.. _program_listing_file_cif++_point.hpp:

Program Listing for File point.hpp
==================================

|exhale_lsh| :ref:`Return to documentation for file <file_cif++_point.hpp>` (``cif++/point.hpp``)

.. |exhale_lsh| unicode:: U+021B0 .. UPWARDS ARROW WITH TIP LEFTWARDS

.. code-block:: cpp

   /*-
    * SPDX-License-Identifier: BSD-2-Clause
    *
    * Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
    *
    * Redistribution and use in source and binary forms, with or without
    * modification, are permitted provided that the following conditions are met:
    *
    * 1. Redistributions of source code must retain the above copyright notice, this
    *    list of conditions and the following disclaimer
    * 2. Redistributions in binary form must reproduce the above copyright notice,
    *    this list of conditions and the following disclaimer in the documentation
    *    and/or other materials provided with the distribution.
    *
    * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
    * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
    * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
    * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
    * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
    * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
    * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
    * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
    * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    */
   
   #pragma once
   
   #include <array>
   #include <cmath>
   #include <complex>
   #include <cstdint>
   #include <functional>
   #include <valarray>
   
   #if __has_include(<clipper/core/coords.h>)
   #define HAVE_LIBCLIPPER 1
   #pragma GCC diagnostic push
   #pragma GCC diagnostic ignored "-Wignored-qualifiers"
   #include <clipper/core/coords.h>
   #pragma GCC diagnostic pop
   #endif
   
   namespace cif
   {
   
   // --------------------------------------------------------------------
   
   const double
       kPI = 3.141592653589793238462643383279502884;
   
   // --------------------------------------------------------------------
   template <typename T>
   class quaternion_type
   {
     public:
       using value_type = T;
   
       constexpr explicit quaternion_type(value_type const &value_a = {}, value_type const &value_b = {}, value_type const &value_c = {}, value_type const &value_d = {})
           : a(value_a)
           , b(value_b)
           , c(value_c)
           , d(value_d)
       {
       }
   
       constexpr explicit quaternion_type(std::complex<value_type> const &z0, std::complex<value_type> const &z1 = std::complex<value_type>())
           : a(z0.real())
           , b(z0.imag())
           , c(z1.real())
           , d(z1.imag())
       {
       }
   
       constexpr quaternion_type(quaternion_type const &) = default; 
       constexpr quaternion_type(quaternion_type &&) = default;      
   
       template <typename X>
       constexpr explicit quaternion_type(quaternion_type<X> const &rhs)
           : a(static_cast<value_type>(rhs.a))
           , b(static_cast<value_type>(rhs.b))
           , c(static_cast<value_type>(rhs.c))
           , d(static_cast<value_type>(rhs.d))
       {
       }
   
       // accessors
   
       constexpr value_type real() const
       {
           return a;
       }
   
       constexpr quaternion_type unreal() const
       {
           return { 0, b, c, d };
       }
   
       constexpr void swap(quaternion_type &o)
       {
           std::swap(a, o.a);
           std::swap(b, o.b);
           std::swap(c, o.c);
           std::swap(d, o.d);
       }
   
       // assignment operators
   
       template <typename X>
       constexpr quaternion_type &operator=(quaternion_type<X> const &rhs)
       {
           a = static_cast<value_type>(rhs.a);
           b = static_cast<value_type>(rhs.b);
           c = static_cast<value_type>(rhs.c);
           d = static_cast<value_type>(rhs.d);
   
           return *this;
       }
   
       constexpr quaternion_type &operator=(quaternion_type const &rhs)
       {
           a = rhs.a;
           b = rhs.b;
           c = rhs.c;
           d = rhs.d;
   
           return *this;
       }
   
       constexpr quaternion_type &operator=(value_type const &rhs)
       {
           a = rhs;
   
           b = c = d = static_cast<value_type>(0);
   
           return *this;
       }
   
       // parts are set to zero.
       constexpr quaternion_type &operator=(std::complex<value_type> const &rhs)
       {
           a = rhs.real();
           b = rhs.imag();
   
           c = d = static_cast<value_type>(0);
   
           return *this;
       }
   
       // other assignment-related operators
   
       constexpr quaternion_type &operator+=(value_type const &rhs)
       {
           a += rhs;
           return *this;
       }
   
       constexpr quaternion_type &operator+=(std::complex<value_type> const &rhs)
       {
           a += std::real(rhs);
           b += std::imag(rhs);
           return *this;
       }
   
