gromacs-dev 4.6.5-1build1 / usr / include / gromacs / gstat.h

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 * check out http://www.gromacs.org for more information.
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#ifndef _gstat_h
#define _gstat_h

#include "typedefs.h"
#include "statutil.h"
#include "mshift.h"
#include "rmpbc.h"

#ifdef __cplusplus
extern "C" {
#endif

/***********************************************
 *
 *     A U T O C O R R E L A T I O N
 *
 ***********************************************/

real LegendreP(real x, unsigned long m);

#define eacNormal (1<<0)
#define eacCos    (1<<1)
#define eacVector (1<<2)
#define eacRcross (1<<3  | eacVector)
#define eacP0     (1<<4  | eacVector)
#define eacP1     (1<<5  | eacVector)
#define eacP2     (1<<6  | eacVector)
#define eacP3     (1<<7  | eacVector)
#define eacP4     (1<<8  | eacVector)
#define eacIden   (1<<9)

enum {
    effnNONE, effnEXP1, effnEXP2, effnEXP3,   effnVAC,
    effnEXP5, effnEXP7, effnEXP9, effnERF, effnERREST, effnNR
};

/* must correspond with 'leg' g_chi.c:727 */
enum {
    edPhi = 0, edPsi, edOmega, edChi1, edChi2, edChi3, edChi4, edChi5, edChi6, edMax
};

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 */

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];

} t_dlist;

extern const int   nfp_ffn[effnNR];

extern const char *s_ffn[effnNR+2];

extern const char *longs_ffn[effnNR];

int sffn2effn(const char **sffn);
/* Returns the ffn enum corresponding to the selected enum option in sffn */

t_pargs *add_acf_pargs(int *npargs, t_pargs *pa);
/* Add options for autocorr to the current set of options.
 * *npargs must be initialised to the number of elements in pa,
 * it will be incremented appropriately.
 */

void cross_corr(int n, real f[], real g[], real corr[]);
/* Simple minded cross correlation algorithm */

real fit_acf(int ncorr, int fitfn, const output_env_t oenv, gmx_bool bVerbose,
             real tbeginfit, real tendfit, real dt, real c1[], real *fit);
/* Fit an ACF to a given function */

void do_autocorr(const char *fn, const output_env_t oenv,
                 const char *title,
                 int nframes, int nitem, real **c1,
                 real dt, unsigned long mode, gmx_bool bAver);
/* Calls low_do_autocorr (see below). After calling add_acf_pargs */

void low_do_autocorr(const char *fn, const output_env_t oenv,
                     const char *title, int  nframes, int nitem,
                     int nout, real **c1, real dt, unsigned long mode,
                     int nrestart, gmx_bool bAver, gmx_bool bNormalize,
                     gmx_bool bVerbose, real tbeginfit, real tendfit,
                     int nfitparm, int nskip);
/*
 * do_autocorr calculates autocorrelation functions for many things.
 * It takes a 2 d array containing nitem arrays of length nframes
 * for each item the ACF is calculated.
 *
 * A number of "modes" exist for computation of the ACF
 *
 * if (mode == eacNormal) {
 *   C(t) = < X (tau) * X (tau+t) >
 * }
 * else if (mode == eacCos) {
 *   C(t) = < cos (X(tau) - X(tau+t)) >
 * }
 * else if (mode == eacIden) { **not fully supported yet**
 *   C(t) = < (X(tau) == X(tau+t)) >
 * }
 * else if (mode == eacVector) {
 *   C(t) = < X(tau) * X(tau+t)
 * }
 * else if (mode == eacP1) {
 *   C(t) = < cos (X(tau) * X(tau+t) >
 * }
 * else if (mode == eacP2) {
 *   C(t) = 1/2 * < 3 cos (X(tau) * X(tau+t) - 1 >
 * }
 * else if (mode == eacRcross) {
 *   C(t) = < ( X(tau) * X(tau+t) )^2 >
 * }
 *
 * For modes eacVector, eacP1, eacP2 and eacRcross the input should be
 * 3 x nframes long, where each triplet is taken as a 3D vector
 *
 * For mode eacCos inputdata must be in radians, not degrees!
 *
 * Other parameters are:
 *
 * fn is output filename (.xvg) where the correlation function(s) are printed
 * title is the title in the output file
 * nframes is the number of frames in the time series
 * nitem is the number of items
 * c1       is an array of dimension [ 0 .. nitem-1 ] [ 0 .. nframes-1 ]
 *          on output, this array is filled with the correlation function
 *          to reduce storage
 * nrestart     is the number of steps between restarts for direct ACFs
 *              (i.e. without FFT) When set to 1 all points are used as
 *              time origin for averaging
 * dt       is the time between frames
 * bAver    If set, all ndih C(t) functions are averaged into a single
 *          C(t)
 * (bFour       If set, will use fast fourier transform (FFT) for evaluating
 *              the ACF: removed option, now on the command line only)
 * bNormalize   If set, all ACFs will be normalized to start at 0
 * nskip        Determines whether steps a re skipped in the output
 */

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, 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.
 *
 * nh      is the number of points
 * histo   is the array of datapoints which is assumed to span
 *         2 M_PI radians
 * start   is the starting angle of the histogram, this can be either 0
 *         or -M_PI
 * nkkk    is the number of karplus sets (multiple coupling constants may be
 *         derived from a single angle)
 * kkk     are the constants for calculating J coupling constants using a
 *         Karplus equation according to
 *
 *                  2
 *         J = A cos theta + B cos theta + C
 *
 *         where theta is phi - offset (phi is the angle in the histogram)
 * offset  is subtracted from phi before substitution in the Karplus
 *         equation
 * S2      is the resulting dihedral order parameter
 *
 */


