FlexPepDockingFlags.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) 199x-2008 Hebrew University, Jerusalem
//
// (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   FlexPepDockingFlags.hh
///
/// @brief flags structure for FlexPepDocking protocols
/// @date January 1, 2009
/// @author Barak Raveh

#ifndef INCLUDED_protocols_flexpep_docking_FlexPepDockingFlags_hh
#define INCLUDED_protocols_flexpep_docking_FlexPepDockingFlags_hh

#include <core/pose/Pose.fwd.hh>
#include <protocols/flexpep_docking/FlexPepDockingFlags.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <map>
// AUTO-REMOVED #include <cstdlib>
#include <string>

#include <utility/vector1.hh>


namespace protocols {
namespace flexpep_docking {


class FlexPepDockingFlags
 : public utility::pointer::ReferenceCount
{
public:

  ///////////////////////////////////////////////
  /// @brief
  /// initialize all flags from cmd-line options
  ///////////////////////////////////////////////
  FlexPepDockingFlags();

  // TODO: documentation
  FlexPepDockingFlagsOP clone() const {
    return new FlexPepDockingFlags( *this );
  }

  // TODO: more documentation
  // validate chain info (if no info specified, choose first two chains)
  void updateChains(core::pose::Pose const& pose);

  // TODO: more documentation
  // set default chain anchors (peptide c.o.m, and nearest receptor residue)
  void setDefaultAnchors(core::pose::Pose& pose); // TODO: pose should be const, but need to fix RB_geometry 4 this

  // update chane boundaries and anchors -
  // support for old params-file format
  //
  // TODO: also take chain-ids from params file
  void updateChainsAndAnchors_fromParamsFile
  ( std::string const& params_file );

  // TODO: documentation
  bool valid_chain_info() const
  {
    return (valid_receptor_chain_ || pep_fold_only) && valid_peptide_chain_ && valid_chain_bounds_;
  }
  
  bool valid_receptor_chain() const
  { return valid_receptor_chain_; }

  bool valid_peptide_chain() const
  { return valid_peptide_chain_; }

  // TODO: documentation
  bool valid_anchors() const
  {
    return
      (peptide_anchors.size() > 0 &&
        peptide_anchors.size() == peptide_cuts.size() + 1 &&
       (receptor_anchor_pos != -1 || pep_fold_only) );
  }


public:
  /////////////////////
  // Accessor Methods:
  /////////////////////

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

  char receptor_chain() const;

  char peptide_chain() const;

  void set_receptor_chain(char ch){
    receptor_chain_ = ch; valid_receptor_chain_ = true;
  }
  
  void set_peptide_chain(char ch){
    peptide_chain_ = ch; valid_peptide_chain_ = true;
  }
  
  int receptor_first_res() const;

  int receptor_last_res() const;

  int receptor_nres() const;

  int peptide_first_res() const;

  int peptide_last_res() const;

  int peptide_nres() const;

  std::string ref_start_struct() const;

  bool valid_ref_start_struct() const;


private:
  // TODO: change all ints to Size, and add access to basic::options::user() to check validity
  // chain info fields
  char receptor_chain_;
  char peptide_chain_;
  int receptor_first_res_;
  int receptor_nres_;
  int peptide_first_res_;
  int peptide_nres_;
  bool valid_receptor_chain_;
  bool valid_peptide_chain_;
  bool valid_chain_bounds_; // refers to fields above
  std::string ref_start_struct_;
  bool valid_ref_start_struct_;
public:
  bool pep_fold_only;
  int receptor_anchor_pos; // anchor position within the receptor protein
  std::map<int,int> peptide_cuts; // peptide internal cuts
  std::map<int,int> peptide_anchors; // anchors for peptide fragments
  std::string params_file; // parameters for describing the complex, anchor residues, etc.
  bool lowres_abinitio;
  bool lowres_preoptimize;
  bool min_only;
  bool pep_refine;
  bool random_phi_psi_pert;
  double random_phi_psi_pert_size;
  bool extend;
  bool randomRBstart;
  bool rbMCM;
  double rb_trans_size;
  double rb_rot_size;
  bool torsionsMCM;
  bool peptide_loop_model;
  double smove_angle_range;
  bool design_peptide;
  bool backrub_opt;
  bool boost_fa_atr;
  bool ramp_fa_rep;
  bool ramp_rama;
  int rep_ramp_cycles;
  int mcm_cycles; // TODO: spearate rigid-body and torsion cycles #
  bool min_receptor_bb;
  bool score_only;
  bool use_cen_score;
  bool ppk_only;
  bool no_prepack1;
  bool no_prepack2;
  double score_filter;
  int    hb_filter;
  int    hotspot_filter;
  double frag3_weight;
  double frag5_weight;
  double frag9_weight;
  bool pSer2Asp_centroid;
  bool pSer2Glu_centroid;
  bool dumpPDB_abinitio;
  bool dumpPDB_lowres;
  bool dumpPDB_hires;
}; // class FlexPepDockingFlags

} // namespace flexpep_docking
} // namespace protocols

#endif