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37 #ifndef GMX_GMXANA_GSTAT_H
38 #define GMX_GMXANA_GSTAT_H
40 #include "../legacyheaders/typedefs.h"
41 #include "../commandline/pargs.h"
42 #include "../legacyheaders/oenv.h"
43 #include "../legacyheaders/index.h"
49 /***********************************************
51 * A U T O C O R R E L A T I O N
53 ***********************************************/
55 real
LegendreP(real x
, unsigned long m
);
57 #define eacNormal (1<<0)
59 #define eacVector (1<<2)
60 #define eacRcross (1<<3 | eacVector)
61 #define eacP0 (1<<4 | eacVector)
62 #define eacP1 (1<<5 | eacVector)
63 #define eacP2 (1<<6 | eacVector)
64 #define eacP3 (1<<7 | eacVector)
65 #define eacP4 (1<<8 | eacVector)
66 #define eacIden (1<<9)
69 effnNONE
, effnEXP1
, effnEXP2
, effnEXP3
, effnVAC
,
70 effnEXP5
, effnEXP7
, effnEXP9
, effnERF
, effnERREST
, effnNR
73 /* must correspond with 'leg' g_chi.c:727 */
75 edPhi
= 0, edPsi
, edOmega
, edChi1
, edChi2
, edChi3
, edChi4
, edChi5
, edChi6
, edMax
79 edPrintST
= 0, edPrintRO
84 #define MAXCHI edMax-NONCHI
85 #define NROT 4 /* number of rotamers: 1=g(-), 2=t, 3=g(+), 0=other */
88 int minCalpha
, minC
, H
, N
, C
, O
, Cn
[MAXCHI
+3];
89 } t_dihatms
; /* Cn[0]=N, Cn[1]=Ca, Cn[2]=Cb etc. */
94 int index
; /* Index for amino acids (histograms) */
95 int j0
[edMax
]; /* Index in dih array (phi angle is first...) */
100 real rot_occ
[edMax
][NROT
];
104 extern const int nfp_ffn
[effnNR
];
106 extern const char *s_ffn
[effnNR
+2];
108 extern const char *longs_ffn
[effnNR
];
110 int sffn2effn(const char **sffn
);
111 /* Returns the ffn enum corresponding to the selected enum option in sffn */
113 t_pargs
*add_acf_pargs(int *npargs
, t_pargs
*pa
);
114 /* Add options for autocorr to the current set of options.
115 * *npargs must be initialised to the number of elements in pa,
116 * it will be incremented appropriately.
119 void cross_corr(int n
, real f
[], real g
[], real corr
[]);
120 /* Simple minded cross correlation algorithm */
122 real
fit_acf(int ncorr
, int fitfn
, const output_env_t oenv
, gmx_bool bVerbose
,
123 real tbeginfit
, real tendfit
, real dt
, real c1
[], real
*fit
);
124 /* Fit an ACF to a given function */
126 void do_autocorr(const char *fn
, const output_env_t oenv
,
128 int nframes
, int nitem
, real
**c1
,
129 real dt
, unsigned long mode
, gmx_bool bAver
);
130 /* Calls low_do_autocorr (see below). After calling add_acf_pargs */
132 void low_do_autocorr(const char *fn
, const output_env_t oenv
,
133 const char *title
, int nframes
, int nitem
,
134 int nout
, real
**c1
, real dt
, unsigned long mode
,
135 int nrestart
, gmx_bool bAver
, gmx_bool bNormalize
,
136 gmx_bool bVerbose
, real tbeginfit
, real tendfit
,
139 * do_autocorr calculates autocorrelation functions for many things.
140 * It takes a 2 d array containing nitem arrays of length nframes
141 * for each item the ACF is calculated.
143 * A number of "modes" exist for computation of the ACF
145 * if (mode == eacNormal) {
146 * C(t) = < X (tau) * X (tau+t) >
148 * else if (mode == eacCos) {
149 * C(t) = < cos (X(tau) - X(tau+t)) >
151 * else if (mode == eacIden) { **not fully supported yet**
152 * C(t) = < (X(tau) == X(tau+t)) >
154 * else if (mode == eacVector) {
155 * C(t) = < X(tau) * X(tau+t)
157 * else if (mode == eacP1) {
158 * C(t) = < cos (X(tau) * X(tau+t) >
160 * else if (mode == eacP2) {
161 * C(t) = 1/2 * < 3 cos (X(tau) * X(tau+t) - 1 >
163 * else if (mode == eacRcross) {
164 * C(t) = < ( X(tau) * X(tau+t) )^2 >
167 * For modes eacVector, eacP1, eacP2 and eacRcross the input should be
168 * 3 x nframes long, where each triplet is taken as a 3D vector
170 * For mode eacCos inputdata must be in radians, not degrees!
