RmsdEvaluatorCreator.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   protocols/simple_filters/RmsdEvaluatorCreator.hh
/// @brief  Header for RmsdEvaluatorCreator
/// @author Matthew O'Meara

// Unit Headers
#include <protocols/simple_filters/RmsdEvaluatorCreator.hh>

// Package Headers
#include <protocols/evaluation/EvaluatorCreator.hh>

// Package Headers
#include <protocols/evaluation/PoseEvaluator.fwd.hh>
#include <protocols/evaluation/PoseEvaluator.hh>
#include <protocols/simple_filters/RmsdEvaluator.hh>

#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/LoopsFileIO.hh>

#include <core/io/silent/silent.fwd.hh>
#include <core/pose/Pose.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/string.functions.hh>

// Utility headers
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>

#include <basic/options/option.hh>
#include <basic/Tracer.hh>

// due to template function
#include <core/io/silent/SilentStruct.hh>


// option key includes
#include <basic/options/option_macros.hh>
#include <basic/options/keys/evaluation.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector0.hh>


#ifdef WIN32
  #include <core/scoring/constraints/Constraint.hh>
#endif


static basic::Tracer tr("protocols.evaluation.RmsdEvaluatorCreator");

namespace protocols {
namespace simple_filters {

RmsdEvaluatorCreator::~RmsdEvaluatorCreator() {}

void RmsdEvaluatorCreator::register_options() {
  using namespace basic::options;
  if ( options_registered_ ) return;
  options_registered_ = true;

  OPT( evaluation::rmsd );
  OPT( evaluation::gdtmm );
  OPT( in::file::native );

}

void RmsdEvaluatorCreator::add_evaluators( evaluation::MetaPoseEvaluator & eval ) const {
  using namespace core;
  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  if ( option[ OptionKeys::evaluation::rmsd ].user() ) {

    core::pose::PoseOP native_pose = NULL;
    if ( option[ in::file::native ].user() ) {
      native_pose = new core::pose::Pose;
      core::import_pose::pose_from_pdb( *native_pose, option[ in::file::native ]() );
    }

    typedef utility::vector1< std::string > RmsdVector;
    RmsdVector const& rmsd( option[ OptionKeys::evaluation::rmsd ]() );

    //the ultimate in RMSD technology:
    //you can have any number of tripletts:
    // each triplett contains  the
    //    target: file or special tags: NATIVE (use in:file:native ) IRMS (use structure in Job object)
    ///   columnname: XXX creates: rms_XXX  gdtmm_XXX
    ///   selection: file or special tag: FULL
    ///   modifier: EXCLUDE ( take the inverse of the selection )
    ///                INLINE r1 r2 r3 ... rm END_INLINE   -- select residues r1, r2, r3, ..., rm
    for ( RmsdVector::const_iterator it=rmsd.begin(); it!=rmsd.end(); ++it ) {
      core::pose::PoseOP target_pose = NULL;
      std::string fname( *it );
      std::string column;
      std::string selection_file;
      bool CA( true );
      bool invert( false );
      bool loop_rms( false );
      bool superimpose_for_looprms( false );
      ++it;
      loops::Loops core;
      while ( it != rmsd.end() && (*it).find('=')!=std::string::npos ) {
        Size pos( it->find('=') );
        std::string key=it->substr(0,pos);
        std::string value=it->substr(pos+1);
        if ( key=="heavy" && value=="yes" ) {
          tr.Info << "switching to full-atom RMSD " << std::endl;
          CA=false;
        } else if ( key == "loop") {
          loop_rms = true;
        } else if ( key == "superimpose") {
          superimpose_for_looprms = (value=="yes");
        } else if ( key == "core" ) {
          std::ifstream is( value.c_str() );
          
