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38 #ifndef GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
39 #define GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
42 #include "gromacs/legacyheaders/typedefs.h"
43 #include "grompp-impl.h"
49 typedef struct gpp_atomtype *gpp_atomtype_t;
51 int get_atomtype_type(const char *str, gpp_atomtype_t at);
52 /* Return atomtype corresponding to case-insensitive str
53 or NOTSET if not found */
55 int get_atomtype_ntypes(gpp_atomtype_t at);
56 /* Return number of atomtypes */
58 char *get_atomtype_name(int nt, gpp_atomtype_t at);
59 /* Return name corresponding to atomtype nt, or NULL if not found */
61 real get_atomtype_massA(int nt, gpp_atomtype_t at);
62 real get_atomtype_massB(int nt, gpp_atomtype_t at);
63 real get_atomtype_qA(int nt, gpp_atomtype_t at);
64 real get_atomtype_qB(int nt, gpp_atomtype_t at);
65 real get_atomtype_radius(int nt, gpp_atomtype_t at);
66 real get_atomtype_vol(int nt, gpp_atomtype_t at);
67 real get_atomtype_surftens(int nt, gpp_atomtype_t at);
68 real get_atomtype_gb_radius(int nt, gpp_atomtype_t at);
69 real get_atomtype_S_hct(int nt, gpp_atomtype_t at);
70 int get_atomtype_ptype(int nt, gpp_atomtype_t at);
71 int get_atomtype_batype(int nt, gpp_atomtype_t at);
72 int get_atomtype_atomnumber(int nt, gpp_atomtype_t at);
74 /* Return the above variable for atomtype nt, or NOTSET if not found */
76 real get_atomtype_nbparam(int nt, int param, gpp_atomtype_t at);
77 /* Similar to the previous but returns the paramth parameter or NOTSET */
79 gpp_atomtype_t init_atomtype(void);
80 /* Return a new atomtype structure */
82 void done_atomtype(gpp_atomtype_t at);
83 /* Free the memory in the structure */
85 int set_atomtype(int nt, gpp_atomtype_t at, struct t_symtab *tab,
86 t_atom *a, const char *name, t_param *nb,
88 real radius, real vol, real surftens, int atomnumber,
89 real gb_radius, real S_hct);
90 /* Set the values of an existing atom type nt. Returns nt on success or
94 set_atomtype_gbparam(gpp_atomtype_t at, int i,
95 real radius, real vol, real surftens,
96 real gb_radius, real S_hct);
98 int add_atomtype(gpp_atomtype_t at, struct t_symtab *tab,
99 t_atom *a, const char *name, t_param *nb,
101 real radius, real vol, real surftens, real atomnumber,
102 real gb_radius, real S_hct);
103 /* Add a complete new atom type to an existing atomtype structure. Returns
104 the number of the atom type. */
106 void print_at (FILE * out, gpp_atomtype_t at);
107 /* Print an atomtype record to a text file */
109 void renum_atype(t_params plist[], gmx_mtop_t *mtop,
111 gpp_atomtype_t at, gmx_bool bVerbose);
113 void copy_atomtype_atomtypes(gpp_atomtype_t atype, t_atomtypes *atypes);
114 /* Copy from one structure to another */