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38 #ifndef GMX_GMXANA_GSTAT_H
39 #define GMX_GMXANA_GSTAT_H
41 #include "gromacs/commandline/pargs.h"
42 #include "gromacs/topology/index.h"
44 struct gmx_output_env_t;
47 /* must correspond with 'leg' g_chi.c:727 */
70 #define MAXCHI (edMax - NONCHI)
71 #define NROT 4 /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
75 int minCalpha, minC, H, N, C, O, Cn[MAXCHI + 3];
76 } t_dihatms; /* Cn[0]=N, Cn[1]=Ca, Cn[2]=Cb etc. */
82 int index; /* Index for amino acids (histograms) */
83 int j0[edMax]; /* Index in dih array (phi angle is first...) */
88 real rot_occ[edMax][NROT];
94 const char* name; /* Description of the J coupling constant */
95 real A, B, C; /* Karplus coefficients */
96 real offset; /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
97 real Jc; /* Resulting Jcoupling */
98 real Jcsig; /* Standard deviation in Jc */
101 void calc_distribution_props(int nh, const int histo[], real start, int nkkk, t_karplus kkk[], real* S2);
102 /* This routine takes a dihedral distribution and calculates
103 * coupling constants and dihedral order parameters of it.
105 * nh is the number of points
106 * histo is the array of datapoints which is assumed to span
108 * start is the starting angle of the histogram, this can be either 0
110 * nkkk is the number of karplus sets (multiple coupling constants may be
111 * derived from a single angle)
112 * kkk are the constants for calculating J coupling constants using a
113 * Karplus equation according to
116 * J = A cos theta + B cos theta + C
118 * where theta is phi - offset (phi is the angle in the histogram)
119 * offset is subtracted from phi before substitution in the Karplus
121 * S2 is the resulting dihedral order parameter
125 void ana_dih_trans(const char* fn_trans,
126 const char* fn_histo,
133 const gmx_output_env_t* oenv);
135 * Analyse dihedral transitions, by counting transitions per dihedral
136 * and per frame. The total number of transitions is printed to
137 * stderr, as well as the average time between transitions.
139 * is wrapper to low_ana_dih_trans, which also passes in and out the
140 number of transitions per dihedral per residue. that uses struc dlist
141 which is not external, so pp2shift.h must be included.
143 * Dihedrals are supposed to be in either of three minima,
144 * (trans, gauche+, gauche-)
146 * fn_trans output file name for #transitions per timeframe
147 * fn_histo output file name for transition time histogram
148 * dih the actual dihedral angles
149 * nframes number of times frames
150 * nangles number of angles
151 * grpname a string for the header of plots
152 * time array (size nframes) of times of trajectory frames
153 * bRb determines whether the polymer convention is used
157 void low_ana_dih_trans(gmx_bool bTrans,
158 const char* fn_trans,
160 const char* fn_histo,
172 const gmx_output_env_t* oenv);
173 /* as above but passes dlist so can copy occupancies into it, and multiplicity[]
174 * (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
175 * rotamers. Also production of xvg output files is conditional
176 * and the fractional width of each rotamer can be set ie for a 3 fold
177 * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
178 * to each rotamer, the rest goes to rotamer zero */
181 void read_ang_dih(const char* trj_fn,
195 const gmx_output_env_t* oenv);
197 * Read a trajectory and calculate angles and dihedrals.
199 * trj_fn file name of trajectory
200 * bAngles do we have to read angles or dihedrals
201 * bSaveAll do we have to store all in the dih array
202 * bRb do we have Ryckaert-Bellemans dihedrals (trans = 0)
203 * bPBC compute angles module 2 Pi
204 * maxangstat number of entries in distribution array
205 * angstat angle distribution
206 * *nframes number of frames read
207 * time simulation time at each time frame
208 * isize number of entries in the index, when angles 3*number of angles
209 * else 4*number of angles
210 * index atom numbers that define the angles or dihedrals
211 * (i,j,k) resp (i,j,k,l)
212 * trans_frac number of dihedrals in trans
213 * aver_angle average angle at each time frame
214 * dih all angles at each time frame
217 void make_histo(FILE* log, int ndata, real data[], int npoints, int histo[], real minx, real maxx);
219 * Make a histogram from data. The min and max of the data array can
220 * be determined (if minx == 0 and maxx == 0)
221 * and the index in the histogram is computed from
222 * ind = npoints/(max(data) - min(data))
224 * log write error output to this file
225 * ndata number of points in data
227 * npoints number of points in histogram
228 * histo histogram array. This is NOT set to zero, to allow you
229 * to add multiple histograms
230 * minx start of the histogram
231 * maxx end of the histogram
232 * if both are 0, these values are computed by the routine itself
235 void normalize_histo(int npoints, const int histo[], real dx, real normhisto[]);
237 * Normalize a histogram so that the integral over the histo is 1
239 * npoints number of points in the histo array
240 * histo input histogram
241 * dx distance between points on the X-axis
242 * normhisto normalized output histogram
245 /* Routines from pp2shift (anadih.c etc.) */
247 void do_pp2shifts(FILE* fp, int nframes, int nlist, t_dlist dlist[], real** dih);
249 gmx_bool has_dihedral(int Dih, t_dlist* dl);
251 t_dlist* mk_dlist(FILE* log,
252 const t_atoms* atoms,
262 void pr_dlist(FILE* fp,
273 int pr_trans(FILE* fp, int nl, t_dlist dl[], real dt, int Xi);
275 void mk_chi_lookup(int** lookup, int maxchi, int nlist, t_dlist dlist[]);
277 void mk_multiplicity_lookup(int* multiplicity, int maxchi, int nlist, t_dlist dlist[], int nangle);
279 void get_chi_product_traj(real** dih,
292 const gmx_output_env_t* oenv);
294 void print_one(const gmx_output_env_t* oenv,
303 /* Routines from g_hbond */
304 void analyse_corr(int n,
315 void compute_derivative(int nn, const real x[], const real y[], real dydx[]);