include/hackblock.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  * Good ROcking Metal Altar for Chronical Sinners
  28  */
  29
  30 #ifndef _hackblock_h
  31 #define _hackblock_h
  32
  33 static char *SRCID_hackblock_h = "$Id$";
  34
  35 #include "typedefs.h"
  36 #include "pdbio.h"
  37
  38 /* Used for reading .rtp/.tdb */
  39 /* ebtsBONDS must be the first, new types can be added to the end */
  40 /* these *MUST* correspond to the arrays in hackblock.c */
  41 enum { ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsNR };
  42 extern char *btsNames[ebtsNR];
  43 extern int btsNiatoms[ebtsNR];
  44
  45 /* if changing any of these structs, make sure that all of the
  46    free/clear/copy/merge_t_* functions stay updated */
  47
  48 /* BONDEDS */
  49 typedef struct {
  50   char  *a[MAXATOMLIST]; /* atom names */
  51   char  *s;              /* optional define string which gets copied from
  52                             .rtp/.tdb to .top and will be parsed by cpp
  53                             during grompp */
  54 } t_rbonded;
  55
  56 typedef struct {
  57   int       nb;          /* number of bondeds */
  58   t_rbonded *b;          /* bondeds */
  59 } t_rbondeds;
  60
  61 /* RESIDUES (rtp) */
  62 typedef struct {
  63   char   *resname;
  64   /* atom data */
  65   int    natom;
  66   t_atom *atom;
  67   char   ***atomname;
  68   int    *cgnr;
  69   /* list of bonded interactions to add */
  70   t_rbondeds rb[ebtsNR];
  71 } t_restp;
  72
  73 /* Block to hack residues */
  74 typedef struct {
  75   int     nr;       /* Number of atoms to hack    */
  76   char    *oname;   /* Old name                   */
  77   char    *nname;   /* New name                   */
  78   /* the type of hack depends on the setting of oname and nname:
  79    * if oname==NULL                we're adding, must have tp>0 also!
  80    * if oname!=NULL && nname==NULL we're deleting
  81    * if oname!=NULL && nname!=NULL we're replacing
  82    */
  83   t_atom  *atom;    /* New atom data              */
  84   int     cgnr;     /* chargegroup number. if not read will be NOTSET */
  85   int     tp;       /* Type of attachment (1..10) */
  86   char    *a[4];    /* Control atoms i,j,k,l      */
  87   rvec    newx;     /* calculated new position    */
  88 } t_hack;
  89
  90 typedef struct {
  91   char      *name;  /* Name of hack block (residue or terminus) */
  92   int       nhack;  /* Number of atoms to hack                  */
  93   int       maxhack;/* used for efficient srenew-ing            */
  94   t_hack    *hack;  /* Hack list                                */
  95   /* list of bonded interactions to add */
  96   t_rbondeds rb[ebtsNR];
  97 } t_hackblock;
  98
  99 extern void free_t_restp(int nrtp, t_restp **rtp);
 100 extern void free_t_hack(int nh, t_hack **h);
 101 extern void free_t_hackblock(int nhb, t_hackblock **hb);
 102 /* free the whole datastructure */
 103
 104 extern void clear_t_hackblock(t_hackblock *hb);
 105 extern void clear_t_hack(t_hack *hack);
 106 /* reset struct */
 107
 108 extern void merge_t_bondeds(t_rbondeds s[], t_rbondeds d[]);
 109 /* add s[].b[] to d[].b[] */
 110
 111 extern void copy_t_restp(t_restp *s, t_restp *d);
 112 extern void copy_t_hack(t_hack *s, t_hack *d);
 113 extern void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
 114 /* make copy of whole datastructure */
 115
 116 extern void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
 117 /* add s[] to *d[] */
 118
 119 extern void merge_hacks(t_hackblock *s, t_hackblock *d);
 120 /* add s->hacks[] to d->hacks[] */
 121
 122 extern void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
 123 /* add s->hacks[] and s->rb[] to d*/
 124
 125 extern void dump_hb(FILE *out, int nres, t_hackblock hb[]);
 126 /* print out whole datastructure */
 127
 128 #endif  /* _hackblock_h */