BALL: solventExcludedSurface.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 // $Id: solventExcludedSurface.h,v 1.39 2005/12/23 17:02:05 amoll Exp $
00005 //
00006 
00007 #ifndef BALL_STRUCTURE_SOLVENTEXCLUDEDSURFACE_H
00008 #define BALL_STRUCTURE_SOLVENTEXCLUDEDSURFACE_H
00009 
00010 #ifndef BALL_STRUCTURE_SESEDGE_H
00011 # include <BALL/STRUCTURE/SESEdge.h>
00012 #endif
00013 
00014 #ifndef BALL_STRUCTURE_SESFACE_H
00015 # include <BALL/STRUCTURE/SESFace.h>
00016 #endif
00017 
00018 #ifndef BALL_STRUCTURE_SESVERTEX_H
00019 # include <BALL/STRUCTURE/SESVertex.h>
00020 #endif
00021 
00022 #ifndef BALL_STRUCTURE_REDUCEDSURFACE_H
00023 # include <BALL/STRUCTURE/reducedSurface.h>
00024 #endif
00025 
00026 #ifndef BALL_MATHS_ANGLE_H
00027 # include <BALL/MATHS/angle.h>
00028 #endif
00029 
00030 #ifndef BALL_MATHS_CIRCLE3_H
00031 # include <BALL/MATHS/circle3.h>
00032 #endif
00033 
00034 #ifndef BALL_MATHS_SPHERE3_H
00035 # include <BALL/MATHS/sphere3.h>
00036 #endif
00037 
00038 #ifndef BALL_MATHS_VECTOR3_H
00039 # include <BALL/MATHS/vector3.h>
00040 #endif
00041 
00042 #ifndef BALL_MATHS_VECTOR4_H
00043 # include <BALL/MATHS/vector4.h>
00044 #endif
00045 
00046 #ifndef BALL_DATATYPE_HASHGRID_H
00047 # include <BALL/DATATYPE/hashGrid.h>
00048 #endif
00049 
00050 #ifndef BALL_DATATYPE_HASHMAP_H
00051 # include <BALL/DATATYPE/hashMap.h>
00052 #endif
00053 
00054 #include <vector>
00055 #include <list>
00056 
00057 
00058 namespace BALL
00059 {
00060   class SESComputer;
00061   class SESSingularityCleaner;
00062   class TriangulatedSES;
00063   class SESTriangulator;
00064 
00068   class BALL_EXPORT SolventExcludedSurface
00069   {
00070     public:
00071 
00080     friend class SESComputer;
00081     friend class SESSingularityCleaner;
00082     friend class TriangulatedSES;
00083     friend class SESTriangulator;
00084 
00085     BALL_CREATE(SolventExcludedSurface)
00086 
00087     
00090 
00091     typedef std::vector<SESVertex*>::iterator
00092             VertexIterator;
00093     typedef std::vector<SESVertex*>::const_iterator
00094             ConstVertexIterator;
00095     typedef std::vector<SESEdge*>::iterator
00096             EdgeIterator;
00097     typedef std::vector<SESEdge*>::const_iterator
00098             ConstEdgeIterator;
00099     typedef std::list<SESEdge*>::iterator
00100             SingularEdgeIterator;
00101     typedef std::list<SESEdge*>::const_iterator
00102             ConstSingularEdgeIterator;
00103     typedef std::vector<SESFace*>::iterator
00104             ContactFaceIterator;
00105     typedef std::vector<SESFace*>::const_iterator
00106             ConstContactFaceIterator;
00107     typedef std::vector<SESFace*>::iterator
00108             SphericFaceIterator;
00109     typedef std::vector<SESFace*>::const_iterator
00110             ConstSphericFaceIterator;
00111     typedef std::vector<SESFace*>::iterator
00112             ToricFaceIterator;
00113     typedef std::vector<SESFace*>::const_iterator
00114             ConstToricFaceIterator;
00115 
00117 
00120 
00124     SolventExcludedSurface()
00125       ;
00126 
00132     SolventExcludedSurface
00133         (const SolventExcludedSurface& ses, bool = false)
00134       ;
00135 
00138     SolventExcludedSurface(ReducedSurface* reduced_surface)
00139       ;
00140 
00144     virtual ~SolventExcludedSurface()
00145       ;
00146 
00148 
00151 
00152     void clear();
00153 
00154     void clean(const double& density);
00155 
00158     void compute()
00159       throw(Exception::GeneralException);
00160 
00161     void splitSphericFaces()
00162       ;
00163 
00164     bool check()
00165       ;
00166 
00168 
00171 
00172     VertexIterator beginVertex()
00173       ;
00174     ConstVertexIterator beginVertex() const
00175       ;
00176     VertexIterator endVertex()
00177       ;
00178     ConstVertexIterator endVertex() const
00179       ;
00180 
00181     EdgeIterator beginEdge()
00182       ;
