IdealBondLengthSet.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/IdealBondLengthSet.cc
/// @brief
/// @author Gordon Lemmon

// Unit headers
#include <core/chemical/IdealBondLengthSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomTypeSet.hh>

// Project headers
#include <basic/Tracer.hh>
#include <utility/string_util.hh>
#include <utility/io/izstream.hh>  

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

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

namespace core {
namespace chemical {

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

IdealBondLengthSet::IdealBondLengthSet():
    bond_lengths_()
{}

IdealBondLengthSet::~IdealBondLengthSet() {}

bool IdealBondLengthSet::contains_bond_length(std::string const & atom_type_name1, std::string const & atom_type_name2) const{
  core::chemical::ChemicalManager *cm= core::chemical::ChemicalManager::get_instance();
  core::chemical::AtomTypeSetCAP atom_type_set= cm->atom_type_set( core::chemical::FA_STANDARD );

  AtomTypeIndex atom_type_index1 = atom_type_set->atom_type_index(atom_type_name1);
  AtomTypeIndex atom_type_index2 = atom_type_set->atom_type_index(atom_type_name2);

  return contains_bond_length(atom_type_index1, atom_type_index2);
}

bool IdealBondLengthSet::contains_bond_length(AtomTypeIndex atom_type_index1, AtomTypeIndex atom_type_index2) const{
  if(atom_type_index1 > atom_type_index2) std::swap(atom_type_index1, atom_type_index2);
  std::pair<AtomTypeIndex,AtomTypeIndex> index_pair(atom_type_index1,atom_type_index2);

  if(bond_lengths_.find(index_pair) == bond_lengths_.end()){
    return false;
  }

  return true;
}

BondLength
IdealBondLengthSet::get_bond_length( std::string const & atom_type_name1, std::string const & atom_type_name2) const{
  core::chemical::ChemicalManager *cm= core::chemical::ChemicalManager::get_instance();
  core::chemical::AtomTypeSetCAP atom_type_set= cm->atom_type_set( core::chemical::FA_STANDARD );

  Size atom_type_index1 = atom_type_set->atom_type_index(atom_type_name1);
  Size atom_type_index2 = atom_type_set->atom_type_index(atom_type_name2);

  if(atom_type_index1 > atom_type_index2) std::swap(atom_type_index1, atom_type_index2);

  if( ! contains_bond_length(atom_type_index1, atom_type_index2) ){
    utility_exit_with_message( "ideal bond_length not defined between these atom types: "+ atom_type_name1+" "+atom_type_name2);
  }
  return get_bond_length(atom_type_index1, atom_type_index2);
}

BondLength
IdealBondLengthSet::get_bond_length(AtomTypeIndex const atom_type_index1, AtomTypeIndex const atom_type_index2) const{
  assert(contains_bond_length(atom_type_index1, atom_type_index2));

  std::pair<AtomTypeIndex,AtomTypeIndex> index_pair(atom_type_index1,atom_type_index2);

  return bond_lengths_.find(index_pair)->second;
}

void
IdealBondLengthSet::add_bond_length(
    std::string const & atom_type_name1,
    std::string const & atom_type_name2,
    BondLength const length
){

  core::chemical::ChemicalManager *cm= core::chemical::ChemicalManager::get_instance();
  core::chemical::AtomTypeSetCAP atom_type_set= cm->atom_type_set( core::chemical::FA_STANDARD );

  Size atom_type_index1 = atom_type_set->atom_type_index(atom_type_name1);
  Size atom_type_index2 = atom_type_set->atom_type_index(atom_type_name2);

  if(atom_type_index1 > atom_type_index2) std::swap(atom_type_index1, atom_type_index2);

  if( contains_bond_length(atom_type_index1, atom_type_index2) ){
    utility_exit_with_message("this pair is already in the table... "+ atom_type_name1+" "+atom_type_name2);
  }else{
    add_bond_length(atom_type_index1, atom_type_index2, length);
  }
}

void
IdealBondLengthSet::add_bond_length(
    AtomTypeIndex const atom_type_index1,
    AtomTypeIndex const atom_type_index2,
    BondLength const length
){
  assert(atom_type_index1 <= atom_type_index2);
  assert(!contains_bond_length(atom_type_index1, atom_type_index2) );

  std::pair<AtomTypeIndex,AtomTypeIndex> index_pair(atom_type_index1,atom_type_index2);
  bond_lengths_[index_pair]= length;
}


void
IdealBondLengthSet::read_file( std::string const & filename )
{
   utility::io::izstream data( filename.c_str() ); 

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

  // now parse the rest of the file

  using namespace basic;

  std::string line;
  // parse the header line
  getline( data, line ); // throw out the header line (currently it is just for file readability)
  while ( getline( data,line ) ) {
    utility::trim(line, " \t\n"); // remove leading and trailing spaces
    if ( line.empty() > 0 ) continue; //skip blank lines
    if ( line.find("#",0) == 0 ) continue; // skip comment lines

    std::istringstream l( line );
    std::string name1, name2;
    Real length;

    l >> name1 >> name2 >> length;

    if ( l.fail() ) {
      utility_exit_with_message("bad line: "+line);
    }

    add_bond_length( name1, name2, length);
  }
}



/// @details This function iterates over each bond_type pair in the bond_length_ map and
/// prints both keys. It is only used for debugging.
void
IdealBondLengthSet::print_all_bond_lengths()
{
  for(
      std::map< std::pair<AtomTypeIndex, AtomTypeIndex>, BondLength >::const_iterator i = bond_lengths_.begin(),
      e = bond_lengths_.end();
      i != e;
      ++i
  ){
      std::cout << i->first.first << " " << i->first.second << " " << i->second << std::endl;
  }
}

} // chemical
} // core