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molshape.h // // molshape.h // // Copyright (C) 1996 Limit Point Systems, Inc. // // Author: Curtis Janssen <cljanss@limitpt.com> // Maintainer: LPS // // This file is part of the SC Toolkit. // // The SC Toolkit is free software; you can redistribute it and/or modify // it under the terms of the GNU Library General Public License as published by // the Free Software Foundation; either version 2, or (at your option) // any later version. // // The SC Toolkit 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 Library General Public License for more details. // // You should have received a copy of the GNU Library General Public License // along with the SC Toolkit; see the file COPYING.LIB. If not, write to // the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA. // // The U.S. Government is granted a limited license as per AL 91-7. // #ifndef _chemistry_molecule_molshape_h #define _chemistry_molecule_molshape_h #ifdef __GNUC__ #pragma interface #endif #include <util/misc/formio.h> #include <math/isosurf/shape.h> #include <chemistry/molecule/atominfo.h> #include <chemistry/molecule/molecule.h> namespace sc { class VDWShape: public UnionShape { private: Ref<AtomInfo> atominfo_; public: VDWShape(const Ref<Molecule>&); VDWShape(const Ref<KeyVal>&); ~VDWShape(); void initialize(const Ref<Molecule>&); }; class DiscreteConnollyShape: public UnionShape { private: double radius_scale_factor_; Ref<AtomInfo> atominfo_; public: DiscreteConnollyShape(const Ref<KeyVal>&); ~DiscreteConnollyShape(); void initialize(const Ref<Molecule>&,double probe_radius); }; #ifndef COUNT_CONNOLLY # define COUNT_CONNOLLY 1 #endif // This is a utility class needed by ConnollyShape2 class CS2Sphere { SCVector3 _v; double _radius; public: #if COUNT_CONNOLLY static int n_no_spheres_; static int n_probe_enclosed_by_a_sphere_; static int n_probe_center_not_enclosed_; static int n_surface_of_s0_not_covered_; static int n_plane_totally_covered_; static int n_internal_edge_not_covered_; static int n_totally_covered_; #endif CS2Sphere(const SCVector3& v, double rad): _v(v),_radius(rad){} CS2Sphere(double x, double y, double z, double rad): _v(x,y,z),_radius(rad){} CS2Sphere(void) {}; void initialize(SCVector3& v, double rad) { _v = v; _radius = rad; } CS2Sphere& operator=(const CS2Sphere&s) { _v = s._v; _radius = s._radius; return *this; } // Return the distance between the centers of the two // spheres double distance(CS2Sphere &asphere) { return sqrt((_v[0]-asphere._v[0])*(_v[0]-asphere._v[0])+ (_v[1]-asphere._v[1])*(_v[1]-asphere._v[1])+ (_v[2]-asphere._v[2])*(_v[2]-asphere._v[2]));} // Return the radius of the circle intersecting the two spheres // Note that this assumes the spheres do overlap! double common_radius(CS2Sphere &asphere); // Return the center const SCVector3& center(void) const { return _v; } double x() const { return _v[0]; } double y() const { return _v[1]; } double z() const { return _v[2]; } // Return the vector3d connecting the two centers SCVector3 center_vec(const CS2Sphere &asphere) { return _v - asphere._v; } double radius(void) const {return _radius;} void recenter(const SCVector3 &v) { _v -= v; } void print(std::ostream& os=ExEnv::out0()) const { os << indent << scprintf("Rad=%lf, Center=(%lf,%lf,%lf), From origin=%lf\n", _radius, _v[0], _v[1], _v[2], _v.norm()); } // Function to determine if there is any portion of this that // is not inside one or more of the spheres in s[]. Returns // 1 if the intersection is empty, otherwise 0 is returned. // Warning: the spheres in s are modified. int intersect(CS2Sphere *s, int n_spheres) const; static void print_counts(std::ostream& = ExEnv::out0()); }; #define CONNOLLYSHAPE_N_WITH_NSPHERE_DIM 10 class ConnollyShape: public Shape { private: CS2Sphere* sphere; double probe_r; double radius_scale_factor_; int n_spheres; Ref<AtomInfo> atominfo_; Arrayint ***box_; double l_; int xmax_; int ymax_; int zmax_; SCVector3 lower_; int get_box(const SCVector3 &v, int &x, int &y, int &z) const; #if COUNT_CONNOLLY static int n_total_; static int n_inside_vdw_; static int n_with_nsphere_[CONNOLLYSHAPE_N_WITH_NSPHERE_DIM]; #endif public: ConnollyShape(const Ref<KeyVal>&); ~ConnollyShape(); void initialize(const Ref<Molecule>&,double probe_radius); void clear(); double distance_to_surface(const SCVector3&r, SCVector3*grad=0) const; void boundingbox(double valuemin, double valuemax, SCVector3& p1, SCVector3& p2); static void print_counts(std::ostream& = ExEnv::out0()); }; } #endif // Local Variables: // mode: c++ // c-file-style: "CLJ" // End: