include/hackblock.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  34  */
  35
  36 #ifndef _hackblock_h
  37 #define _hackblock_h
  38
  39 #include "typedefs.h"
  40 #include "pdbio.h"
  41 #include "grompp.h"
  42 #include "gpp_atomtype.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 /* Used for reading .rtp/.tdb */
  49 /* ebtsBONDS must be the first, new types can be added to the end */
  50 /* these *MUST* correspond to the arrays in hackblock.c */
  51 enum { ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR };
  52 extern const char *btsNames[ebtsNR];
  53 extern const int btsNiatoms[ebtsNR];
  54
  55 /* if changing any of these structs, make sure that all of the
  56    free/clear/copy/merge_t_* functions stay updated */
  57
  58 /* BONDEDS */
  59 typedef struct {
  60   char  *a[MAXATOMLIST]; /* atom names */
  61   char  *s;              /* optional define string which gets copied from
  62                             .rtp/.tdb to .top and will be parsed by cpp
  63                             during grompp */
  64 } t_rbonded;
  65
  66 typedef struct {
  67   int       nb;          /* number of bondeds */
  68   t_rbonded *b;          /* bondeds */
  69 } t_rbondeds;
  70
  71 /* RESIDUES (rtp) */
  72 typedef struct {
  73   char   *resname;
  74   /* atom data */
  75   int    natom;
  76   t_atom *atom;
  77   char   ***atomname;
  78   int    *cgnr;
  79   /* list of bonded interactions to add */
  80   t_rbondeds rb[ebtsNR];
  81 } t_restp;
  82
  83 /* Block to hack residues */
  84 typedef struct {
  85   int     nr;       /* Number of atoms to hack    */
  86   char    *oname;   /* Old name                   */
  87   char    *nname;   /* New name                   */
  88   /* the type of hack depends on the setting of oname and nname:
  89    * if oname==NULL                we're adding, must have tp>0 also!
  90    * if oname!=NULL && nname==NULL we're deleting
  91    * if oname!=NULL && nname!=NULL we're replacing
  92    */
  93   t_atom  *atom;    /* New atom data              */
  94   int     cgnr;     /* chargegroup number. if not read will be NOTSET */
  95   int     tp;       /* Type of attachment (1..11) */
  96   int     nctl;     /* How many control atoms there are */
  97   char    *a[4];    /* Control atoms i,j,k,l      */
  98   rvec    newx;     /* calculated new position    */
  99   atom_id newi;     /* new atom index number (after additions) */
 100 } t_hack;
 101
 102 typedef struct {
 103   char      *name;  /* Name of hack block (residue or terminus) */
 104   int       nhack;  /* Number of atoms to hack                  */
 105   int       maxhack;/* used for efficient srenew-ing            */
 106   t_hack    *hack;  /* Hack list                                */
 107   /* list of bonded interactions to add */
 108   t_rbondeds rb[ebtsNR];
 109 } t_hackblock;
 110
 111 /* all libraries and other data to protonate a structure or trajectory */
 112 typedef struct {
 113   bool        bInit; /* true after init; set false by init_t_protonate */
 114   /* force field name: */
 115   char        FF[10];
 116   /* libarary data: */
 117   int         *nab;
 118   t_hack      **ab;
 119   t_hackblock *ah, *ntdb, *ctdb;
 120   t_hackblock **sel_ntdb, **sel_ctdb;
 121   int         nah;
 122   t_symtab    tab;
 123   /* residue indices (not numbers!) of the N and C termini */
 124   int         *rN, *rC;
 125   gpp_atomtype_t atype;
 126   /* protonated topology: */
 127   t_atoms     *patoms;
 128   /* unprotonated topology: */
 129   t_atoms     *upatoms;
 130
 131 } t_protonate;
 132
 133 typedef struct {
 134   char *res1, *res2;
 135   char *atom1,*atom2;
 136   char *newres1,*newres2;
 137   int  nbond1,nbond2;
 138   real length;
 139 } t_specbond;
 140
 141 extern t_specbond *get_specbonds(int *nspecbond);
 142 extern void done_specbonds(int nsb,t_specbond sb[]);
 143
 144 extern void free_t_restp(int nrtp, t_restp **rtp);
 145 extern void free_t_hack(int nh, t_hack **h);
 146 extern void free_t_hackblock(int nhb, t_hackblock **hb);
 147 /* free the whole datastructure */
 148
 149 extern void clear_t_hackblock(t_hackblock *hb);
 150 extern void clear_t_hack(t_hack *hack);
 151 /* reset struct */
 152
 153 extern void merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
 154                             bool bMin, bool bPlus);
 155 /* add s[].b[] to d[].b[]
 156  * If bMin==TRUE, don't copy bondeds with atoms starting with '-'
 157  * If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
 158  */
 159
 160 extern void copy_t_restp(t_restp *s, t_restp *d);
 161 extern void copy_t_hack(t_hack *s, t_hack *d);
 162 extern void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
 163 /* make copy of whole datastructure */
 164
 165 extern void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
 166 /* add s[] to *d[] */
 167
 168 extern void merge_hacks(t_hackblock *s, t_hackblock *d);
 169 /* add s->hacks[] to d->hacks[] */
 170
 171 extern void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
 172 /* add s->hacks[] and s->rb[] to d*/
 173
 174 extern void dump_hb(FILE *out, int nres, t_hackblock hb[]);
 175 /* print out whole datastructure */
 176
 177 extern void init_t_protonate(t_protonate *protonate);
 178 /* initialize t_protein struct */
 179
 180 #ifdef __cplusplus
 181 }
 182 #endif
 183
 184 #endif  /* _hackblock_h */