       template <class X>
       constexpr quaternion_type &operator+=(quaternion_type<X> const &rhs)
       {
           a += rhs.a;
           b += rhs.b;
           c += rhs.c;
           d += rhs.d;
           return *this;
       }
   
       constexpr quaternion_type &operator-=(value_type const &rhs)
       {
           a -= rhs;
           return *this;
       }
   
       constexpr quaternion_type &operator-=(std::complex<value_type> const &rhs)
       {
           a -= std::real(rhs);
           b -= std::imag(rhs);
           return *this;
       }
   
       template <class X>
       constexpr quaternion_type &operator-=(quaternion_type<X> const &rhs)
       {
           a -= rhs.a;
           b -= rhs.b;
           c -= rhs.c;
           d -= rhs.d;
           return *this;
       }
   
       constexpr quaternion_type &operator*=(value_type const &rhs)
       {
           a *= rhs;
           b *= rhs;
           c *= rhs;
           d *= rhs;
           return *this;
       }
   
       constexpr quaternion_type &operator*=(std::complex<value_type> const &rhs)
       {
           value_type ar = rhs.real();
           value_type br = rhs.imag();
           quaternion_type result(a * ar - b * br, a * br + b * ar, c * ar + d * br, -c * br + d * ar);
           swap(result);
           return *this;
       }
   
       friend constexpr quaternion_type operator*(const quaternion_type &a, const quaternion_type &b)
       {
           auto result = a;
           result *= b;
           return result;
       }
   
       template <typename X>
       constexpr quaternion_type &operator*=(quaternion_type<X> const &rhs)
       {
           value_type ar = static_cast<value_type>(rhs.a);
           value_type br = static_cast<value_type>(rhs.b);
           value_type cr = static_cast<value_type>(rhs.c);
           value_type dr = static_cast<value_type>(rhs.d);
   
           quaternion_type result(a * ar - b * br - c * cr - d * dr, a * br + b * ar + c * dr - d * cr, a * cr - b * dr + c * ar + d * br, a * dr + b * cr - c * br + d * ar);
           swap(result);
           return *this;
       }
   
       constexpr quaternion_type &operator/=(value_type const &rhs)
       {
           a /= rhs;
           b /= rhs;
           c /= rhs;
           d /= rhs;
           return *this;
       }
   
       constexpr quaternion_type &operator/=(std::complex<value_type> const &rhs)
       {
           value_type ar = rhs.real();
           value_type br = rhs.imag();
           value_type denominator = ar * ar + br * br;
           quaternion_type result((+a * ar + b * br) / denominator, (-a * br + b * ar) / denominator, (+c * ar - d * br) / denominator, (+c * br + d * ar) / denominator);
           swap(result);
           return *this;
       }
   
       template <typename X>
       constexpr quaternion_type &operator/=(quaternion_type<X> const &rhs)
       {
           value_type ar = static_cast<value_type>(rhs.a);
           value_type br = static_cast<value_type>(rhs.b);
           value_type cr = static_cast<value_type>(rhs.c);
           value_type dr = static_cast<value_type>(rhs.d);
   
           value_type denominator = ar * ar + br * br + cr * cr + dr * dr;
           quaternion_type result((+a * ar + b * br + c * cr + d * dr) / denominator, (-a * br + b * ar - c * dr + d * cr) / denominator, (-a * cr + b * dr + c * ar - d * br) / denominator, (-a * dr - b * cr + c * br + d * ar) / denominator);
           swap(result);
           return *this;
       }
   
       friend constexpr quaternion_type normalize(quaternion_type q)
       {
           std::valarray<value_type> t(4);
   
           t[0] = q.a;
           t[1] = q.b;
           t[2] = q.c;
           t[3] = q.d;
   
           t *= t;
   
           value_type length = std::sqrt(t.sum());
   
           if (length > 0.001)
               q /= static_cast<value_type>(length);
           else
               q = quaternion_type(1, 0, 0, 0);
   
           return q;
       }
   
       friend constexpr quaternion_type conj(quaternion_type q)
       {
           return quaternion_type{ +q.a, -q.b, -q.c, -q.d };
       }
   
       constexpr value_type get_a() const { return a; } 
       constexpr value_type get_b() const { return b; } 
       constexpr value_type get_c() const { return c; } 
       constexpr value_type get_d() const { return d; } 
   
       constexpr bool operator==(const quaternion_type &rhs) const
       {
           return a == rhs.a and b == rhs.b and c == rhs.c and d == rhs.d;
       }
   
       constexpr bool operator!=(const quaternion_type &rhs) const
       {
           return a != rhs.a or b != rhs.b or c != rhs.c or d != rhs.d;
       }
   
       constexpr operator bool() const
       {
           return a != 0 or b != 0 or c != 0 or d != 0;
       }
   
     private:
       value_type a, b, c, d;
   };
   
   template <typename T>
   inline quaternion_type<T> spherical(T const &rho, T const &theta, T const &phi1, T const &phi2)
   {
       T cos_phi1 = std::cos(phi1);
       T cos_phi2 = std::cos(phi2);
   
