SigmoidFilter.hh

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//
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/// @file protocols/simple_filters/SigmoidFilter.hh

#ifndef INCLUDED_protocols_simple_filters_SigmoidFilter_hh
#define INCLUDED_protocols_simple_filters_SigmoidFilter_hh

//unit headers
#include <protocols/simple_filters/SigmoidFilter.fwd.hh>

// Project Headers
#include <core/types.hh>
#include <protocols/filters/Filter.hh>
#include <core/pose/Pose.fwd.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <protocols/moves/Mover.fwd.hh>

namespace protocols {
namespace simple_filters {

///@brief transform the output from a regular filter into a sigmoid ranging from 0-1 according to:
/// fx = 1/[1 + exp[ ( x - offset ) * steepness ]
/// The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset
class Sigmoid : public filters::Filter
{
  public:
    Sigmoid();
    virtual ~Sigmoid();
    filters::FilterOP clone() const {
      return new Sigmoid( *this );
    }
    filters::FilterOP fresh_instance() const{
      return new Sigmoid();
    }

    virtual bool apply( core::pose::Pose const & pose ) const;
    virtual void report( std::ostream & out, core::pose::Pose const & pose ) const;
    virtual core::Real report_sm( core::pose::Pose const & pose ) const;
    void parse_my_tag( utility::tag::TagPtr const tag, moves::DataMap &, filters::Filters_map const &filters, moves::Movers_map const &, core::pose::Pose const & );
    core::Real compute( core::pose::Pose const & pose ) const;
    core::Real steepness() const{ return steepness_; }
    void steepness( core::Real const s ){ steepness_ = s; }
    core::Real offset(){ return offset_; }
    void offset( core::Real const o ){ offset_ = o; }
    bool negate() const{ return negate_; }
    void negate( bool const b ){ negate_ = b; }
    protocols::filters::FilterOP filter() const;
    void filter( protocols::filters::FilterOP f );
    void reset_baseline( core::pose::Pose const & pose, bool const attempt_read_from_checkpoint ); /// allows within-trajectory resetting of the baseline. Notice this is nonconst, so can't be called from apply. attempt_read_from_checkpoint should be true for MC trials > 1, but false otherwise
    core::Real threshold() const{ return threshold_; }
    void threshold( core::Real const t ){ threshold_ = t; }
    void baseline_checkpointing_filename( std::string const s ){ baseline_checkpointing_filename_ = s; }
    std::string baseline_checkpointing_filename() const{ return baseline_checkpointing_filename_; }
  private:
    protocols::filters::FilterOP filter_; /// dflt NULL
    core::Real steepness_; //dflt 1
    core::Real offset_;/// dflt 0
    core::Real baseline_; /// dflt 0; this is tricky; used internally to keep track of where the pose started. It is only reset by reset_baseline, and cannot, due to constness, be changed by apply
    bool negate_; /// dflt false
    core::Real threshold_; /// dflt 0 (always accept)
    std::string baseline_checkpointing_filename_; // dflt ""; If this is set, the baseline value is saved to a checkpointing file to allow for recovery of the baseline after failure.
};
}
}

#endif