00183     ConstEdgeIterator beginEdge() const
00184       ;
00185     EdgeIterator endEdge()
00186       ;
00187     ConstEdgeIterator endEdge() const
00188       ;
00189 
00190     SingularEdgeIterator beginSingularEdge()
00191       ;
00192     ConstSingularEdgeIterator beginSingularEdge() const
00193       ;
00194     SingularEdgeIterator endSingularEdge()
00195       ;
00196     ConstSingularEdgeIterator endSingularEdge() const
00197       ;
00198 
00199     ContactFaceIterator beginContactFace()
00200       ;
00201     ConstContactFaceIterator beginContactFace() const
00202       ;
00203     ContactFaceIterator endContactFace()
00204       ;
00205     ConstContactFaceIterator endContactFace() const
00206       ;
00207 
00208     SphericFaceIterator beginSphericFace()
00209       ;
00210     ConstSphericFaceIterator beginSphericFace() const
00211       ;
00212     SphericFaceIterator endSphericFace()
00213       ;
00214     ConstSphericFaceIterator endSphericFace() const
00215       ;
00216 
00217     ToricFaceIterator beginToricFace()
00218       ;
00219     ConstToricFaceIterator beginToricFace() const
00220       ;
00221     ToricFaceIterator endToricFace()
00222       ;
00223     ConstToricFaceIterator endToricFace() const
00224       ;
00225 
00227 
00228     private:
00229 
00230     void splitSphericFace(Position i)
00231       ;
00232 
00233     void deleteSmallToricFace(SESFace* face)
00234       ;
00235 
00236     void deleteSmallSingularToricFace(SESFace* face)
00237       ;
00238 
00239     bool cleanToricFace(SESFace* face, const double& sqrt_density)
00240       ;
00241 
00242     bool cleanSingularToricFace(SESFace* face, const double& sqrt_density)
00243       ;
00244 
00245     void cleanVertices()
00246       ;
00247 
00248     void cleanEdges()
00249       ;
00250 
00251     void cleanContactFaces()
00252       ;
00253 
00254     void cleanToricFaces()
00255       ;
00256 
00257     void cleanSphericFaces()
00258       ;
00259 
00260 
00261     protected:
00262 
00263     /*_ the number of vertices of the solvent exluded surface
00264     */
00265     Position number_of_vertices_;
00266     /*_ the vertices of the solvent exluded surface
00267     */
00268     ::std::vector<SESVertex*> vertices_;
00269     /*_ the number of edges of the solvent exluded surface
00270     */
00271     Position number_of_edges_;
00272     /*_ the edges of the solvent exluded surface
00273     */
00274     ::std::vector<SESEdge*> edges_;
00275     /*_ the number of singular edges of the solvent exluded surface
00276     */
00277     Position number_of_singular_edges_;
00278     /*_ the singular edges of the solvent exluded surface
00279     */
00280     ::std::list<SESEdge*> singular_edges_;
00281     /*_ the number of contact faces of the solvent exluded surface
00282     */
00283     Position number_of_contact_faces_;
00284     /*_ the contact faces of the solvent exluded surface
00285     */
00286     ::std::vector<SESFace*> contact_faces_;
00287     /*_ the number of toric reentrant faces of the solvent exluded surface
00288     */
00289     Position number_of_toric_faces_;
00290     /*_ the toric reentrant faces of the solvent exluded surface
00291     */
00292     ::std::vector<SESFace*> toric_faces_;
00293     /*_ the number of spheric reentrant faces of the solvent exluded surface
00294     */
00295     Position number_of_spheric_faces_;
00296     /*_ the spheric reentrant faces of the solvent exluded surface
00297     */
00298     ::std::vector<SESFace*> spheric_faces_;
00299     /*_ the corresponding reduced surface
00300     */
00301     ReducedSurface* reduced_surface_;
00302 
00303   };
00304 
00305 
00309 
00312   BALL_EXPORT std::ostream& operator <<
00313       (std::ostream& s, const SolventExcludedSurface& ses);
00314 
00316 
00317 
00318 
00322   class BALL_EXPORT SESComputer
00323   {
00324     public:
00325 
00326     BALL_CREATE(SESComputer)
00327 
00328     
00331 
00335     SESComputer()
