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00020 #ifndef OST_ACCESSIBILITY_HH
00021 #define OST_ACCESSIBILITY_HH
00022
00023 #include <ost/mol/entity_view.hh>
00024 #include <ost/mol/entity_handle.hh>
00025
00026 namespace ost { namespace mol { namespace alg {
00027
00028 typedef enum {
00029 NACCESS, DSSP
00030 } AccessibilityAlgorithm;
00031
00032 class NACCESSAccessibilityParam {
00033
00034 public:
00035
00036 static const NACCESSAccessibilityParam& GetInstance() {
00037 static NACCESSAccessibilityParam instance;
00038 return instance;
00039 }
00040
00041 Real GetVdWRadius(const String& rname, const String& aname,
00042 const String& ele) const;
00043
00044 Real GetResidueAccessibility(const String& rname) const;
00045
00046 private:
00047
00048
00049 NACCESSAccessibilityParam();
00050
00051 Real GuessRadius(const String& ele) const;
00052
00053
00054 std::map<String, std::map<String, Real> > vdw_radii_;
00055 std::map<String, Real> accessibilities_;
00056 };
00057
00058 class DSSPAccessibilityParam {
00059
00060 public:
00061
00062 static const DSSPAccessibilityParam& GetInstance() {
00063 static DSSPAccessibilityParam instance;
00064 return instance;
00065 }
00066
00067 Real GetVdWRadius(const String& aname) const;
00068
00069 Real GetResidueAccessibility(const String& rname) const;
00070
00071 const std::vector<Real>& GetFibonacciX() const { return fibonacci_x_; }
00072 const std::vector<Real>& GetFibonacciY() const { return fibonacci_y_; }
00073 const std::vector<Real>& GetFibonacciZ() const { return fibonacci_z_; }
00074 Real GetPointWeight() const { return point_weight_; }
00075
00076 private:
00077
00078
00079 DSSPAccessibilityParam();
00080
00081 std::map<String, std::map<String, Real> > vdw_radii_;
00082 std::map<String, Real> accessibilities_;
00083 std::vector<Real> fibonacci_x_;
00084 std::vector<Real> fibonacci_y_;
00085 std::vector<Real> fibonacci_z_;
00086 Real point_weight_;
00087 };
00088
00089 Real Accessibility(ost::mol::EntityView& ent,
00090 Real probe_radius = 1.4,
00091 bool include_hydrogens = false,
00092 bool include_hetatm = false,
00093 bool include_water = false,
00094 bool oligo_mode = false,
00095 const String& selection = "",
00096 const String& asa_abs = "asaAbs",
00097 const String& asa_rel = "asaRel",
00098 const String& asa_atom = "asaAtom",
00099 AccessibilityAlgorithm algorithm = NACCESS);
00100
00101
00102 Real Accessibility(ost::mol::EntityHandle& ent,
00103 Real probe_radius = 1.4,
00104 bool include_hydrogens = false,
00105 bool include_hetatm = false,
00106 bool include_water = false,
00107 bool oligo_mode = false,
00108 const String& selection = "",
00109 const String& asa_abs = "asaAbs",
00110 const String& asa_rel = "asaRel",
00111 const String& asa_atom = "asaAtom",
00112 AccessibilityAlgorithm algorithm = NACCESS);
00113
00114 }}}
00115
00116 #endif