/usr/include/BALL/STRUCTURE/triangulatedSAS.h is in libball1.4-dev 1.4.1+20111206-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 | // -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#ifndef BALL_STRUCTURE_TRIANGULATEDSAS_H
#define BALL_STRUCTURE_TRIANGULATEDSAS_H
#ifndef BALL_STRUCTURE_SASEDGE_H
# include <BALL/STRUCTURE/SASEdge.h>
#endif
#ifndef BALL_STRUCTURE_SASFACE_H
# include <BALL/STRUCTURE/SASFace.h>
#endif
#ifndef BALL_TRUCTURE_SOLVENTEXCLUDEDSURFACE_H
# include <BALL/STRUCTURE/solventAccessibleSurface.h>
#endif
#ifndef BALL_STRUCTURE_TRIANGULATEDSURFACE_H
# include <BALL/STRUCTURE/triangulatedSurface.h>
#endif
#ifndef BALL_STRUCTURE_TRIANGLE_H
# include <BALL/STRUCTURE/triangle.h>
#endif
#ifndef BALL_STRUCTURE_TRIANGLEEDGE_H
# include <BALL/STRUCTURE/triangleEdge.h>
#endif
#ifndef BALL_STRUCTURE_TRIANGLEPOINT_H
# include <BALL/STRUCTURE/trianglePoint.h>
#endif
#ifndef BALL_MATHS_ANGLE_H
# include <BALL/MATHS/angle.h>
#endif
#ifndef BALL_MATHS_CIRCLE3_H
# include <BALL/MATHS/circle3.h>
#endif
#ifndef BALL_MATHS_VECTOR3_H
# include <BALL/MATHS/vector3.h>
#endif
#ifndef BALL_DATATYPE_HASHGRID_H
# include <BALL/DATATYPE/hashGrid.h>
#endif
#include <list>
#include <vector>
namespace BALL
{
class SASTriangulator;
/** Generic TriangulatedSAS Class.
\ingroup Surface
*/
class BALL_EXPORT TriangulatedSAS : public TriangulatedSurface
{
public:
/** @name Class friends
- class SASTriangulator
*/
friend class SASTriangulator;
BALL_CREATE(TriangulatedSAS)
/** @name Constructors and Destructors
*/
//@{
/** Default constructor.
This method creates a new TriangulatedSAS object.
*/
TriangulatedSAS();
/** Copy constructor.
Create a new TriangulatedSAS object from another.
@param surface the TriangulatedSAS object to be copied
@param bool ignored - just for interface consistency
*/
TriangulatedSAS(const TriangulatedSAS& surface, bool = true);
/** Detailed constructor.
Create a new empty TriangulatedSAS object and set its SAS.
@param sas a pointer to the corresponding SAS
@param density the density to use by triangulation
*/
TriangulatedSAS(SolventAccessibleSurface* sas, const double& density);
/** Destructor.
Destructs the TriangulatedSAS object.
*/
virtual ~TriangulatedSAS();
//@}
/** @name Assignment
*/
//@{
/** Assign from another TriangulatedSAS.
@param surface the TriangulatedSAS object to assign from
@param bool ignored - just for interface consistency
*/
void set(const TriangulatedSAS& surface, bool = true);
/** Assign from another TriangulatedSAS.
@param surface the TriangulatedSAS object to assign from
*/
TriangulatedSAS& operator = (const TriangulatedSAS& surface);
//@}
/** @name Accessors
*/
//@{
/** Set the density used by triangulation.
*/
void setDensity(const double& density);
/** Get the density used by triangulation.
*/
double getDensity() const;
/** Compute the solvent-accessible surface
*/
void compute();
//@}
protected:
/*_ @name Attributes
*/
//@{
SolventAccessibleSurface* sas_;
double density_;
//@}
};
/** Generic SASTriangulator Class.
\par
\par
\ingroup Surface
*/
class BALL_EXPORT SASTriangulator
{
public:
#ifdef debug_triangulation
void printToHINFile(string filename);
void Contour2HIN(const std::list<TriangleEdge*>& contour, const string& file);
void SASEdge2HIN(SASEdge* edge, const string& file);
#endif
BALL_CREATE(SASTriangulator)
/** @name Constructors and Destructors
*/
//@{
/** Default constructor.
This method creates a new SASTriangulator object.
*/
SASTriangulator();
/** Detailed constructor.
Create a new empty SASTriangulator object and set its SAS.
@param tsas a pointer to the corresponding SAS
*/
SASTriangulator(TriangulatedSAS* tsas);
/** Destructor.
Destructs the SASTriangulator object.
*/
virtual ~SASTriangulator();
//@}
/** @name Accessors
*/
//@{
void run();
private:
void triangulateFace(SASFace* face);
void createPlanes(SASFace* face,
std::list< std::pair<TPlane3<double>,double> >& planes);
void tagPoints(TriangulatedSurface& part,
const std::list< std::pair<TPlane3<double>,double> >& planes);
void removeInsideTriangles(TriangulatedSurface& part);
HashGrid3<TrianglePoint*> createHashGrid(const TriangulatedSurface& part);
void createPoints(TriangulatedSurface& part,
const std::list< std::pair<TPlane3<double>,double> >& planes,
HashGrid3<TrianglePoint*>& grid);
void createNewTriangles(TriangulatedSurface& part, HashGrid3<TrianglePoint*>& grid);
void onePointOutside(Index outside, Triangle* t,
TriangulatedSurface& part, HashGrid3<TrianglePoint*>& grid);
void twoPointsOutside(Position outside1, Position outside2,
Triangle* t, TriangulatedSurface& part, HashGrid3<TrianglePoint*>& grid);
TrianglePoint* vertexExists(const TVector3<double>& point, HashGrid3<TrianglePoint*>& grid);
Size numberOfRefinements(const double& density, const double& radius);
void buildTemplateSpheres();
//@}
protected:
/** @name Attributes
*/
//@{
TriangulatedSAS* tsas_;
double sqrt_density_;
std::vector< std::list< TVector3<double> > > edge_;
HashMap<Size,TriangulatedSurface> template_spheres_;
//@}
};
} // namespace BALL
#endif // BALL_STRUCTURE_TRIANGULATEDSAS_H
|