| /** | |
| @file | |
| @author Simon Mitternacht | |
| Functions to compute neighbor lists. The function | |
| freesasa_nb_contact() is mainly intended for checking consistency, | |
| in performance-critical code it is advisible to use the struct (as | |
| demonstrated in sasa_lr.c and sasa_sr.c). | |
| */ | |
| //! Neighbor list | |
| typedef struct { | |
| int n; //!< number of elements | |
| int **nb; //!< neighbors to each element | |
| int *nn; //!< number of neighbors to each element | |
| double **xyd; //!< distance between neighbors in xy-plane | |
| double **xd; //!< signed distance between neighbors along x-axis | |
| double **yd; //!< signed distance between neighbors along y-axis | |
| int *capacity; //!< keeps track of memory chunks (don't change this) | |
| } nb_list; | |
| /** | |
| Creates a neigbor list based on a set of coordinates with | |
| corresponding sphere radii. | |
| Implemented using cell lists, giving O(N) performance. Should be | |
| freed with freesasa_nb_free(). For efficient calculations | |
| using this list the members of the returned struct should be used | |
| directly and not freesasa_nb_contact(). | |
| @param coord a set of coordinates | |
| @param radii radii for the coordinates | |
| @return a neigbor list. Returns NULL if either argument is null or | |
| if there were any problems constructing the list (see error | |
| messages). | |
| */ | |
| nb_list * | |
| freesasa_nb_new(const coord_t *coord, | |
| const double *radii); | |
| /** | |
| Frees a neigbor list created by freesasa_nb_new(). | |
| @param nb The neigbor list to free | |
| */ | |
| void | |
| freesasa_nb_free(nb_list *nb); | |
| /** | |
| Checks if two atoms are in contact. Only included for reference. | |
| @param nb The neigbor list | |
| @param i Index of first coordinate | |
| @param j Index of second coordinate | |
| @return 1 if contact, 0 else. | |
| */ | |
| int | |
| freesasa_nb_contact(const nb_list *nb, | |
| int i, | |
| int j); | |