util.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:
// :noTabs=false:tabSize=4:indentSize=4:
//
// (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/util.cc
/// @brief Utilities for modifying and utilizing Residues and other core::chemical classes.


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

// Package Headers
// AUTO-REMOVED #include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/AtomType.hh>

// Project Headers
#include <core/types.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <utility/file/file_sys_util.hh>
#include <basic/Tracer.hh>

namespace core {
namespace chemical {

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

core::chemical::ResidueTypeSetCAP
rsd_set_from_cmd_line() {
  using namespace basic::options;
  using namespace basic::options::OptionKeys;
  using namespace core::chemical;

  std::string const type_set_name( option[ in::file::residue_type_set ]() );
  ResidueTypeSetCAP set = ChemicalManager::get_instance()->residue_type_set(
    type_set_name
  );

  return set;
}


/// @brief  Add additional parameter files not present in <atom-set-name>/extras.txt. Called by ChemicalManager at time of AtomTypeSet creation.

void
add_atom_type_set_parameters_from_command_line(
                                               std::string const & atom_type_set_tag,
                                               AtomTypeSet & atom_type_set
                                               )
{
  if ( !( basic::options::option[ basic::options::OptionKeys::chemical::add_atom_type_set_parameters ].user() ) ) {
    /// do nothing if flag not present
    return;
  }
  utility::vector1< std::string > paramstring
    ( basic::options::option[ basic::options::OptionKeys::chemical::add_atom_type_set_parameters ]() );
  if ( paramstring.size()%2 != 0 ) {
    utility_exit_with_message("bad format for -add_atom_type_set_parameters; should be: -add_atom_type_set_parameters <tag1> <filename1> <tag2> <filename2> ...");
  }
  Size const nparams( paramstring.size()/2 );
  for ( Size i=0; i< nparams; ++i ) {
    std::string const tag( paramstring[2*i+1] ), filename( paramstring[2*i+2] );
    TR.Trace << "add_atom_type_set_parameters_from_command_line: desired_tag= " << atom_type_set_tag <<
      " cmdline-tag= " << tag << " filename= " << filename << std::endl;
    if ( tag == atom_type_set_tag ) {
      if ( !utility::file::file_exists( filename ) ) {
        utility_exit_with_message("unable to locate/open file: "+filename );
      }
      TR.Trace << "add_atom_type_set_parameters_from_command_line: tag= " << tag << " filename= " << filename <<
        std::endl;
      atom_type_set.add_parameters_from_file( filename );
    }
  }
}


/// @brief Modify atom_type properties from the command line. Called by ChemicalManager at time of AtomTypeSet creation.
void
modify_atom_properties_from_command_line(
                                         std::string const & atom_type_set_tag,
                                         AtomTypeSet & atom_type_set
                                         )
{


  if ( basic::options::option[ basic::options::OptionKeys::chemical::set_atom_properties ].user() ) {
    utility::vector1< std::string > const & mods
      ( basic::options::option[ basic::options::OptionKeys::chemical::set_atom_properties ]);

    std::string const errmsg( "-set_atom_properties format should be:: -set_atom_properties <set1>:<atom1>:<param1>:<setting1> <set2>:<atom2>:<param2>:<setting2> ...; for example: '-chemical:set_atom_properties fa_standard:OOC:LK_DGFREE:-5 fa_standard:ONH2:LJ_RADIUS:0.5' ");

    for ( Size i=1; i<= mods.size(); ++i ) {
      ///
      /// mod should look like (for example):  "fa_standard:OOC:LK_RADIUS:4.5"
      ///
      std::string const & mod( mods[i] );

      Size const pos1( mod.find(":") );
      if ( pos1 == std::string::npos ) utility_exit_with_message(errmsg);
      std::string const atomset_tag( mod.substr(0,pos1) );
      if ( atomset_tag != atom_type_set_tag ) continue;

      Size const pos2( mod.substr(pos1+1).find(":") );
      if ( pos2 == std::string::npos ) utility_exit_with_message(errmsg);
      std::string const atom_name( mod.substr(pos1+1,pos2) );
      if ( !atom_type_set.has_atom( atom_name ) ) utility_exit_with_message(errmsg+". Nonexistent atomname: "+atom_name);

      Size const pos3( mod.substr(pos1+1+pos2+1).find(":") );
      if ( pos3 == std::string::npos ) utility_exit_with_message(errmsg);
      std::string const param( mod.substr(pos1+1+pos2+1,pos3) );

      std::string const stringsetting( mod.substr(pos1+1+pos2+1+pos3+1) );
      if ( !ObjexxFCL::is_float( stringsetting ) ) utility_exit_with_message(errmsg);
      Real const setting( ObjexxFCL::float_of( stringsetting ) );

      TR.Trace << "modify_atom_properties_from_command_line: setting " << atomset_tag << ' ' << atom_name << ' ' <<
        param << ' ' << setting << std::endl;

      Size const atom_index( atom_type_set.atom_type_index( atom_name ) );

      /// I would like to uncomment the following if-check, but right now there is an extra parameter file
      /// that defines a parameter with the name LK_DGFREE (memb_fa_params.txt). That's kind of confusing...
      ///
      // if ( atom_type_set.has_extra_parameter( param ) ) {
      //  Size const param_index( atom_type_set.extra_parameter_index( param ) );
      //  atom_type_set[ atom_index ].set_extra_parameter( param_index, setting );
      // } else {
      atom_type_set[ atom_index ].set_parameter( param, setting );
    }
  }
}

} // namespace chemical
} // namespace core