172 * Other parameters are:
174 * fn is output filename (.xvg) where the correlation function(s) are printed
175 * title is the title in the output file
176 * nframes is the number of frames in the time series
177 * nitem is the number of items
178 * c1 is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ]
179 * on output, this array is filled with the correlation function
181 * nrestart is the number of steps between restarts for direct ACFs
182 * (i.e. without FFT) When set to 1 all points are used as
183 * time origin for averaging
184 * dt is the time between frames
185 * bAver If set, all ndih C(t) functions are averaged into a single
187 * (bFour If set, will use fast fourier transform (FFT) for evaluating
188 * the ACF: removed option, now on the command line only)
189 * bNormalize If set, all ACFs will be normalized to start at 0
190 * nskip Determines whether steps a re skipped in the output
194 const char *name
; /* Description of the J coupling constant */
195 real A
, B
, C
; /* Karplus coefficients */
196 real offset
; /* Offset for dihedral angle in histogram (e.g. -M_PI/3) */
197 real Jc
; /* Resulting Jcoupling */
198 real Jcsig
; /* Standard deviation in Jc */
201 void calc_distribution_props(int nh
, int histo
[],
202 real start
, int nkkk
, t_karplus kkk
[],
204 /* This routine takes a dihedral distribution and calculates
205 * coupling constants and dihedral order parameters of it.
207 * nh is the number of points
208 * histo is the array of datapoints which is assumed to span
210 * start is the starting angle of the histogram, this can be either 0
212 * nkkk is the number of karplus sets (multiple coupling constants may be
213 * derived from a single angle)
214 * kkk are the constants for calculating J coupling constants using a
215 * Karplus equation according to
218 * J = A cos theta + B cos theta + C
220 * where theta is phi - offset (phi is the angle in the histogram)
221 * offset is subtracted from phi before substitution in the Karplus
223 * S2 is the resulting dihedral order parameter
228 /***********************************************
230 * F I T R O U T I N E S
232 ***********************************************/
233 void do_expfit(int ndata
, real c1
[], real dt
,
234 real begintimefit
, real endtimefit
);
236 void expfit(int n
, real x
[], real y
[], real Dy
[],
239 /* This procedure fits y=exp(a+bx) for n (x,y) pairs to determine a and b.
240 * The uncertainties in the y values must be in the vector Dy.
241 * The standard deviations of a and b, sa and sb, are also calculated.
243 * Routine from Computers in physics, 7(3) (1993), p. 280-285.
246 void ana_dih_trans(const char *fn_trans
, const char *fn_histo
,
247 real
**dih
, int nframes
, int nangles
,
248 const char *grpname
, real
*time
, gmx_bool bRb
,
249 const output_env_t oenv
);
251 * Analyse dihedral transitions, by counting transitions per dihedral
252 * and per frame. The total number of transitions is printed to
253 * stderr, as well as the average time between transitions.
255 * is wrapper to low_ana_dih_trans, which also passes in and out the
256 number of transitions per dihedral per residue. that uses struc dlist
257 which is not external, so pp2shift.h must be included.
259 * Dihedrals are supposed to be in either of three minima,
260 * (trans, gauche+, gauche-)
262 * fn_trans output file name for #transitions per timeframe
263 * fn_histo output file name for transition time histogram
264 * dih the actual dihedral angles
265 * nframes number of times frames
266 * nangles number of angles
267 * grpname a string for the header of plots
268 * time array (size nframes) of times of trajectory frames
269 * bRb determines whether the polymer convention is used
273 void low_ana_dih_trans(gmx_bool bTrans
, const char *fn_trans
,
274 gmx_bool bHisto
, const char *fn_histo
, int maxchi
,
275 real
**dih
, int nlist
, t_dlist dlist
[],
276 int nframes
, int nangles
, const char *grpname
,
277 int multiplicity
[], real
*time
, gmx_bool bRb
,
278 real core_frac
, const output_env_t oenv
);
279 /* as above but passes dlist so can copy occupancies into it, and multiplicity[]
280 * (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
281 * rotamers. Also production of xvg output files is conditional
282 * and the fractional width of each rotamer can be set ie for a 3 fold
283 * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
284 * to each rotamer, the rest goes to rotamer zero */
288 void read_ang_dih(const char *trj_fn
,
289 gmx_bool bAngles
, gmx_bool bSaveAll
, gmx_bool bRb
, gmx_bool bPBC
,
290 int maxangstat
, int angstat
[],
291 int *nframes
, real
**time
,
292 int isize
, atom_id index
[],
296 const output_env_t oenv
);
298 * Read a trajectory and calculate angles and dihedrals.
