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# molshape.h

    00001 //
    00002 // molshape.h
    00003 //
    00004 // Copyright (C) 1996 Limit Point Systems, Inc.
    00005 //
    00006 // Author: Curtis Janssen <cljanss@limitpt.com>
    00007 // Maintainer: LPS
    00008 //
    00009 // This file is part of the SC Toolkit.
    00010 //
    00011 // The SC Toolkit is free software; you can redistribute it and/or modify
    00012 // it under the terms of the GNU Library General Public License as published by
    00013 // the Free Software Foundation; either version 2, or (at your option)
    00014 // any later version.
    00015 //
    00016 // The SC Toolkit is distributed in the hope that it will be useful,
    00017 // but WITHOUT ANY WARRANTY; without even the implied warranty of
    00018 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    00019 // GNU Library General Public License for more details.
    00020 //
    00021 // You should have received a copy of the GNU Library General Public License
    00022 // along with the SC Toolkit; see the file COPYING.LIB.  If not, write to
    00023 // the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
    00024 //
    00025 // The U.S. Government is granted a limited license as per AL 91-7.
    00026 //
    00027
    00028 #ifndef _chemistry_molecule_molshape_h
    00029 #define _chemistry_molecule_molshape_h
    00030
    00031 #ifdef __GNUC__
    00032 #pragma interface
    00033 #endif
    00034
    00035 #include <util/misc/formio.h>
    00036
    00037 #include <math/isosurf/shape.h>
    00038 #include <chemistry/molecule/atominfo.h>
    00039 #include <chemistry/molecule/molecule.h>
    00040
    00041 namespace sc {
    00042
    00047 class VDWShape: public UnionShape {
    00048  private:
    00049     Ref<AtomInfo> atominfo_;
    00050  public:
    00051     VDWShape(const Ref<Molecule>&);
    00052     VDWShape(const Ref<KeyVal>&);
    00053     ~VDWShape();
    00054     void initialize(const Ref<Molecule>&);
    00055 };
    00056
    00061 class DiscreteConnollyShape: public UnionShape {
    00062   private:
    00063     double radius_scale_factor_;
    00064     Ref<AtomInfo> atominfo_;
    00065  public:
    00066     DiscreteConnollyShape(const Ref<KeyVal>&);
    00067     ~DiscreteConnollyShape();
    00068     void initialize(const Ref<Molecule>&,double probe_radius);
    00069 };
    00070
    00071 #ifndef COUNT_CONNOLLY
    00072 # define COUNT_CONNOLLY 1
    00073 #endif
    00074
    00075 // This is a utility class needed by ConnollyShape2
    00076 class CS2Sphere
    00077 {
    00078     SCVector3 _v;
    00079     double _radius;
    00080
    00081   public:
    00082 #if COUNT_CONNOLLY
    00083     static int n_no_spheres_;
    00084     static int n_probe_enclosed_by_a_sphere_;
    00085     static int n_probe_center_not_enclosed_;
    00086     static int n_surface_of_s0_not_covered_;
    00087     static int n_plane_totally_covered_;
    00088     static int n_internal_edge_not_covered_;
    00089     static int n_totally_covered_;
    00090 #endif
    00091
    00092     CS2Sphere(const SCVector3& v, double rad):
    00093     _v(v),_radius(rad){}
    00094     CS2Sphere(double x, double y, double z, double rad):
    00095     _v(x,y,z),_radius(rad){}
    00096     CS2Sphere(void) {};
    00097     void initialize(SCVector3& v, double rad) {
    00098         _v = v; _radius = rad; }
    00099
    00100     CS2Sphere& operator=(const CS2Sphere&s) {
    00101         _v = s._v; _radius = s._radius; return *this; }
    00102
    00103     // Return the distance between the centers of the two
    00104     // spheres
    00105     double distance(CS2Sphere &asphere)
    00106     { return sqrt((_v[0]-asphere._v[0])*(_v[0]-asphere._v[0])+
    00107                   (_v[1]-asphere._v[1])*(_v[1]-asphere._v[1])+
    00108                   (_v[2]-asphere._v[2])*(_v[2]-asphere._v[2]));}
    00109
    00110     // Return the radius of the circle intersecting the two spheres
    00111     // Note that this assumes the spheres do overlap!
    00112     double common_radius(CS2Sphere &asphere);
    00113
    00114     // Return the center
    00115     const SCVector3& center(void) const { return _v; }
    00116     double x() const { return _v[0]; }
    00117     double y() const { return _v[1]; }
    00118     double z() const { return _v[2]; }
    00119
    00120     // Return the vector3d connecting the two centers
    00121     SCVector3 center_vec(const CS2Sphere &asphere) { return _v - asphere._v; }
    00122
    00123     double radius(void) const {return _radius;}
    00124
    00125     void recenter(const SCVector3 &v) { _v -= v; }
    00126     void print(std::ostream& os=ExEnv::out0()) const
    00127     {
    00128       os << indent
    00129          << scprintf("Rad=%lf, Center=(%lf,%lf,%lf), From origin=%lf\n",
    00130                      _radius, _v[0], _v[1], _v[2], _v.norm());
    00131     }
    00132
    00133     // Function to determine if there is any portion of this that
    00134     // is not inside one or more of the spheres in s[].  Returns
    00135     // 1 if the intersection is empty, otherwise 0 is returned.
    00136     // Warning: the spheres in s are modified.
    00137     int intersect(CS2Sphere *s,
    00138                   int n_spheres) const;
    00139
    00140     static void print_counts(std::ostream& = ExEnv::out0());
    00141 };
    00142
    00143 #define CONNOLLYSHAPE_N_WITH_NSPHERE_DIM 10
    00144
    00148 class ConnollyShape: public Shape {
    00149   private:
    00150     CS2Sphere* sphere;
    00151     double probe_r;
    00152     double radius_scale_factor_;
    00153     int n_spheres;
    00154     Ref<AtomInfo> atominfo_;
    00155
    00156     std::vector<int> ***box_;
    00157     double l_;
    00158     int xmax_;
    00159     int ymax_;
    00160     int zmax_;
    00161     SCVector3 lower_;
    00162
    00163     int get_box(const SCVector3 &v, int &x, int &y, int &z) const;
    00164
    00165 #if COUNT_CONNOLLY
    00166     static int n_total_;
    00167     static int n_inside_vdw_;
    00168     static int n_with_nsphere_[CONNOLLYSHAPE_N_WITH_NSPHERE_DIM];
    00169 #endif
    00170
    00171   public:
    00172     ConnollyShape(const Ref<KeyVal>&);
    00173     ~ConnollyShape();
    00174     void initialize(const Ref<Molecule>&,double probe_radius);
    00175     void clear();
    00176     double distance_to_surface(const SCVector3&r,
    00177                                SCVector3*grad=0) const;
    00178     void boundingbox(double valuemin,
    00179                      double valuemax,
    00180                      SCVector3& p1, SCVector3& p2);
    00181
    00182     static void print_counts(std::ostream& = ExEnv::out0());
    00183 };
    00184
    00185 }
    00186
    00187 #endif
    00188
    00189 // Local Variables:
    00190 // mode: c++
    00191 // c-file-style: "CLJ"
    00192 // End: