SymmetricMotifFilter.hh

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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:
//
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// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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/// @file protocols/simplefilters/SymmetricMotifFilter.hh
/// @brief position-independent RMS filter evaluating how close a set of interfaces is to symmetric
/// @author Frank DiMaio

#ifndef INCLUDED_protocols_simple_filters_SymmetricMotifFilter_hh
#define INCLUDED_protocols_simple_filters_SymmetricMotifFilter_hh


#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <protocols/filters/Filter.hh>
#include <utility/tag/Tag.fwd.hh>
#include <list>

#include <utility/vector1.hh>

#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyz.functions.hh>


namespace protocols {
namespace simple_filters {

struct Quat { core::Real x,y,z,w; };
void R2quat( numeric::xyzMatrix< core::Real > R, Quat &Q );
void quat2R( Quat &Q ,numeric::xyzMatrix< core::Real > R );
core::Real RMSwrapper( utility::vector1 <numeric::xyzVector< core::Real > > chainA,
                       utility::vector1 <numeric::xyzVector< core::Real > > chainB,
                       numeric::xyzMatrix< core::Real > &R, 
                      numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT);

//
class SymmetricMotifFilter : public protocols::filters::Filter
{
public:
  SymmetricMotifFilter();
  SymmetricMotifFilter(
    utility::vector1<core::pose::PoseOP> reference_motifs,
    std::string symm_type_in="D2");

  void set_defaults();

  bool apply( core::pose::Pose const & pose ) const;

  void add_motif( core::pose::PoseOP motif );
  void set_symm( std::string symm_type_in ) { symm_type_ = symm_type_in; };

  void set_thresholds( core::Real angle_thresh_in, core::Real trans_thresh_in, core::Real rmsd_thresh_in, core::Size /*clash_thresh_in*/ ) {
    angle_thresh_ = angle_thresh_in;
    trans_thresh_ = trans_thresh_in;
    rmsd_thresh_ = rmsd_thresh_in;
  }

  void set_weights( core::Real angle_thresh_in, core::Real trans_thresh_in, core::Real rmsd_thresh_in ) { 
    angle_thresh_ = angle_thresh_in;
    trans_thresh_ = trans_thresh_in;
    rmsd_thresh_ = rmsd_thresh_in;
  }

  // call after all motifs are added; verifies motifs are of correct symmetry & precomputes all transformations
  void process_motifs();

  protocols::filters::FilterOP clone() const;
  protocols::filters::FilterOP fresh_instance() const { return new SymmetricMotifFilter(); }

  void report( std::ostream & out, core::pose::Pose const & pose ) const;

  // compute angle and rms offsets
  bool compute( core::pose::Pose const & pose, core::Real &best_score, std::string &motifhit ) const;

  // symmetry-specific variants
  bool compute_d2( core::pose::Pose const & pose, core::Real &best_score, std::string &motifhit ) const;
  core::Real score_d2( core::Real rms, core::Real angle, core::Real trans, core::Size clash ) const {
    if (rms<=rmsd_thresh_ && angle<=angle_thresh_ && clash<=clash_thresh_) { 
      return(
        angle_wt_ * (angle-angle_thresh_)
        + rmsd_wt_ * (rms-rmsd_thresh_)
        + trans_wt_ * (trans-trans_thresh_)
        + clash_wt_ * (clash-((int)clash_thresh_)) );
    } else {
      return(999);  // very large
    }
  }


  core::Real report_sm( core::pose::Pose const & pose ) const;

  virtual ~SymmetricMotifFilter();

  void parse_my_tag(
    utility::tag::TagPtr const tag,
    protocols::moves::DataMap & data_map,
    protocols::filters::Filters_map const &,
    protocols::moves::Movers_map const &,
    core::pose::Pose const & reference_pose );

private:
  // symmetry group and motifs
  std::string symm_type_;
  utility::vector1<core::pose::PoseOP> ref_motifs_;
  core::Size nsegs_;

  // filter parameters
  //  * cutoffs for pass/fail
  core::Real angle_thresh_, trans_thresh_,  rmsd_thresh_;
  core::Size clash_thresh_;
  //  * weights for report_sm
  core::Real angle_wt_, trans_wt_,  rmsd_wt_, clash_wt_;

  // force the motifs to a particular location
  utility::vector1< int > forced_pos_;

  // motif coords & transformations
  utility::vector1< Quat > Qs;
  utility::vector1< numeric::xyzMatrix< core::Real > > Rdimers;
  utility::vector1< numeric::xyzVector< core::Real > > delta_coms;
  utility::vector1< numeric::xyzVector< core::Real > > symm_axes;
  utility::vector1< core::Real  > symm_orders;
  utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > cas_chainA, cas_chainB;
  utility::vector1< utility::vector1< core::Size > > motif_cuts;
};

} // filters
}

#endif //INCLUDED_protocols_protein_interface_design_filters_SymmetricMotifFilter_HH_