fpocket/headers/voronoi.h

/*
 * Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
 * Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

 */

#ifndef DH_VORONOI
#define DH_VORONOI

// ---------------------------------INCLUDES----------------------------------*/

#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <sys/types.h>
#include <unistd.h>
#include <time.h>
#include "rpdb.h"
#include "writepdb.h"
#include "calc.h"
#include "utils.h"

#include "../src/qhull/src//qvoronoi/qvoronoi.h"
#include "../src/qhull/src/qconvex/qconvex.h"

#include "memhandler.h"

/* ----------------------------------MACROS--------------------------------- */

#define M_VORONOI_SUCCESS 0 /**< alpha sphere type - hydrophobic alpha sphere */
#define M_APOLAR_AS 0       /**< alpha sphere type - hydrophilic alpha sphere */
#define M_POLAR_AS 1
#define M_PREC_TOLERANCE 1e-3 /**< tolerance for coordinate imprecion during alpha sphere search*/

#define M_BUFSIZE 1e6  /**< buffer size*/
#define M_N_REPLICAS 1 /**< currently not used anymore : number of times we do the voronoi tesselation for translated coordinates to avoid precision problems with qhull */

/* --------------------------------STRUCTURES-------------------------------- */

/**
 Container of the Voronoi vertice
 */
typedef struct s_vvertice
{
        int resid;   /**< residue ID*/
        int id,      /**< vertice ID*/
            seen,    /**< Say if we have seen this vertice during a neighbor search */
            qhullId, /**< ID of the vertice in qhull output*/
            type;    /**< 0 if apolar contacts, 1 if polar */

        float ray; /**< Ray of voronoi vertice */
        float x,   /**< X coord */
            y,     /**< Y coord */
            z;     /**< Z coord */

        int sort_x;          /**< Index in the sorted tab by X coord */
        int apol_neighbours; /**< number of neighbouring apolar alpha spheres */

        int vneigh[4];   /**< vertice neighbours (4 contact atoms)*/
        s_atm *neigh[4]; /**< The theorical 4 contacted atoms */

        float bary[3];              /**< Barycenter of the pocket */
        float electrostatic_energy; /**<estimate of electrostatic energy around the alpha sphere */

} s_vvertice;

/**
 vertice list container
 */
typedef struct s_lst_vvertice
{
        s_vvertice *vertices;   /**< List of voronoi vertices */
        s_vvertice **pvertices; /**< list of pointers to vertices*/

        /* Indexes of heavy atoms used as input for qhull in the s_pdb list of atoms */
        int *h_tr;

        /* Size of h_tr */
        int n_h_tr;

        int *tr,       /**< translation of voronoi vertice indices*/
            nvert,     /**< no of vertices*/
            qhullSize; /**< number of vertices in qhull*/

} s_lst_vvertice;

/**
 * clusterlib vertice info container
 */

typedef struct s_clusterlib_vertices
{
        double **pos;     /**< Positions (xyz) of Voronoi vertices*/
        int **mask;       /**< Mask for position array*/
        double weight[3]; /**< column (coordinate weights for distance matrix calculation*/
        int transpose;    /**< cluster by rows (transpose=0) or column(transpose=1)*/
        char dist;        /**< char defining distance measure used*/
        char method;      /**< char defining method used (clustering)*/

} s_clusterlib_vertices;

/* -----------------------------PROTOTYPES----------------------------------- */

s_lst_vvertice *load_vvertices(s_pdb *pdb, s_fparams *params, float xshift, float yshift, float zshift);

void fill_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms, int natoms,
                    s_fparams *params,
                    float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb);

void add_missing_vvertices(s_lst_vvertice *lvvert, const char fpath[], s_atm *atoms,
                           s_fparams *params,
                           float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb);

unsigned short check_if_similar_vertice_in_list(s_vvertice *v, s_lst_vvertice *lvvert);
void add_vertice_to_vertice_list(s_lst_vvertice *lvvert, s_vvertice *v);
void copy_vertice(s_vvertice *v1, s_vvertice *v2, int n);

float testVvertice(float xyz[3], int curNbIdx[4], s_atm *atoms,
                   s_fparams *params,
                   s_lst_vvertice *lvvert,
                   float xshift, float yshift, float zshift, float avg_bfactor, s_pdb *pdb);

float atom_in_explicit_pocket(s_atm *cura, s_fparams *params);

s_lst_vvertice *compare_vvertice_shifted_lists(s_lst_vvertice *lvvert,
                                               s_lst_vvertice *list_shifted, float xshift, float yshift, float zshift);

double **get_3d_array_from_vvertice_list(s_lst_vvertice *lvvert);
s_clusterlib_vertices *prepare_vertices_for_cluster_lib(s_lst_vvertice *lvvert, char c_method, char d_method);
void set_barycenter(s_vvertice *v);
int is_in_lst_vert(s_vvertice **lst_vert, int nb_vert, int v_id);
int is_in_lst_vert_p(s_vvertice **lst_vert, int nb_vert, s_vvertice *vert);

void write_pqr_vert(FILE *f, s_vvertice *v, int i);
void write_pdb_vert(FILE *f, s_vvertice *v, int i);
void write_mmcif_vert(FILE *f, s_vvertice *v, int i);
float get_verts_volume_ptr(s_vvertice **verts, int nvert, int niter, float correct);
float get_convex_hull_volume(s_vvertice **verts, int nvert);

void print_vvertices(FILE *f, s_lst_vvertice *lvvert);
void free_vert_lst(s_lst_vvertice *lvvert);

void transferClustersToVertices(int **clusterIds, s_lst_vvertice *lvert);

double frand_a_b(double a, double b);
int free_cluster_lib_vertices(s_clusterlib_vertices *clusterlib_vertices, int nvert);

#endif