class ResidueType;
/* must correspond with 'leg' g_chi.c:727 */
-enum {
- edPhi = 0, edPsi, edOmega, edChi1, edChi2, edChi3, edChi4, edChi5, edChi6, edMax
+enum
+{
+ edPhi = 0,
+ edPsi,
+ edOmega,
+ edChi1,
+ edChi2,
+ edChi3,
+ edChi4,
+ edChi5,
+ edChi6,
+ edMax
};
-enum {
- edPrintST = 0, edPrintRO
+enum
+{
+ edPrintST = 0,
+ edPrintRO
};
#define NHISTO 360
#define NONCHI 3
-#define MAXCHI (edMax-NONCHI)
-#define NROT 4 /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
+#define MAXCHI (edMax - NONCHI)
+#define NROT 4 /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
-typedef struct {
- int minCalpha, minC, H, N, C, O, Cn[MAXCHI+3];
+typedef struct
+{
+ int minCalpha, minC, H, N, C, O, Cn[MAXCHI + 3];
} t_dihatms; /* Cn[0]=N, Cn[1]=Ca, Cn[2]=Cb etc. */
-typedef struct {
- char name[12];
- int resnr;
- int index; /* Index for amino acids (histograms) */
- int j0[edMax]; /* Index in dih array (phi angle is first...) */
- t_dihatms atm;
- int b[edMax];
- int ntr[edMax];
- real S2[edMax];
- real rot_occ[edMax][NROT];
+typedef struct
+{
+ char name[12];
+ int resnr;
+ int index; /* Index for amino acids (histograms) */
+ int j0[edMax]; /* Index in dih array (phi angle is first...) */
+ t_dihatms atm;
+ int b[edMax];
+ int ntr[edMax];
+ real S2[edMax];
+ real rot_occ[edMax][NROT];
} t_dlist;
-typedef struct {
- const char *name; /* Description of the J coupling constant */
+typedef struct
+{
+ const char* name; /* Description of the J coupling constant */
real A, B, C; /* Karplus coefficients */
real offset; /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
real Jc; /* Resulting Jcoupling */
real Jcsig; /* Standard deviation in Jc */
} t_karplus;
-void calc_distribution_props(int nh, const int histo[],
- real start, int nkkk, t_karplus kkk[],
- real *S2);
+void calc_distribution_props(int nh, const int histo[], real start, int nkkk, t_karplus kkk[], real* S2);
/* This routine takes a dihedral distribution and calculates
* coupling constants and dihedral order parameters of it.
*
*
*/
-void ana_dih_trans(const char *fn_trans, const char *fn_histo,
- real **dih, int nframes, int nangles,
- const char *grpname, real *time, gmx_bool bRb,
- const gmx_output_env_t *oenv);
+void ana_dih_trans(const char* fn_trans,
+ const char* fn_histo,
+ real** dih,
+ int nframes,
+ int nangles,
+ const char* grpname,
+ real* time,
+ gmx_bool bRb,
+ const gmx_output_env_t* oenv);
/*
* Analyse dihedral transitions, by counting transitions per dihedral
* and per frame. The total number of transitions is printed to
* (trans = 0)
*/
-void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
- gmx_bool bHisto, const char *fn_histo, int maxchi,
- real **dih, int nlist, t_dlist dlist[],
- int nframes, int nangles, const char *grpname,
- int multiplicity[], real *time, gmx_bool bRb,
- real core_frac, const gmx_output_env_t *oenv);
+void low_ana_dih_trans(gmx_bool bTrans,
+ const char* fn_trans,
+ gmx_bool bHisto,
+ const char* fn_histo,
+ int maxchi,
+ real** dih,
+ int nlist,
+ t_dlist dlist[],
+ int nframes,
+ int nangles,
+ const char* grpname,
+ int multiplicity[],
+ real* time,
+ gmx_bool bRb,
+ real core_frac,
+ const gmx_output_env_t* oenv);
/* as above but passes dlist so can copy occupancies into it, and multiplicity[]
* (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
* rotamers. Also production of xvg output files is conditional
* to each rotamer, the rest goes to rotamer zero */
-
-void read_ang_dih(const char *trj_fn,
- gmx_bool bAngles, gmx_bool bSaveAll, gmx_bool bRb, gmx_bool bPBC,
- int maxangstat, int angstat[],
- int *nframes, real **time,
- int isize, int index[],
- real **trans_frac,
- real **aver_angle,
- real *dih[],
- const gmx_output_env_t *oenv);
+void read_ang_dih(const char* trj_fn,
+ gmx_bool bAngles,
+ gmx_bool bSaveAll,
+ gmx_bool bRb,
+ gmx_bool bPBC,
+ int maxangstat,
+ int angstat[],
+ int* nframes,
+ real** time,
+ int isize,
+ int index[],
+ real** trans_frac,
+ real** aver_angle,
+ real* dih[],
+ const gmx_output_env_t* oenv);
/*
* Read a trajectory and calculate angles and dihedrals.
