accessibility.hh

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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------
 
#ifndef OST_ACCESSIBILITY_HH
#define OST_ACCESSIBILITY_HH
 
#include <ost/mol/entity_view.hh>
#include <ost/mol/entity_handle.hh>
 
namespace ost { namespace mol { namespace alg {
 
typedef enum {
NACCESS, DSSP
} AccessibilityAlgorithm;
 
class NACCESSAccessibilityParam {
 
public:
  // Singleton access to one constant instance
  static const NACCESSAccessibilityParam& GetInstance() {
    static NACCESSAccessibilityParam instance;
    return instance;
  }
  // Data access
  Real GetVdWRadius(const String& rname, const String& aname, 
                    const String& ele) const;
 
  Real GetResidueAccessibility(const String& rname) const;
 
private:
 
  // construction only inside here
  NACCESSAccessibilityParam();
 
  Real GuessRadius(const String& ele) const;
  
 
  std::map<String, std::map<String, Real> > vdw_radii_;
  std::map<String, Real> accessibilities_;
};
 
class DSSPAccessibilityParam {
  
  public:
    // Singleton access to one constant instance
    static const DSSPAccessibilityParam& GetInstance() {
      static DSSPAccessibilityParam instance;
      return instance;
    }
    // Data access
    Real GetVdWRadius(const String& aname) const;
  
    Real GetResidueAccessibility(const String& rname) const;
 
    const std::vector<Real>& GetFibonacciX() const { return fibonacci_x_; }
    const std::vector<Real>& GetFibonacciY() const { return fibonacci_y_; }
    const std::vector<Real>& GetFibonacciZ() const { return fibonacci_z_; }
    Real GetPointWeight() const { return point_weight_; }
  
  private:
  
    // construction only inside here
    DSSPAccessibilityParam();
  
    std::map<String, std::map<String, Real> > vdw_radii_;
    std::map<String, Real> accessibilities_;
    std::vector<Real> fibonacci_x_;
    std::vector<Real> fibonacci_y_;
    std::vector<Real> fibonacci_z_;
    Real point_weight_;
  };
 
Real Accessibility(ost::mol::EntityView& ent, 
                   Real probe_radius = 1.4,
                   bool include_hydrogens = false,  
                   bool include_hetatm = false,
                   bool include_water = false,
                   bool oligo_mode = false,
                   const String& selection = "",
                   const String& asa_abs = "asaAbs",
                   const String& asa_rel = "asaRel",
                   const String& asa_atom = "asaAtom",
                   AccessibilityAlgorithm algorithm = NACCESS);
 
 
Real Accessibility(ost::mol::EntityHandle& ent, 
                   Real probe_radius = 1.4,
                   bool include_hydrogens = false,
                   bool include_hetatm = false,
                   bool include_water = false,
                   bool oligo_mode = false,
                   const String& selection = "",
                   const String& asa_abs = "asaAbs",
                   const String& asa_rel = "asaRel",
                   const String& asa_atom = "asaAtom",
                   AccessibilityAlgorithm algorithm = NACCESS);
 
}}} //ns
 
#endif