periodic_box.h

/*
 * This file is a part of
 *
 * ============================================
 * ###   Pteros molecular modeling library  ###
 * ============================================
 *
 * https://github.com/yesint/pteros
 *
 * (C) 2009-2021, Semen Yesylevskyy
 *
 * All works, which use Pteros, should cite the following papers:
 *
 *  1.  Semen O. Yesylevskyy, "Pteros 2.0: Evolution of the fast parallel
 *      molecular analysis library for C++ and python",
 *      Journal of Computational Chemistry, 2015, 36(19), 1480–1488.
 *      doi: 10.1002/jcc.23943.
 *
 *  2.  Semen O. Yesylevskyy, "Pteros: Fast and easy to use open-source C++
 *      library for molecular analysis",
 *      Journal of Computational Chemistry, 2012, 33(19), 1632–1636.
 *      doi: 10.1002/jcc.22989.
 *
 * This is free software distributed under Artistic License:
 * http://www.opensource.org/licenses/artistic-license-2.0.php
 *
*/
 
 
#pragma once
 
#include <string>
#include <Eigen/Core>
#include "pteros/core/typedefs.h"
 
namespace pteros {
 
class PeriodicBox {
public:
 
    PeriodicBox();
 
    PeriodicBox(Matrix3f_const_ref m);
 
    PeriodicBox(Vector3f_const_ref vectors, Vector3f_const_ref angles);
 
    PeriodicBox(const PeriodicBox& other);
 
    PeriodicBox& operator=(const PeriodicBox& other);
 
    // Get box element
    float get_element(int i, int j) const;
 
    // Set box element
    void set_element(int i, int j, float val);
 
    Eigen::Vector3f get_vector(int i) const;
 
    void set_vector(Vector3f_const_ref vec, int i);
 
    Eigen::Matrix3f get_matrix() const;
 
    void set_matrix(Matrix3f_const_ref box);
 
    void scale_vectors(Vector3f_const_ref scale);
 
    Eigen::Matrix3f get_inv_matrix() const;
 
    Eigen::Vector3f lab_to_box(Vector3f_const_ref point) const;
 
    Eigen::Matrix3f lab_to_box_transform() const;
 
    Eigen::Vector3f box_to_lab(Vector3f_const_ref point) const;
 
    Eigen::Matrix3f box_to_lab_transform() const;
 
    float extent(int i) const;
 
    Eigen::Vector3f extents() const;
 
    bool is_triclinic() const {return _is_triclinic;}
 
    bool is_periodic() const {return _is_periodic;}
 
    float distance(Vector3f_const_ref point1,
                   Vector3f_const_ref point2,         
                   Array3i_const_ref pbc = fullPBC) const;
 
    float distance_squared(Vector3f_const_ref point1,
                   Vector3f_const_ref point2,                   
                   Array3i_const_ref pbc = fullPBC) const;
 
    void wrap_point(Vector3f_ref point,
                    Array3i_const_ref pbc = fullPBC,
                    Vector3f_const_ref origin = Eigen::Vector3f::Zero()) const;
 
    bool in_box(Vector3f_const_ref point, Vector3f_const_ref origin = Eigen::Vector3f::Zero()) const;
 
    Eigen::Vector3f closest_image(Vector3f_const_ref point,
                                      Vector3f_const_ref target,
                                      Array3i_const_ref pbc = fullPBC) const;
 
    Eigen::Vector3f shortest_vector(Vector3f_const_ref point1,
                                    Vector3f_const_ref point2,
                                    Array3i_const_ref pbc = fullPBC) const;
 
    float volume();
 
    void from_pdb_box(const char *line);
 
    std::string to_pdb_box() const;
 
    void to_vectors_angles(Vector3f_ref vectors, Vector3f_ref angles) const;
 
    void from_vectors_angles(Vector3f_const_ref vectors, Vector3f_const_ref angles);
 
 
private:
    Eigen::Matrix3f _box;
    Eigen::Matrix3f _box_inv;    
    bool _is_triclinic;
    bool _is_periodic;
 
    void recompute_internals();
};
 
}