/***********************************************
 *
 *     F I T   R O U T I N E S
 *
 ***********************************************/
void do_expfit(int ndata, real c1[], real dt,
               real begintimefit, real endtimefit);

void expfit(int n, real x[], real y[], real Dy[],
            real *a, real *sa,
            real *b, real *sb);
/* This procedure fits y=exp(a+bx) for n (x,y) pairs to determine a and b.
 * The uncertainties in the y values must be in the vector Dy.
 * The standard deviations of a and b, sa and sb, are also calculated.
 *
 * Routine from Computers in physics, 7(3) (1993), p. 280-285.
 */

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 output_env_t oenv);
/*
 * Analyse dihedral transitions, by counting transitions per dihedral
 * and per frame. The total number of transitions is printed to
 * stderr, as well as the average time between transitions.
 *
 * is wrapper to low_ana_dih_trans, which also passes in and out the
     number of transitions per dihedral per residue. that uses struc dlist
     which is not external, so pp2shift.h must be included.

 * Dihedrals are supposed to be in either of three minima,
 * (trans, gauche+, gauche-)
 *
 * fn_trans  output file name for #transitions per timeframe
 * fn_histo  output file name for transition time histogram
 * dih       the actual dihedral angles
 * nframes   number of times frames
 * nangles   number of angles
 * grpname   a string for the header of plots
 * time      array (size nframes) of times of trajectory frames
 * bRb       determines whether the polymer convention is used
 *           (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 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
 * and the fractional width of each rotamer can be set ie for a 3 fold
 * dihedral with core_frac = 0.5 only the central 60 degrees is assigned
 * 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, atom_id index[],
                  real **trans_frac,
                  real **aver_angle,
                  real *dih[],
                  const output_env_t oenv);
/*
 * Read a trajectory and calculate angles and dihedrals.
 *
 * trj_fn      file name of trajectory
 * tpb_fn      file name of tpb file
 * bAngles     do we have to read angles or dihedrals
 * bSaveAll    do we have to store all in the dih array
 * bRb         do we have Ryckaert-Bellemans dihedrals (trans = 0)
 * bPBC        compute angles module 2 Pi
 * maxangstat  number of entries in distribution array
 * angstat     angle distribution
 * *nframes    number of frames read
 * time        simulation time at each time frame
 * isize       number of entries in the index, when angles 3*number of angles
 *             else 4*number of angles
 * index       atom numbers that define the angles or dihedrals
 *             (i,j,k) resp (i,j,k,l)
 * trans_frac  number of dihedrals in trans
 * aver_angle  average angle at each time frame
 * dih         all angles at each time frame
 */

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)
 * and the index in the histogram is computed from
 * ind = npoints/(max(data) - min(data))
 *
 * log       write error output to this file
 * ndata     number of points in data
 * data      data points
 * npoints   number of points in histogram
 * histo     histogram array. This is NOT set to zero, to allow you
 *           to add multiple histograms
 * minx      start of the histogram
 * maxx      end of the histogram
 *           if both are 0, these values are computed by the routine itself
 */

void normalize_histo(int npoints, int histo[], real dx, real normhisto[]);
/*
 * Normalize a histogram so that the integral over the histo is 1
 *
 * npoints    number of points in the histo array
 * histo      input histogram
 * dx         distance between points on the X-axis
 * normhisto  normalized output histogram
 */

real fit_function(int eFitFn, real *parm, real x);
/* Returns the value of fit function eFitFn at x */

/* Use Levenberg-Marquardt method to fit to a nfitparm parameter exponential */
/* or to a transverse current autocorrelation function */
/* Or: "There is no KILL like OVERKILL", Dr. Ir. D. van der Spoel */
real do_lmfit(int ndata, real c1[], real sig[], real dt, real *x,
              real begintimefit, real endtimefit, const output_env_t oenv,
              gmx_bool bVerbose, int eFitFn, real fitparms[], int fix);
/* Returns integral.
 * If x == NULL, the timestep dt will be used to create a time axis.
 * fix fixes fit parameter i at it's starting value, when the i'th bit
 * of fix is set.
 */

real evaluate_integral(int n, real x[], real y[], real dy[],
                       real aver_start, real *stddev);
/* Integrate data in y, and, if given, use dy as weighting
 * aver_start should be set to a value where the function has
 * converged to 0.
 */

real print_and_integrate(FILE *fp, int n, real dt,
                         real c[], real *fit, int nskip);
/* Integrate the data in c[] from 0 to n using trapezium rule.
 * If fp != NULL output is written to it
 * nskip determines whether all elements are written to the output file
 * (written when i % nskip == 0)
 * If fit != NULL the fit is also written.
 */

int get_acfnout(void);
/* Return the output length for the correlation function
 * Works only AFTER do_auto_corr has been called!
 */

int get_acffitfn(void);
/* Return the fit function type.
 * Works only AFTER do_auto_corr has been called!
 */

/* Routines from pp2shift (anadih.c etc.) */

void do_pp2shifts(FILE *fp, int nframes,
                  int nlist, t_dlist dlist[], real **dih);

gmx_bool has_dihedral(int Dih, t_dlist *dl);

t_dlist *mk_dlist(FILE *log,
                  t_atoms *atoms, int *nlist,
                  gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
                  int maxchi, int r0, gmx_residuetype_t 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);

int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi);

void mk_chi_lookup (int **lookup, int maxchi, real **dih,
                    int nlist, t_dlist dlist[]);

void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih,
                             int nlist, t_dlist dlist[], int nangle);

void get_chi_product_traj (real **dih, int nframes, int nangles,
                           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 output_env_t oenv);

void print_one (const 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, real smooth_tail_start,
                  const output_env_t oenv);

void compute_derivative(int nn, real x[], real y[], real dydx[]);

#ifdef __cplusplus
}
#endif

#endif