitespace);
      }
      atom_type_index_[ name_wo_whitespace ] = atoms_.size();
      tr.Debug << "New MM atom type: " << name_wo_whitespace << std::endl;
    }
  }
}

/// @details This function iterates over each element in the atom_type_index_ map and
/// prints both keys. It is only used for debugging.
void
MMAtomTypeSet::print_all_types()
{
  for( std::map< std::string, int >::const_iterator i = atom_type_index_.begin(), e = atom_type_index_.end(); i != e; ++i )
    {
      std::cout << (*i).first << " " << (*i).second << std::endl;
    }
}

} // chemical
} // core