          if (!is.good()) {
            utility_exit_with_message( "[ERROR] Error opening RBSeg file '" + value + "'" );
          }
          loops::PoseNumberedLoopFileReader reader;
          reader.hijack_loop_reading_code_set_loop_line_begin_token( "RIGID" );
          loops::SerializedLoopList loops = reader.read_pose_numbered_loops_file(is, value, false );
          core = loops::Loops( loops );
      } else {
          utility_exit_with_message( "key not recognized: "+key+" possible keys: { heavy }" );
        }
        tr.Info << "detected option: " << key << " : " << value << std::endl;
        ++it;
      }
      if ( it != rmsd.end() ) {
        column = *it;
      } else {
        utility_exit_with_message(
               "need to specify tripletts <target> [key/value pairs] <column> <selection/FULL> with option -evaluation:rmsd   last read: "+fname );
      }
      ++it;
      if ( it != rmsd.end() ) {
        selection_file = *it;
      } else {
        utility_exit_with_message(
               "need to specify tripletts <target> <column> <selection/FULL> with option -evaluation:rmsd   last read: "+column );
      }
      if ( fname == "NATIVE" ) target_pose = native_pose;
      else if ( fname != "IRMS" ) {
        target_pose = new pose::Pose;
        core::import_pose::pose_from_pdb( *target_pose, fname );
      }

      if ( selection_file == "EXCLUDE" ) {
        invert = true;
        ++it;
        if ( it != rmsd.end() ) {
          selection_file = *it;  //read next tag
        } else {
          utility_exit_with_message(
            "need to specify a <selection/FULL> after 'EXCLUDE' with option -evaluation:rmsd    last read: "+column );
        }
      }
      loops::Loops loops;
      utility::vector1< Size> selection; //figure out selection
      if ( selection_file == "INLINE" ) {
        std::string next_tag( "" );
        ++it;
        if ( it != rmsd.end() ) {
          next_tag = *it;
        } else {
          utility_exit_with_message(
            "need to find END_INLINE after INLINE in option -evaluation:rmsd    last read: "+column );
        } //error condition
        while( next_tag != "END_INLINE" ) {
          selection.push_back( utility::string2int( next_tag ) );
          ++it;
          if ( it != rmsd.end() ) {
            next_tag = *it;
          } else {
            utility_exit_with_message(
              "need to find END_INLINE after INLINE in option -evaluation:rmsd    last read: "+column );
          } //error condition
        }
      } else if ( selection_file != "FULL" ) {
        std::ifstream is( selection_file.c_str() );
        
        if (!is.good()) {
          utility_exit_with_message( "[ERROR] Error opening RBSeg file '" + selection_file + "'" );
        }
        loops::SerializedLoopList list_of_loops;
        if ( loop_rms ) {
          loops::PoseNumberedLoopFileReader reader;
          list_of_loops = reader.read_pose_numbered_loops_file(is, selection_file, false );
          loops = loops::Loops( list_of_loops );
        } else {
          loops::PoseNumberedLoopFileReader reader;
          reader.hijack_loop_reading_code_set_loop_line_begin_token( "RIGID" );
          list_of_loops = reader.read_pose_numbered_loops_file(is, selection_file, false );
          loops::Loops core = loops::Loops( list_of_loops );
          core.get_residues( selection );
        }
      }
      if ( invert ) {
        utility::vector1< Size > inverted_selection;
        for ( Size i = 1; i<=target_pose->total_residue(); ++i) {
          bool found( false );
          for ( Size j = 1; j<=selection.size() && !found; ++j ) {
            if ( selection[ j ]==i ) {
              found = true;
            }
          }
          if ( !found) inverted_selection.push_back( i );
        }
        selection = inverted_selection;
      }
      if ( selection_file != "FULL" ) {
        if ( !loop_rms ) {
          eval.add_evaluation( new simple_filters::SelectRmsdEvaluator( target_pose, selection, column, CA ) );
        } else {
          eval.add_evaluation( new simple_filters::LoopRmsdEvaluator( target_pose, loops, core, column, CA, superimpose_for_looprms ) );
        }
        if ( option[ OptionKeys::evaluation::gdtmm ]() ) {
          eval.add_evaluation( new simple_filters::SelectGdtEvaluator( target_pose, selection, column) );
        }
      } else {
        eval.add_evaluation( new simple_filters::SelectRmsdEvaluator( target_pose, column, CA ) );
        if ( option[ OptionKeys::evaluation::gdtmm ]() ) {
          eval.add_evaluation( new simple_filters::SelectGdtEvaluator( target_pose, column ) );
        }
      } // no selection
    } // iterate over tripletts in option -rmsd
  } // option -rmsd

}

std::string RmsdEvaluatorCreator::type_name() const {
  return "RmsdEvaluatorCreator";
}

} //namespace
} //namespace