src/gromacs/gmxana/hxprops.h

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  37
  38 #ifndef _hxprops_h
  39 #define _hxprops_h
  40
  41 #include <stdio.h>
  42
  43 #include "gromacs/math/vectypes.h"
  44 #include "gromacs/topology/idef.h"
  45 #include "gromacs/utility/basedefinitions.h"
  46 #include "gromacs/utility/real.h"
  47
  48 struct t_atom;
  49 struct t_resinfo;
  50
  51 #define PHI_AHX (-55.0)
  52 #define PSI_AHX (-45.0)
  53 /* Canonical values of the helix phi/psi angles */
  54
  55
  56 /*! \internal \brief Struct containing properties of a residue in a protein backbone. */
  57 struct t_bb {
  58     //! Protein backbone phi angle.
  59     real     phi;
  60     //! Protein backbone psi angle.
  61     real     psi;
  62     //! RMS distance of phi and psi angles from ideal helix
  63     real     pprms2;
  64     //! Estimated J-coupling value
  65     real     jcaha;
  66     //! Value of 3 turn helix?
  67     real     d3;
  68     //! Value of 4 turn helix?
  69     real     d4;
  70     //! Value of 5 turn?
  71     real     d5;
  72     //! Average of RMS for analysis.
  73     real     rmsa;
  74     //! If the structure is helical.
  75     gmx_bool bHelix;
  76     //! Number of elliptical elements
  77     int      nhx;
  78     //! Average RMS Deviation when atoms of this residue are fitted to ideal helix
  79     int      nrms;
  80     //! Residue index for output, relative to gmx_helix -r0 value
  81     int      resno;
  82     //! Index for previous carbon.
  83     int      Cprev;
  84     //! Index for backbone nitrogen.
  85     int      N;
  86     //! Index for backbone NH hydrogen.
  87     int      H;
  88     //! Index for alpha carbon.
  89     int      CA;
  90     //! Index for carbonyl carbon.
  91     int      C;
  92     //! Index for carbonyl oxygen.
  93     int      O;
  94     //! Index for next backbone nitrogen.
  95     int      Nnext;
  96     //! Name for this residue.
  97     char     label[32];
  98 };
  99
 100 enum {
 101     efhRAD,  efhTWIST, efhRISE, efhLEN,
 102     efhDIP,  efhRMS,   efhRMSA, efhCD222,
 103     efhPPRMS, efhCPHI,  efhPHI,  efhPSI,
 104     efhHB3,  efhHB4,   efhHB5,  efhJCA,
 105     efhAHX,  efhNR
 106 };
 107
 108 extern real ahx_len(int gnx, const int index[], rvec x[]);
 109 /* Assume we have a list of Calpha atoms only! */
 110
 111 extern real ellipticity(int nres, t_bb bb[]);
 112
 113 extern real radius(FILE *fp, int nca, const int ca_index[], rvec x[]);
 114 /* Assume we have calphas */
 115
 116 extern real twist(int nca, const int caindex[], rvec x[]);
 117 /* Calculate the twist of the helix */
 118
 119 extern real pprms(FILE *fp, int nbb, t_bb bb[]);
 120 /* Calculate the average RMS from canonical phi/psi values
 121  * and the distance per residue
 122  */
 123
 124 extern real ca_phi(int gnx, const int index[], rvec x[]);
 125 /* Assume we have a list of Calpha atoms only! */
 126
 127 extern real dip(int nbb, const int bbind[], const rvec x[], const t_atom atom[]);
 128
 129 extern real rise(int gnx, const int index[], rvec x[]);
 130 /* Assume we have a list of Calpha atoms only! */
 131
 132 extern void av_hblen(FILE *fp3, FILE *fp3a,
 133                      FILE *fp4, FILE *fp4a,
 134                      FILE *fp5, FILE *fp5a,
 135                      real t, int nres, t_bb bb[]);
 136
 137 extern void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
 138                       real t, int nres, t_bb bb[]);
 139
 140 /*! \brief Allocate and fill an array of information about residues in a protein backbone.
 141  *
 142  * The user is propted for an index group of protein residues (little
 143  * error checking occurs). For the number of residues found in the
 144  * selected group, nbb entries are made in the returned array.  Each
 145  * entry contains the atom indices of the N, H, CA, C and O atoms (for
 146  * PRO, H means CD), as well as the C of the previous residue and the
 147  * N of the next (-1 if not found).
 148  *
 149  * In the output array, the first residue will be numbered starting
 150  * from res0. */
 151 extern t_bb *mkbbind(const char *fn, int *nres, int *nbb, int res0,
 152                      int *nall, int **index,
 153                      char ***atomname, t_atom atom[],
 154                      t_resinfo *resinfo);
 155
 156 extern void do_start_end(int nres, t_bb bb[], int *nbb,
 157                          int bbindex[], int *nca, int caindex[],
 158                          gmx_bool bRange, int rStart, int rEnd);
 159
 160 extern void calc_hxprops(int nres, t_bb bb[], const rvec x[]);
 161
 162 extern void pr_bb(FILE *fp, int nres, t_bb bb[]);
 163
 164 #endif