00336       ;
00337 
00340     SESComputer(SolventExcludedSurface* ses)
00341       ;
00342 
00346     virtual ~SESComputer()
00347       ;
00348 
00350 
00353 
00356     void run()
00357       throw(Exception::GeneralException);
00358 
00360 
00361     private:
00362 
00363     /*_ @name SES computation (private)
00364     */
00366 
00367     void preProcessing()
00368       ;
00369 
00370     void get()
00371       ;
00372 
00373     void createSphericFace(Position j)
00374       ;
00375 
00376     SESVertex* createVertex
00377       (const TVector3<double>& probe_center,
00378        Index index)
00379       ;
00380 
00381     void pushVertex
00382       (SESFace* face,
00383        const TSphere3<double>& probe,
00384        RSVertex* rsvertex)
00385       ;
00386 
00387     SESEdge* createConcaveEdge
00388       (SESFace* spheric_face,
00389        Position p1,
00390        Position p2,
00391        Index index,
00392        const double& radius_of_probe)
00393       ;
00394 
00395     void pushConcaveEdge
00396       (SESFace* face,
00397        Position p1,
00398        Position p2,
00399        const double& radius_of_probe)
00400       ;
00401 
00402     SESEdge* createConvexEdge
00403       (SESFace* toric_face,
00404        RSVertex* rsvertex)
00405       ;
00406 
00407     void createToricFace(Position i)
00408       ;
00409 
00410     void treatSingularToricFace(Position i)
00411       ;
00412 
00413     void createFreeToricFace(Position i)
00414       ;
00415 
00416     SESVertex* createSingularVertex
00417         (Position ip,
00418          const TVector3<double>& dir,
00419          SESFace* face0,
00420          SESFace* face1,
00421          SESFace* face2,
00422          SESEdge* edge0,
00423          SESEdge* edge1,
00424          SESEdge* edge2)
00425       ;
00426 
00427     void updateEdge
00428         (SESEdge*   edge,
00429          SESVertex* vertex1,
00430          SESVertex* vertex2,
00431          bool           is_new)
00432       ;
00433 
00434     void getPoint
00435       (const TVector3<double>& p1,
00436        const TVector3<double>& p2,
00437        const double&            dist,
00438        TVector3<double>&        result)
00439       ;
00440 
00441     Index vertexExists(const TVector3<double>& point)
00442       ;
00443 
00445 
00446 
00447     protected:
00448 
00449     /*_ a pointer to the solvent excluded surface to compute
00450     */
00451     SolventExcludedSurface* ses_;
00452     /*_ a HashGrid to store and find the vertices in an efficient way
00453     */
00454     HashGrid3<Index> vertex_grid_;
00455 
00456   };
00457 
00458 
00459 
00460 
00464   class BALL_EXPORT SESSingularityCleaner
00465   {
00466     public:
00467 
00468     BALL_CREATE(SESSingularityCleaner)
00469 
00470     typedef std::pair< std::pair<TAngle<double>,Index>,TVector3<double> > Intersection;
00471 
00472     struct ProbeIntersection
00473     {
00474       TVector3<double> point[2];
00475     };
00476 
00477     friend class SESComputer;
00478 
00482 
00486     SESSingularityCleaner()
00487       ;
00488 
00491     SESSingularityCleaner
00492         (SolventExcludedSurface*  ses,
00493          HashGrid3<Index>*        vertex_grid_)
00494       ;
00495 
00499     virtual ~SESSingularityCleaner()
00500       ;
00501 
00503 
00506 
00509     bool run()
00510       throw(Exception::GeneralException);
00511 
00513 
00514     private:
00515 
00519 
00520     Index vertexExists(TVector3<double> point)
00521       ;
00522 
00523     void treatSingularities()
00524       ;
00525 
00526     void getSingularFaces(std::list<SESFace*>& faces)
00527       ;
00528 
00529     bool treatFirstCategory()
00530       ;
00531 
00532     void treatSecondCategory()
00533       ;
00534 
00535     void getFirstCategoryFaces(std::list<SESFace*>& first_category_faces)
00536       ;
00537 
00538     void noCut(SESFace* face1, SESFace* face2)
00539       ;
00540 
00541     void twoCuts(SESFace* face1, SESFace* face2)
