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 #ifdef __cplusplus
  52 extern "C"
  53 {
  54 #endif
  55
  56 #define PHI_AHX (-55.0)
  57 #define PSI_AHX (-45.0)
  58 /* Canonical values of the helix phi/psi angles */
  59
  60
  61 /*! \internal \brief Struct containing properties of a residue in a protein backbone. */
  62 struct t_bb {
  63     //! Protein backbone phi angle.
  64     real     phi;
  65     //! Protein backbone psi angle.
  66     real     psi;
  67     //! RMS distance of phi and psi angles from ideal helix
  68     real     pprms2;
  69     //! Estimated J-coupling value
  70     real     jcaha;
  71     //! Value of 3 turn helix?
  72     real     d3;
  73     //! Value of 4 turn helix?
  74     real     d4;
  75     //! Value of 5 turn?
  76     real     d5;
  77     //! Average of RMS for analysis.
  78     real     rmsa;
  79     //! If the structure is helical.
  80     gmx_bool bHelix;
  81     //! Number of elliptical elements
  82     int      nhx;
  83     //! Average RMS Deviation when atoms of this residue are fitted to ideal helix
  84     int      nrms;
  85     //! Residue index for output, relative to gmx_helix -r0 value
  86     int      resno;
  87     //! Index for previous carbon.
  88     int      Cprev;
  89     //! Index for backbone nitrogen.
  90     int      N;
  91     //! Index for backbone NH hydrogen.
  92     int      H;
  93     //! Index for alpha carbon.
  94     int      CA;
  95     //! Index for carbonyl carbon.
  96     int      C;
  97     //! Index for carbonyl oxygen.
  98     int      O;
  99     //! Index for next backbone nitrogen.
 100     int      Nnext;
 101     //! Name for this residue.
 102     char     label[32];
 103 };
 104
 105 enum {
 106     efhRAD,  efhTWIST, efhRISE, efhLEN,
 107     efhDIP,  efhRMS,   efhRMSA, efhCD222,
 108     efhPPRMS, efhCPHI,  efhPHI,  efhPSI,
 109     efhHB3,  efhHB4,   efhHB5,  efhJCA,
 110     efhAHX,  efhNR
 111 };
 112
 113 extern real ahx_len(int gnx, int index[], rvec x[]);
 114 /* Assume we have a list of Calpha atoms only! */
 115
 116 extern real ellipticity(int nres, t_bb bb[]);
 117
 118 extern real radius(FILE *fp, int nca, int ca_index[], rvec x[]);
 119 /* Assume we have calphas */
 120
 121 extern real twist(int nca, int caindex[], rvec x[]);
 122 /* Calculate the twist of the helix */
 123
 124 extern real pprms(FILE *fp, int nbb, t_bb bb[]);
 125 /* Calculate the average RMS from canonical phi/psi values
 126  * and the distance per residue
 127  */
 128
 129 extern real ca_phi(int gnx, int index[], rvec x[]);
 130 /* Assume we have a list of Calpha atoms only! */
 131
 132 extern real dip(int nbb, const int bbind[], const rvec x[], const t_atom atom[]);
 133
 134 extern real rise(int gnx, int index[], rvec x[]);
 135 /* Assume we have a list of Calpha atoms only! */
 136
 137 extern void av_hblen(FILE *fp3, FILE *fp3a,
 138                      FILE *fp4, FILE *fp4a,
 139                      FILE *fp5, FILE *fp5a,
 140                      real t, int nres, t_bb bb[]);
 141
 142 extern void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
 143                       real t, int nres, t_bb bb[]);
 144
 145 /*! \brief Allocate and fill an array of information about residues in a protein backbone.
 146  *
 147  * The user is propted for an index group of protein residues (little
 148  * error checking occurs). For the number of residues found in the
 149  * selected group, nbb entries are made in the returned array.  Each
 150  * entry contains the atom indices of the N, H, CA, C and O atoms (for
 151  * PRO, H means CD), as well as the C of the previous residue and the
 152  * N of the next (-1 if not found).
 153  *
 154  * In the output array, the first residue will be numbered starting
 155  * from res0. */
 156 extern t_bb *mkbbind(const char *fn, int *nres, int *nbb, int res0,
 157                      int *nall, int **index,
 158                      char ***atomname, t_atom atom[],
 159                      t_resinfo *resinfo);
 160
 161 extern void do_start_end(int nres, t_bb bb[], int *nbb,
 162                          int bbindex[], int *nca, int caindex[],
 163                          gmx_bool bRange, int rStart, int rEnd);
 164
 165 extern void calc_hxprops(int nres, t_bb bb[], const rvec x[]);
 166
 167 extern void pr_bb(FILE *fp, int nres, t_bb bb[]);
 168
 169 #ifdef __cplusplus
 170 }
 171 #endif
 172
 173 #endif