OrbitalTypeSet.cc

Go to the documentation of this file.

// -*- 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.
//////////////////////////////////////////////////////////////////////
/// @begin AtomTypeSet
///
/// @brief
/// A class for reading in the orbital type properties
///
/// @detailed
/// This class reads in the orbital_properties.txt file which contains the "chemical" information for orbitals.
/// This does not contain the actual properties, but sets the properties through the OrbitalType class.
/// This class is called by the ChemicalManager. Modeled off of atomtypeset.
///
///
///
/// @authors
/// Steven Combs
///
///
/// @last_modified December 12 2010
/////////////////////////////////////////////////////////////////////////


#include <fstream>
#include <iostream>

#include <basic/Tracer.hh>
#include <core/chemical/orbitals/OrbitalTypeSet.hh>

#include <core/chemical/orbitals/OrbitalType.hh>
#include <utility/io/izstream.hh>

#include <utility/exit.hh>
#include <utility/vector1.hh>


namespace core{
namespace chemical{
namespace orbitals{

/// @details Auto-generated virtual destructor
OrbitalTypeSet::~OrbitalTypeSet() {}

static basic::Tracer TR("core.chemical.orbitals");

OrbitalTypeSet::OrbitalTypeSet(std::string const & directory)
{
  directory_ = directory;
  read_file( directory + "/orbital_properties.txt" );

  //currently commented out. This is if someone down the line wants to add extras, like
  //in the atomtype extras.
/*  std::ifstream data( ( directory+"/extras.txt" ).c_str() );
  if ( data.good() ) { // add extra data
    std::string line;
    while( getline( data, line ) ) {
      if ( line.size() && line[0] == '#' ) continue;
      add_parameters_from_file( directory+"/"+line );
    }
  }
  data.close();*/

}


//function take from AtomTypeSet.cc. Modified slightly for OrbitalTypeSet.cc.
//basically reads the file orbital_properties.txt found in your directory.
//
void OrbitalTypeSet::read_file(std::string const & filename)
{
  utility::io::izstream data( filename.c_str() ); 

  if ( !data.good() ) utility_exit_with_message( "Unable to open atomset file: "+filename );

  // parse the header line currently should look like orbital_type atom_type hybridization distance
  utility::vector1< std::string > tags;
  { // scope
    std::string line, tag, tag2;
    getline( data, line );
    std::istringstream l( line );
    l >> tag >> tag2;
    if ( tag != "orbital_type" || tag2 != "atom_type" ) {
      utility_exit_with_message("AtomTypeSet::read_file: bad first line: "+ line );
    }
    l >> tag;
    while ( !l.fail() ) {
      tags.push_back( tag );
      l >> tag;
    }
  }

  // now parse the rest of the file
  core::Size 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 ( l.fail() || name_wo_whitespace.find("#",0) == 0 ) continue; // skip comment,blank lines
      l >> tag;
      if ( l.fail() || tag.size() < 1 ) {
        utility_exit_with_message("bad line: "+line);
      }

      //      std::string const name( line.substr(0,4) );
      std::string atom_type_name( tag );
      OrbitalType* orbital_type_ptr( new OrbitalType( name_wo_whitespace, atom_type_name ) );

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

      // now parse the properties
      l >> tag;
      while ( !l.fail() && tag.find("#",0) != 0) {
        orbital_type_ptr->set_property( tag, true );
        l >> tag;
      }

      // add this to the list
      orbitals_.push_back( orbital_type_ptr );
      //    atom_type_index_[ name ] = atoms_.size();
      if ( orbital_type_index_.count( name_wo_whitespace ) ) {
        utility_exit_with_message("AtomTypeSet:: duplicate atom name "+name_wo_whitespace);
      }
      orbital_type_index_[ name_wo_whitespace ] = orbitals_.size();
      TR.Debug << "New atom type: " << name_wo_whitespace << ' ' << atom_type_name << std::endl; //std::endl;
    }
  } // scope


}

int
OrbitalTypeSet::orbital_type_index( std::string const & orbital_type_name ) const
{
  std::map< std::string, int >::const_iterator
    iter( orbital_type_index_.find( orbital_type_name ) );
  if ( iter == orbital_type_index_.end() ) {
    utility_exit_with_message("unrecognized orbital type name "+orbital_type_name);
  }
  return iter->second;
}


int
OrbitalTypeSet::orbital_type_index( std::string & orbital_type_name ) const
{
  std::map< std::string, int >::const_iterator
    iter( orbital_type_index_.find( orbital_type_name ) );
  if ( iter == orbital_type_index_.end() ) {
    utility_exit_with_message("unrecognized orbital type name "+orbital_type_name);
  }
  return iter->second;
}

}
}
}