00542       ;
00543 
00544     void treatSingularEdge
00545       (SESEdge*               edge,
00546        HashGrid3<Position>&   grid,
00547        ::std::list<SESEdge*>& deletable_edges)
00548       ;
00549 
00550     void getIntersectionsOfSingularEdge
00551       (SESEdge*                 edge,
00552        const TAngle<double>&              phi,
00553        HashGrid3<Position>&     grid,
00554        std::list<Intersection>& intersections)
00555       ;
00556 
00557     bool getIntersectionPointsAndAngles
00558       (const TCircle3<double>&  circle,
00559        const TVector3<double>&  point,
00560        Position       index1,
00561        Position       index2,
00562        Position       probe_index,
00563        TAngle<double>&          phi1,
00564        TVector3<double>&        point1,
00565        TAngle<double>&          phi2,
00566        TVector3<double>&        point2)
00567       ;
00568 
00569     bool isIntersection
00570        (const TAngle<double>&  min_phi,
00571         const TAngle<double>&  max_phi,
00572         const TAngle<double>&  phi,
00573         const TVector3<double>& middle,
00574         const TSphere3<double>& probe)
00575       ;
00576 
00577     void buildEndEdges
00578       (SESEdge*                       edge,
00579        const std::list<Intersection>& min,
00580        const std::list<Intersection>& max,
00581        SESVertex*&                    vertex1,
00582        SESVertex*&                    vertex2,
00583        Index&                         actual_min,
00584        Index&                         actual_max)
00585       ;
00586 
00587     void buildEdge
00588       (SESEdge*               edge,
00589        Index                  face1,
00590        Index&                 face2,
00591        Index                  end,
00592        SESVertex*&            vertex,
00593        const HashSet<Index>&  indices,
00594        bool                   minimum)
00595       ;
00596 
00597     void getExtrema
00598         (const std::list<Intersection>& intersections,
00599          std::list<Intersection>& min,
00600          std::list<Intersection>& max)
00601       ;
00602 
00603     void buildEndEdge
00604       (SESEdge*                       edge,
00605        const std::list<Intersection>& extrema,
00606        SESVertex*&                    vertex,
00607        Index&                         actual_extremum,
00608        bool                           min)
00609       ;
00610 
00611     bool probeIntersection
00612        (Index    face1,
00613         Index    face2,
00614         Index    face3,
00615         TVector3<double>& point1,
00616         TVector3<double>& point2)
00617       ;
00618 
00619     void sort
00620         (SESFace* face1,
00621          SESFace* face2,
00622          std::vector<SESEdge*>& sesedge1,
00623          std::vector<SESEdge*>& sesedge2,
00624          std::vector<SESVertex*>& sesvertex1,
00625          std::vector<SESVertex*>& sesvertex2)
00626       ;
00627 
00628     void sort
00629        (Index   u1, Index   u2, Index   u3,
00630         Index&  s1, Index&  s2, Index&  s3)
00631       ;
00632 
00634 
00635 
00636     protected:
00637 
00638     /*_ a pointer to the solvent excluded surface to compute
00639     */
00640     SolventExcludedSurface* ses_;
00641     /*_ a pointer to a HashGrid to store and find the vertices
00642         in an efficient way
00643     */
00644     HashGrid3<Index>* vertex_grid_;
00645     /*_ for each triple of probe spheres its intersections
00646     */
00647     HashMap< Position,
00648              HashMap< Position,
00649                       HashMap< Position,
00650                                ProbeIntersection*
00651                              >
00652                     >
00653            > probe_intersections_;
00654 
00655   };
00656 
00657    
00658 } // namespace BALL
00659 
00660 #endif  // BALL_STRUCTURE_SOLVENTEXCLUDEDSURFACE_H