       T a = std::cos(theta) * cos_phi1 * cos_phi2;
       T b = std::sin(theta) * cos_phi1 * cos_phi2;
       T c = std::sin(phi1) * cos_phi2;
       T d = std::sin(phi2);
   
       quaternion_type result(a, b, c, d);
       result *= rho;
   
       return result;
   }
   
   using quaternion = quaternion_type<float>;
   
   // --------------------------------------------------------------------
   
   template <typename F>
   struct point_type
   {
       using value_type = F;
   
       value_type m_x, 
           m_y,        
           m_z;        
   
       constexpr point_type()
           : m_x(0)
           , m_y(0)
           , m_z(0)
       {
       }
   
       constexpr point_type(value_type x, value_type y, value_type z)
           : m_x(x)
           , m_y(y)
           , m_z(z)
       {
       }
   
       template <typename PF>
       constexpr point_type(const point_type<PF> &pt)
           : m_x(static_cast<F>(pt.m_x))
           , m_y(static_cast<F>(pt.m_y))
           , m_z(static_cast<F>(pt.m_z))
       {
       }
   
       constexpr point_type(const std::tuple<value_type, value_type, value_type> &pt)
           : point_type(std::get<0>(pt), std::get<1>(pt), std::get<2>(pt))
       {
       }
   
   #if HAVE_LIBCLIPPER
       constexpr point_type(const clipper::Coord_orth &pt)
           : m_x(pt[0])
           , m_y(pt[1])
           , m_z(pt[2])
       {
       }
   
       constexpr point_type &operator=(const clipper::Coord_orth &rhs)
       {
           m_x = rhs[0];
           m_y = rhs[1];
           m_z = rhs[2];
           return *this;
       }
   #endif
   
       template <typename PF>
       constexpr point_type &operator=(const point_type<PF> &rhs)
       {
           m_x = static_cast<F>(rhs.m_x);
           m_y = static_cast<F>(rhs.m_y);
           m_z = static_cast<F>(rhs.m_z);
           return *this;
       }
   
       constexpr value_type &get_x() { return m_x; }      
       constexpr value_type get_x() const { return m_x; } 
       constexpr void set_x(value_type x) { m_x = x; }    
   
       constexpr value_type &get_y() { return m_y; }      
       constexpr value_type get_y() const { return m_y; } 
       constexpr void set_y(value_type y) { m_y = y; }    
   
       constexpr value_type &get_z() { return m_z; }      
       constexpr value_type get_z() const { return m_z; } 
       constexpr void set_z(value_type z) { m_z = z; }    
   
       constexpr point_type &operator+=(const point_type &rhs)
       {
           m_x += rhs.m_x;
           m_y += rhs.m_y;
           m_z += rhs.m_z;
   
           return *this;
       }
   
       constexpr point_type &operator+=(value_type d)
       {
           m_x += d;
           m_y += d;
           m_z += d;
   
           return *this;
       }
   
       template <typename F2>
       friend constexpr auto operator+(const point_type &lhs, const point_type<F2> &rhs)
       {
           return point_type<std::common_type_t<value_type, F2>>(lhs.m_x + rhs.m_x, lhs.m_y + rhs.m_y, lhs.m_z + rhs.m_z);
       }
   
       constexpr point_type &operator-=(const point_type &rhs)
       {
           m_x -= rhs.m_x;
           m_y -= rhs.m_y;
           m_z -= rhs.m_z;
   
           return *this;
       }
   
       constexpr point_type &operator-=(value_type d)
       {
           m_x -= d;
           m_y -= d;
           m_z -= d;
   
           return *this;
       }
   
       template <typename F2>
       friend constexpr auto operator-(const point_type &lhs, const point_type<F2> &rhs)
       {
           return point_type<std::common_type_t<value_type, F2>>(lhs.m_x - rhs.m_x, lhs.m_y - rhs.m_y, lhs.m_z - rhs.m_z);
       }
   