*
* dih all angles at each time frame
*/
-void make_histo(FILE *log,
- int ndata, real data[], int npoints, int histo[],
- real minx, real maxx);
+void make_histo(FILE* log, int ndata, real data[], int npoints, int histo[], real minx, real maxx);
/*
* Make a histogram from data. The min and max of the data array can
* be determined (if minx == 0 and maxx == 0)
/* Routines from pp2shift (anadih.c etc.) */
-void do_pp2shifts(FILE *fp, int nframes,
- int nlist, t_dlist dlist[], real **dih);
+void do_pp2shifts(FILE* fp, int nframes, int nlist, t_dlist dlist[], real** dih);
-gmx_bool has_dihedral(int Dih, t_dlist *dl);
+gmx_bool has_dihedral(int Dih, t_dlist* dl);
-t_dlist *mk_dlist(FILE *log,
- const t_atoms *atoms, int *nlist,
- gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
- int maxchi, int r0, ResidueType *rt);
+t_dlist* mk_dlist(FILE* log,
+ const t_atoms* atoms,
+ int* nlist,
+ gmx_bool bPhi,
+ gmx_bool bPsi,
+ gmx_bool bChi,
+ gmx_bool bHChi,
+ int maxchi,
+ int r0,
+ ResidueType* rt);
-void pr_dlist(FILE *fp, int nl, t_dlist dl[], real dt, int printtype,
- gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, int maxchi);
+void pr_dlist(FILE* fp,
+ int nl,
+ t_dlist dl[],
+ real dt,
+ int printtype,
+ gmx_bool bPhi,
+ gmx_bool bPsi,
+ gmx_bool bChi,
+ gmx_bool bOmega,
+ int maxchi);
-int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi);
+int pr_trans(FILE* fp, int nl, t_dlist dl[], real dt, int Xi);
-void mk_chi_lookup (int **lookup, int maxchi,
- int nlist, t_dlist dlist[]);
+void mk_chi_lookup(int** lookup, int maxchi, int nlist, t_dlist dlist[]);
-void mk_multiplicity_lookup (int *multiplicity, int maxchi,
- int nlist, t_dlist dlist[], int nangle);
+void mk_multiplicity_lookup(int* multiplicity, int maxchi, int nlist, t_dlist dlist[], int nangle);
-void get_chi_product_traj (real **dih, int nframes,
- int nlist, int maxchi, t_dlist dlist[],
- real time[], int **lookup, int *multiplicity,
- gmx_bool bRb, gmx_bool bNormalize,
- real core_frac, gmx_bool bAll, const char *fnall,
- const gmx_output_env_t *oenv);
+void get_chi_product_traj(real** dih,
+ int nframes,
+ int nlist,
+ int maxchi,
+ t_dlist dlist[],
+ real time[],
+ int** lookup,
+ int* multiplicity,
+ gmx_bool bRb,
+ gmx_bool bNormalize,
+ real core_frac,
+ gmx_bool bAll,
+ const char* fnall,
+ const gmx_output_env_t* oenv);
-void print_one (const gmx_output_env_t *oenv, const char *base,
- const char *name,
- const char *title, const char *ylabel, int nf,
- real time[], real data[]);
+void print_one(const gmx_output_env_t* oenv,
+ const char* base,
+ const char* name,
+ const char* title,
+ const char* ylabel,
+ int nf,
+ real time[],
+ real data[]);
/* Routines from g_hbond */
-void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
- real sigma_ct[], real sigma_nt[], real sigma_kt[],
- real fit_start, real temp);
+void analyse_corr(int n,
+ real t[],
+ real ct[],
+ real nt[],
+ real kt[],
+ real sigma_ct[],
+ real sigma_nt[],
+ real sigma_kt[],
+ real fit_start,
+ real temp);
void compute_derivative(int nn, const real x[], const real y[], real dydx[]);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff