v2_parser.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   /src/core/chemical/sdf/v2_parser.cc
/// @author Sam DeLuca

#include <core/chemical/sdf/v2_parser.hh>
#include <core/chemical/ResidueType.hh>
#include <utility/string_util.hh>

#include <utility/vector1.hh>


namespace core {
namespace chemical {
namespace sdf {

V2Parser::V2Parser(utility::vector1<std::string> const & connection_table_lines,
    core::chemical::ResidueTypeOP molecule_container, MolData const & mol_data):
    CtabBase(connection_table_lines,molecule_container,mol_data)
{ }

void V2Parser::ParseTable()
{
  std::string counts_line = this->connection_table_line(1);
  core::Size atom_count = atoi(counts_line.substr(0,3).c_str());
  core::Size bond_count = atoi(counts_line.substr(3,3).c_str());

  //ctabParserTracer.Debug << atom_count << " atoms and " << bond_count << " bonds" <<std::endl;
  //std::map<core::Size, std::string> atom_type_data = this->ParseAtomTypeData();
  std::string version_tag = counts_line.substr(34,5);

  assert(version_tag == "V2000");

  core::Size last_atom = atom_count;
  core::Size last_bond = last_atom+bond_count;

  for(core::Size line_number = 1; line_number < this->connection_table_length(); ++line_number)
  {
    if(line_number <= last_atom)
    {
      ParseAtom(this->connection_table_line(line_number+1),line_number);
    }else if(line_number <= last_bond)
    {
      ParseBond(this->connection_table_line(line_number+1));
    }
  }

  //Iterate across the atoms, finding their types
  this->fix_atom_types();
  /*
  core::chemical::ResidueTypeOP residue(this->GetResidueType());
  for(core::Size atom_index = 1; atom_index <= atom_count; ++atom_index)
  {
    std::string atom_name(this->atom_name_from_index(atom_index));
    core::Size atomno = residue->atom_index(atom_name);
    this->set_atom_type(atomno,atom_name);
  }
  */
}

void V2Parser::ParseAtom(std::string const atom_line, core::Size const atom_number)
{
  core::Real x_coord = atof(atom_line.substr(0,10).c_str());
  core::Real y_coord = atof(atom_line.substr(10,10).c_str());
  core::Real z_coord = atof(atom_line.substr(20,10).c_str());
  //ctabParserTracer.Debug << "atom " <<atom_number << " has coordinates " << x_coord << ',' << y_coord << ',' << z_coord << std::endl;
  std::string element_name = atom_line.substr(31,3).c_str();
  if(element_name.at(1)==' ') {
    element_name=element_name.substr(0,1);
  } else if (element_name.at(2)==' ') {
    element_name=element_name.substr(0,2);
  }

  std::string atom_number_string= utility::to_string<core::Size>(atom_number);

  //atom_number_string = convert_stream.str();

  //Set the atom type to a default based on the element.
  std::string atom_type = element_to_default_type.get(element_name);

  std::string element_id = element_name+ atom_number_string;
  utility::add_spaces_left_align(element_id,4);

  core::Size charge = atoi(atom_line.substr(36,3).c_str());
  numeric::xyzVector<core::Real> coordinates(x_coord,y_coord,z_coord);
  this->add_index_name_pair(atom_number,element_id);

  core::chemical::ResidueTypeOP residue(this->GetResidueType());
  residue->add_atom(element_id,atom_type,DEFAULT_MM_ATOM_TYPE_,charge);
  residue->set_ideal_xyz(element_id,coordinates);
  //residue->finalize();
}

void V2Parser::ParseBond(std::string const bond_line)
{
  core::Size atom1_index = atoi(bond_line.substr(0,3).c_str());
  core::Size atom2_index = atoi(bond_line.substr(3,3).c_str());
  core::chemical::BondName bond_type = static_cast<core::chemical::BondName>(atoi(bond_line.substr(6,3).c_str()));
  if(this->check_for_aromatic(atom1_index,atom2_index))
  {
    bond_type = core::chemical::AromaticBond;
  }
  std::string atom1_id(this->atom_name_from_index(atom1_index));
  std::string atom2_id(this->atom_name_from_index(atom2_index));

  core::chemical::ResidueTypeOP residue(this->GetResidueType());
  residue->add_bond(atom1_id,atom2_id,bond_type);
  //residue->finalize();

}

}
}
}