       friend constexpr point_type operator-(const point_type &pt)
       {
           return point_type(-pt.m_x, -pt.m_y, -pt.m_z);
       }
   
       constexpr point_type &operator*=(value_type rhs)
       {
           m_x *= rhs;
           m_y *= rhs;
           m_z *= rhs;
           return *this;
       }
   
       template <typename F2>
       friend constexpr auto operator*(const point_type &pt, F2 f)
       {
           return point_type<std::common_type_t<value_type, F2>>(pt.m_x * f, pt.m_y * f, pt.m_z * f);
       }
   
       template <typename F2>
       friend constexpr auto operator*(F2 f, const point_type &pt)
       {
           return point_type<std::common_type_t<value_type, F2>>(pt.m_x * f, pt.m_y * f, pt.m_z * f);
       }
   
       constexpr point_type &operator/=(value_type rhs)
       {
           m_x /= rhs;
           m_y /= rhs;
           m_z /= rhs;
           return *this;
       }
   
       template <typename F2>
       friend constexpr auto operator/(const point_type &pt, F2 f)
       {
           return point_type<std::common_type_t<value_type, F2>>(pt.m_x / f, pt.m_y / f, pt.m_z / f);
       }
   
       constexpr value_type normalize()
       {
           auto length = m_x * m_x + m_y * m_y + m_z * m_z;
           if (length > 0)
           {
               length = std::sqrt(length);
               operator/=(length);
           }
           return length;
       }
   
       constexpr void rotate(const quaternion &q)
       {
           quaternion_type<value_type> p(0, m_x, m_y, m_z);
   
           p = q * p * conj(q);
   
           m_x = p.get_b();
           m_y = p.get_c();
           m_z = p.get_d();
       }
   
       constexpr void rotate(const quaternion &q, point_type pivot)
       {
           operator-=(pivot);
           rotate(q);
           operator+=(pivot);
       }
   
   #if HAVE_LIBCLIPPER
       operator clipper::Coord_orth() const
       {
           return clipper::Coord_orth(m_x, m_y, m_z);
       }
   #endif
   
       constexpr operator std::tuple<const value_type &, const value_type &, const value_type &>() const
       {
           return std::make_tuple(std::ref(m_x), std::ref(m_y), std::ref(m_z));
       }
   
       constexpr operator std::tuple<value_type &, value_type &, value_type &>()
       {
           return std::make_tuple(std::ref(m_x), std::ref(m_y), std::ref(m_z));
       }
   
   #if defined(__cpp_impl_three_way_comparison)
       constexpr auto operator<=>(const point_type &rhs) const = default;
   #else
       constexpr bool operator==(const point_type &rhs) const
       {
           return m_x == rhs.m_x and m_y == rhs.m_y and m_z == rhs.m_z;
       }
   
       constexpr bool operator!=(const point_type &rhs) const
       {
           return not operator==(rhs);
       }
   #endif
   
       // consider point as a vector... perhaps I should rename point?
   
       constexpr value_type length_sq() const
       {
           return m_x * m_x + m_y * m_y + m_z * m_z;
       }
   
       constexpr value_type length() const
       {
           return std::sqrt(length_sq());
       }
   
       friend std::ostream &operator<<(std::ostream &os, const point_type &pt)
       {
           os << '(' << pt.m_x << ',' << pt.m_y << ',' << pt.m_z << ')';
           return os;
       }
   };
   
   using point = point_type<float>;
   
   // --------------------------------------------------------------------
   // several standard 3d operations
   
   template <typename F1, typename F2>
   constexpr auto distance_squared(const point_type<F1> &a, const point_type<F2> &b)
   {
       return (a.m_x - b.m_x) * (a.m_x - b.m_x) +
              (a.m_y - b.m_y) * (a.m_y - b.m_y) +
              (a.m_z - b.m_z) * (a.m_z - b.m_z);
   }
   
   template <typename F1, typename F2>
   constexpr auto distance(const point_type<F1> &a, const point_type<F2> &b)
   {
       return std::sqrt(
           (a.m_x - b.m_x) * (a.m_x - b.m_x) +
           (a.m_y - b.m_y) * (a.m_y - b.m_y) +
           (a.m_z - b.m_z) * (a.m_z - b.m_z));
   }
   
   template <typename F1, typename F2>
   inline constexpr auto dot_product(const point_type<F1> &a, const point_type<F2> &b)
   {
       return a.m_x * b.m_x + a.m_y * b.m_y + a.m_z * b.m_z;
   }
   
