src/tools/cdist.h

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Great Red Oystrich Makes All Chemists Sane
  28  */
  29 static char *SRCID_cdist_h = "$Id$";
  30
  31 #define HEAD_LOADED
  32 #include <stdio.h>
  33 #include <math.h>
  34 #include "typedefs.h"
  35 #include "statutil.h"
  36 #include "fatal.h"
  37 #include "physics.h"
  38 #include "string2.h"
  39 #include "smalloc.h"
  40 #include "macros.h"
  41 #include "futil.h"
  42 #include "copyrite.h"
  43 #include "vec.h"
  44 #include "pdbio.h"
  45
  46 typedef struct {
  47   real lb,ub,len;
  48 } t_dist;
  49
  50 /* LIST OF FUNCTIONS */
  51
  52 extern void pdih_lengths(int ai,int aj,int ak,int al,
  53                          t_ilist ilist[],t_iparams iparams[],
  54                          real *lb,real *ub,t_atoms *atoms);
  55
  56 extern real idih_lengths(int ai,int aj,int ak,int al,
  57                          t_ilist ilist[],t_iparams iparams[],t_atoms *atoms);
  58
  59 extern bool dist_set(t_dist *d,int natoms,int ai,int aj);
  60
  61 extern void set_dist(t_dist *d,int natoms,int ai,int aj,real lb,real ub,
  62                      real len);
  63
  64 extern void read_O_dist(void);
  65
  66 #define NOBOND -666
  67 extern real lookup_bondlength(int ai,int aj,t_ilist ilist[],
  68                               t_iparams iparams[],bool bFail,t_atoms *atoms);
  69 /* Return the bondlength in Angstrom, or NOBOND if not found.
  70  * If not found and bFail, a fatal_error will be issued
  71  */
  72
  73 extern real lookup_angle(int ai,int aj,int ak,t_ilist ilist[],
  74                          t_iparams iparams[],t_atoms *atoms);
  75 /* Return the angle between atoms in radians */
  76
  77 extern real angle_length(int ai,int aj,int ak,real theta,
  78                          t_ilist ilist[],t_iparams iparams[],t_atoms *atoms);
  79 /* Return the distance corresponding to atoms in Angstrom
  80  */
  81
  82 extern void gauche(int ai,int aj,int ak,int al,t_ilist ilist[],
  83                    t_iparams iparams[],real *lb,t_atoms *atoms);
  84
  85 extern void gauche15(int ai,int aj,int ak,int al,int am,real omega1,
  86                      real omega2,real omega3,
  87                      t_ilist ilist[],t_iparams iparams[],real *lb,
  88                      t_atoms *atoms);
  89
  90 extern real d_len(t_dist *d,int natoms,int ai,int aj);
  91 extern real d_ub(t_dist *d,int natoms,int ai,int aj);
  92 extern real d_lb(t_dist *d,int natoms,int ai,int aj);
  93
  94 /* FUNCTIONS cdist.c calls */
  95
  96 void do_smooth (t_dist *d,t_atoms *atoms,real tol);
  97 int do_triangle (t_dist *d,t_atoms *atoms,real tol);
  98 int triangle_upper_bound (t_dist *d,int natoms,real tol);
  99 int triangle_lower_bound (t_dist *d,int natoms,real tol);
 100 /* Return the number of smoothing operations */
 101
 102 /* OTHER FUNCTIONS */
 103 extern int set_virtual (int *ATMS,int N,real margin,t_dist *d,int natoms);
 104
 105 /* Routines from residues.c */
 106 extern void peptide_bonds (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,
 107                            real weight[], real pep_margin,
 108                            t_ilist ilist[],t_iparams iparams[],bool bVir);
 109
 110 extern void arg (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 111                  real arg_margin,t_ilist ilist[],
 112                  t_iparams iparams[],bool bVir);
 113
 114 extern void asn (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 115                  real end_margin,t_ilist ilist[],
 116                  t_iparams iparams[],bool bVir);
 117
 118 extern void gln (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 119                  real end_margin,t_ilist ilist[],
 120                  t_iparams iparams[],bool bVir);
 121
 122 extern void phe (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 123                  real ring_margin,t_ilist ilist[],
 124                  t_iparams iparams[],bool bVir);
 125
 126 extern void tyr (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 127                  real ring_margin,t_ilist ilist[],
 128                  t_iparams iparams[],bool bVir);
 129
 130 extern void trp (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 131                  real ring_margin,t_ilist ilist[],
 132                  t_iparams iparams[],bool bVir);
 133
 134 extern void hisb(FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 135                  real ring_margin,t_ilist ilist[],
 136                  t_iparams iparams[],bool bVir);
 137
 138 extern void val (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 139                  real val_margin,t_ilist ilist[],t_iparams iparams[]);
 140
 141 extern void leu (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 142                  real leu_margin,t_ilist ilist[],t_iparams iparams[]);
 143
 144 extern void ile (FILE *log,t_dist *d,t_idef *idef,t_atoms *atoms,real weight[],
 145                  real ile_margin,t_ilist ilist[],t_iparams iparams[]);
 146
 147
 148 #endif