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43 #include "gromacs/legacyheaders/typedefs.h"
45 #define PHI_AHX (-55.0)
46 #define PSI_AHX (-45.0)
47 /* Canonical values of the helix phi/psi angles */
51 real phi, psi, pprms2;
53 real d3, d4, d5, rmsa;
57 int Cprev, N, H, CA, C, O, Nnext;
62 efhRAD, efhTWIST, efhRISE, efhLEN,
63 efhDIP, efhRMS, efhRMSA, efhCD222,
64 efhPPRMS, efhCPHI, efhPHI, efhPSI,
65 efhHB3, efhHB4, efhHB5, efhJCA,
69 extern real ahx_len(int gnx, atom_id index[], rvec x[]);
70 /* Assume we have a list of Calpha atoms only! */
72 extern real ellipticity(int nres, t_bb bb[]);
74 extern real radius(FILE *fp, int nca, atom_id ca_index[], rvec x[]);
75 /* Assume we have calphas */
77 extern real twist(int nca, atom_id caindex[], rvec x[]);
78 /* Calculate the twist of the helix */
80 extern real pprms(FILE *fp, int nbb, t_bb bb[]);
81 /* Calculate the average RMS from canonical phi/psi values
82 * and the distance per residue
85 extern real ca_phi(int gnx, atom_id index[], rvec x[]);
86 /* Assume we have a list of Calpha atoms only! */
88 extern real dip(int nbb, atom_id bbind[], rvec x[], t_atom atom[]);
90 extern real rise(int gnx, atom_id index[], rvec x[]);
91 /* Assume we have a list of Calpha atoms only! */
93 extern void av_hblen(FILE *fp3, FILE *fp3a,
94 FILE *fp4, FILE *fp4a,
95 FILE *fp5, FILE *fp5a,
96 real t, int nres, t_bb bb[]);
98 extern void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
99 real t, int nres, t_bb bb[]);
101 extern t_bb *mkbbind(const char *fn, int *nres, int *nbb, int res0,
102 int *nall, atom_id **index,
103 char ***atomname, t_atom atom[],
106 extern void do_start_end(int nres, t_bb bb[], int *nbb,
107 atom_id bbindex[], int *nca, atom_id caindex[],
108 gmx_bool bRange, int rStart, int rEnd);
110 extern void calc_hxprops(int nres, t_bb bb[], rvec x[]);
112 extern void pr_bb(FILE *fp, int nres, t_bb bb[]);