SheetFilter.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:
//
// (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/protocols/filters/SheetFilters.hh
/// @brief header file for SheetSheetFilter class.
/// @detailed
/// @author Robert Vernon
/// @author James Thompson

#ifndef INCLUDED_protocols_simple_filters_SheetFilter_hh
#define INCLUDED_protocols_simple_filters_SheetFilter_hh

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

// Project Headers
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
// AUTO-REMOVED #include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>

// ObjexxFCL Headers
// AUTO-REMOVED #include <ObjexxFCL/FArray1D.hh>
// AUTO-REMOVED #include <ObjexxFCL/FArray2D.hh>
// AUTO-REMOVED #include <ObjexxFCL/FArray1A.hh>
// AUTO-REMOVED #include <ObjexxFCL/FArray2A.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>
#include <ObjexxFCL/FArray2D.fwd.hh>
#include <ObjexxFCL/FArray1A.fwd.hh>
#include <ObjexxFCL/FArray2A.fwd.hh>

// Utility headers

//// C++ headers
// AUTO-REMOVED #include <cstdlib>
#include <string>
// AUTO-REMOVED #include <vector>

#include <utility/vector1.hh>


namespace protocols {
namespace simple_filters {

class SheetFilter : public AbinitioBaseFilter {
public:

  /// c-tor and d-tor
  SheetFilter() {
    using namespace basic::options;
    using namespace basic::options::OptionKeys;
  }
  virtual ~SheetFilter() {}

  filters::FilterOP clone() const {
    return new SheetFilter( *this ); }

  filters::FilterOP fresh_instance() const{
    return new SheetFilter(); }


  /// @brief Returns true if the given pose passes the filter, false otherwise.
  virtual
  bool apply( core::pose::Pose const & pose ) const;

  static int const max_nstr = 50;

  virtual std::string name() const {
    return "SheetFilter";
  }

private:

  // data
  /// @brief initialized_ is true if init() has been called, false otherwise.
  bool initialized_;
  mutable float handedness_score_;

  // methods

  void ingo_diamers(
    int const & nres,
    ObjexxFCL::FArray1A_int strnm,
    int natm,
    ObjexxFCL::FArray2D_float const & atmps,
    ObjexxFCL::FArray1D_int & rnm,
    ObjexxFCL::FArray1D_int & indC,
    ObjexxFCL::FArray1D_int & indN,
    ObjexxFCL::FArray2A_float strdm,
    ObjexxFCL::FArray1A_int inddm
  ) const;

  void
  ingo_find_dir(
    int shnm,
    int hm,
    int & nstr,
    ObjexxFCL::FArray1A_int slct,
    ObjexxFCL::FArray1A_int order,
    ObjexxFCL::FArray1A_int strlbl,
    ObjexxFCL::FArray2A_float strdr,
    // int & proper, // Not used
    ObjexxFCL::FArray1A_int directions
  ) const;

  void
  ingo_find_ord(
    int shnm,
    int hm,
    int & nstr,
    ObjexxFCL::FArray1A_int strlbl,
    ObjexxFCL::FArray2A_float dstrmin,
    float ngbhct,
    ObjexxFCL::FArray1A_int order,
    ObjexxFCL::FArray1A_int sequence,
    ObjexxFCL::FArray1A_int slct,
    int & rubbish
  ) const;

  void
  ingo_hand(
    int const k,
    int const hm,
    ObjexxFCL::FArray1A_int stpppt,
    ObjexxFCL::FArray1A_int strtpt,
    int const str1,
    int const str2,
    ObjexxFCL::FArray1A_int order,
    ObjexxFCL::FArray2A_float strdr,
    int const nstr,
    int const nres,
    ObjexxFCL::FArray1A_int sequence,
    ObjexxFCL::FArray1A_int directions,
    ObjexxFCL::FArray1A_int scstr,
    ObjexxFCL::FArray2A_float lctn,
    bool const use_whole_helix,
    int & rubbish
  ) const;

  void
  ingo_ident_sheets(
    int &nstr,
    ObjexxFCL::FArray2A_float dstrmin,
    float ngbhct,
    ObjexxFCL::FArray2A_int strprs,
    int & nsht,
    ObjexxFCL::FArray1A_int strsht,
    ObjexxFCL::FArray1A_int strlbl,
    int & rubbish
  ) const;

  void
  ingo_lnl(
   int hm,
   ObjexxFCL::FArray1A_int order,
   int & nloc,
   int & nnloc
 ) const;

  void
  ingo_locations(
    int const & nres,
    int natm,
    ObjexxFCL::FArray1D_int & indCA,
    ObjexxFCL::FArray2D_float const & atmps,
    ObjexxFCL::FArray2A_float lctn
  ) const;

  void
  ingo_number_of_strands(
    int const & nres,
    ObjexxFCL::FArray1A_int scstr,
    int & nstr
  ) const;

  void
  ingo_proper_sheets(
    int & nstr,
    int & nsht,
    float ngbhct,
    ObjexxFCL::FArray2A_float dstrmin,
    ObjexxFCL::FArray2A_float strdr,
    ObjexxFCL::FArray1A_int strsht,
    ObjexxFCL::FArray1A_int strlbl,
    int & rubbish,
    float & maxdist,
    float & mindotprodabs,
    ObjexxFCL::FArray1A_int strtpt,
    ObjexxFCL::FArray1A_int stpppt,
    ObjexxFCL::FArray2A_int locdsm,
    ObjexxFCL::FArray2A_float lctn,
    int const & nres
  ) const;

  void
  ingo_sheet_stuff(
    int const & nres,
    ObjexxFCL::FArray1A_int scstr,
    int natm,
    ObjexxFCL::FArray2D_float const & atmps,
    ObjexxFCL::FArray1D_int & indN,
    ObjexxFCL::FArray1D_int & indCA,
    ObjexxFCL::FArray1D_int & indC,
    ObjexxFCL::FArray1D_int & rnm,
    float ngbhct,
    int & nstr,
    int & nsht,
    float & maxdt,
    float & mindp,
    int & nloc,
    int & nnloc,
    int & rubbish
  ) const;

  void
  ingo_start_stop(
    int const & nres,
    ObjexxFCL::FArray1A_int scstr,
    int & nstr,
    ObjexxFCL::FArray1A_int strnm,
    ObjexxFCL::FArray1A_int strtpt,
    ObjexxFCL::FArray1A_int stpppt
  ) const;

  void
  ingo_strand_dirs(
    int const & nres,
    int & nstr,
    ObjexxFCL::FArray1A_int strtpt,
    ObjexxFCL::FArray1A_int stpppt,
    ObjexxFCL::FArray2A_float lctn,
    ObjexxFCL::FArray2A_float strdr
  ) const;

  void
  ingo_strand_dists_min(
    int const & nres,
    int & nstr,
    ObjexxFCL::FArray1A_int inddm,
    ObjexxFCL::FArray1A_int strnm,
    ObjexxFCL::FArray2A_float strdm,
    ObjexxFCL::FArray2A_float dstrmin,
    ObjexxFCL::FArray2A_int locdsm
  ) const;

  void ingo_clean_ss(
    int const & nres,
    ObjexxFCL::FArray1A_int scstr
  ) const;
};

} // filters
} // protocols

#endif