300 * trj_fn file name of trajectory
301 * tpb_fn file name of tpb file
302 * bAngles do we have to read angles or dihedrals
303 * bSaveAll do we have to store all in the dih array
304 * bRb do we have Ryckaert-Bellemans dihedrals (trans = 0)
305 * bPBC compute angles module 2 Pi
306 * maxangstat number of entries in distribution array
307 * angstat angle distribution
308 * *nframes number of frames read
309 * time simulation time at each time frame
310 * isize number of entries in the index, when angles 3*number of angles
311 * else 4*number of angles
312 * index atom numbers that define the angles or dihedrals
313 * (i,j,k) resp (i,j,k,l)
314 * trans_frac number of dihedrals in trans
315 * aver_angle average angle at each time frame
316 * dih all angles at each time frame
319 void make_histo(FILE *log
,
320 int ndata
, real data
[], int npoints
, int histo
[],
321 real minx
, real maxx
);
323 * Make a histogram from data. The min and max of the data array can
324 * be determined (if minx == 0 and maxx == 0)
325 * and the index in the histogram is computed from
326 * ind = npoints/(max(data) - min(data))
328 * log write error output to this file
329 * ndata number of points in data
331 * npoints number of points in histogram
332 * histo histogram array. This is NOT set to zero, to allow you
333 * to add multiple histograms
334 * minx start of the histogram
335 * maxx end of the histogram
336 * if both are 0, these values are computed by the routine itself
339 void normalize_histo(int npoints
, int histo
[], real dx
, real normhisto
[]);
341 * Normalize a histogram so that the integral over the histo is 1
343 * npoints number of points in the histo array
344 * histo input histogram
345 * dx distance between points on the X-axis
346 * normhisto normalized output histogram
349 real
fit_function(int eFitFn
, real
*parm
, real x
);
350 /* Returns the value of fit function eFitFn at x */
352 /* Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential */
353 /* or to a transverse current autocorrelation function */
354 /* Or: "There is no KILL like OVERKILL", Dr. Ir. D. van der Spoel */
355 real
do_lmfit(int ndata
, real c1
[], real sig
[], real dt
, real
*x
,
356 real begintimefit
, real endtimefit
, const output_env_t oenv
,
357 gmx_bool bVerbose
, int eFitFn
, real fitparms
[], int fix
);
359 * If x == NULL, the timestep dt will be used to create a time axis.
360 * fix fixes fit parameter i at it's starting value, when the i'th bit
364 real
evaluate_integral(int n
, real x
[], real y
[], real dy
[],
365 real aver_start
, real
*stddev
);
366 /* Integrate data in y, and, if given, use dy as weighting
367 * aver_start should be set to a value where the function has
371 real
print_and_integrate(FILE *fp
, int n
, real dt
,
372 real c
[], real
*fit
, int nskip
);
373 /* Integrate the data in c[] from 0 to n using trapezium rule.
374 * If fp != NULL output is written to it
375 * nskip determines whether all elements are written to the output file
376 * (written when i % nskip == 0)
377 * If fit != NULL the fit is also written.
380 int get_acfnout(void);
381 /* Return the output length for the correlation function
382 * Works only AFTER do_auto_corr has been called!
385 int get_acffitfn(void);
386 /* Return the fit function type.
387 * Works only AFTER do_auto_corr has been called!
390 /* Routines from pp2shift (anadih.c etc.) */
392 void do_pp2shifts(FILE *fp
, int nframes
,
393 int nlist
, t_dlist dlist
[], real
**dih
);
395 gmx_bool
has_dihedral(int Dih
, t_dlist
*dl
);
397 t_dlist
*mk_dlist(FILE *log
,
398 t_atoms
*atoms
, int *nlist
,
399 gmx_bool bPhi
, gmx_bool bPsi
, gmx_bool bChi
, gmx_bool bHChi
,
400 int maxchi
, int r0
, gmx_residuetype_t rt
);
402 void pr_dlist(FILE *fp
, int nl
, t_dlist dl
[], real dt
, int printtype
,
403 gmx_bool bPhi
, gmx_bool bPsi
, gmx_bool bChi
, gmx_bool bOmega
, int maxchi
);
405 int pr_trans(FILE *fp
, int nl
, t_dlist dl
[], real dt
, int Xi
);
407 void mk_chi_lookup (int **lookup
, int maxchi
,
408 int nlist
, t_dlist dlist
[]);
410 void mk_multiplicity_lookup (int *multiplicity
, int maxchi
,
411 int nlist
, t_dlist dlist
[], int nangle
);
413 void get_chi_product_traj (real
**dih
, int nframes
,
414 int nlist
, int maxchi
, t_dlist dlist
[],
415 real time
[], int **lookup
, int *multiplicity
,
416 gmx_bool bRb
, gmx_bool bNormalize
,
417 real core_frac
, gmx_bool bAll
, const char *fnall
,
418 const output_env_t oenv
);
420 void print_one (const output_env_t oenv
, const char *base
,
422 const char *title
, const char *ylabel
, int nf
,
423 real time
[], real data
[]);
425 /* Routines from g_hbond */
426 void analyse_corr(int n
, real t
[], real ct
[], real nt
[], real kt
[],
427 real sigma_ct
[], real sigma_nt
[], real sigma_kt
[],
428 real fit_start
, real temp
, real smooth_tail_start
,
429 const output_env_t oenv
);
431 void compute_derivative(int nn
, real x
[], real y
[], real dydx
[]);