   template <typename F1, typename F2>
   inline constexpr auto cross_product(const point_type<F1> &a, const point_type<F2> &b)
   {
       return point_type<std::common_type_t<F1, F2>>(
           a.m_y * b.m_z - b.m_y * a.m_z,
           a.m_z * b.m_x - b.m_z * a.m_x,
           a.m_x * b.m_y - b.m_x * a.m_y);
   }
   
   template <typename F>
   constexpr auto angle(const point_type<F> &p1, const point_type<F> &p2, const point_type<F> &p3)
   {
       point_type<F> v1 = p1 - p2;
       point_type<F> v2 = p3 - p2;
   
       return std::acos(dot_product(v1, v2) / (v1.length() * v2.length())) * 180 / kPI;
   }
   
   template <typename F>
   constexpr auto dihedral_angle(const point_type<F> &p1, const point_type<F> &p2, const point_type<F> &p3, const point_type<F> &p4)
   {
       point_type<F> v12 = p1 - p2; // vector from p2 to p1
       point_type<F> v43 = p4 - p3; // vector from p3 to p4
   
       point_type<F> z = p2 - p3; // vector from p3 to p2
   
       point_type<F> p = cross_product(z, v12);
       point_type<F> x = cross_product(z, v43);
       point_type<F> y = cross_product(z, x);
   
       auto u = dot_product(x, x);
       auto v = dot_product(y, y);
   
       F result = 360;
       if (u > 0 and v > 0)
       {
           u = dot_product(p, x) / std::sqrt(u);
           v = dot_product(p, y) / std::sqrt(v);
           if (u != 0 or v != 0)
               result = std::atan2(v, u) * static_cast<F>(180 / kPI);
       }
   
       return result;
   }
   
   template <typename F>
   constexpr auto cosinus_angle(const point_type<F> &p1, const point_type<F> &p2, const point_type<F> &p3, const point_type<F> &p4)
   {
       point_type<F> v12 = p1 - p2;
       point_type<F> v34 = p3 - p4;
   
       auto x = dot_product(v12, v12) * dot_product(v34, v34);
   
       return x > 0 ? dot_product(v12, v34) / std::sqrt(x) : 0;
   }
   
   template <typename F>
   constexpr auto distance_point_to_line(const point_type<F> &l1, const point_type<F> &l2, const point_type<F> &p)
   {
       auto line = l2 - l1;
       auto p_to_l1 = p - l1;
       auto p_to_l2 = p - l2;
       auto cross = cross_product(p_to_l1, p_to_l2);
       return cross.length() / line.length();
   }
   
   // --------------------------------------------------------------------
   point nudge(point p, float offset);
   
   // --------------------------------------------------------------------
   
   quaternion construct_from_angle_axis(float angle, point axis);
   
   std::tuple<double, point> quaternion_to_angle_axis(quaternion q);
   
   quaternion construct_for_dihedral_angle(point p1, point p2, point p3, point p4,
       float angle, float esd);
   
   point centroid(const std::vector<point> &pts);
   
   point center_points(std::vector<point> &pts);
   
   quaternion align_points(const std::vector<point> &a, const std::vector<point> &b);
   
   double RMSd(const std::vector<point> &a, const std::vector<point> &b);
   
   // --------------------------------------------------------------------
   template <int N>
   class spherical_dots
   {
     public:
       constexpr static int P = 2 * N * 1;
   
       constexpr static double W = (4 * kPI) / P;
   
       using array_type = typename std::array<point, P>;
   
       using iterator = typename array_type::const_iterator;
   
       static spherical_dots &instance()
       {
           static spherical_dots sInstance;
           return sInstance;
       }
   
       std::size_t size() const { return P; }
   
       const point operator[](uint32_t inIx) const { return m_points[inIx]; }
   
       iterator begin() const { return m_points.begin(); }
   
       iterator end() const { return m_points.end(); }
   
       double weight() const { return W; }
   
       spherical_dots()
       {
           const double
               kGoldenRatio = (1 + std::sqrt(5.0)) / 2;
   
           auto p = m_points.begin();
   
           for (int32_t i = -N; i <= N; ++i)
           {
               double lat = std::asin((2.0 * i) / P);
               double lon = std::fmod(i, kGoldenRatio) * 2 * kPI / kGoldenRatio;
   
               p->m_x = std::sin(lon) * std::cos(lat);
               p->m_y = std::cos(lon) * std::cos(lat);
               p->m_z = std::sin(lat);
   
               ++p;
           }
       }
   
     private:
       array_type m_points;
   };
   
   } // namespace cif