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
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  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       type;        /* The type of bonded interaction */
  68   int       nb;          /* number of bondeds */
  69   t_rbonded *b;          /* bondeds */
  70 } t_rbondeds;
  71
  72 /* RESIDUES (rtp) */
  73 typedef struct {
  74   char   *resname;
  75   /* The base file name this rtp entry was read from */
  76   char   *filebase;
  77   /* atom data */
  78   int    natom;
  79   t_atom *atom;
  80   char   ***atomname;
  81   int    *cgnr;
  82   /* Bonded interaction setup */
  83   gmx_bool      bKeepAllGeneratedDihedrals;
  84   int       nrexcl;
  85   gmx_bool      bGenerateHH14Interactions;
  86   gmx_bool      bRemoveDihedralIfWithImproper;
  87   /* list of bonded interactions to add */
  88   t_rbondeds rb[ebtsNR];
  89 } t_restp;
  90
  91 /* Block to hack residues */
  92 typedef struct {
  93   int     nr;       /* Number of atoms to hack    */
  94   char    *oname;   /* Old name                   */
  95   char    *nname;   /* New name                   */
  96   /* the type of hack depends on the setting of oname and nname:
  97    * if oname==NULL                we're adding, must have tp>0 also!
  98    * if oname!=NULL && nname==NULL we're deleting
  99    * if oname!=NULL && nname!=NULL we're replacing
 100    */
 101   t_atom  *atom;    /* New atom data              */
 102   int     cgnr;     /* chargegroup number. if not read will be NOTSET */
 103   int     tp;       /* Type of attachment (1..11) */
 104   int     nctl;     /* How many control atoms there are */
 105   char    *a[4];    /* Control atoms i,j,k,l      */
 106   gmx_bool    bAlreadyPresent;
 107   gmx_bool    bXSet;
 108   rvec    newx;     /* calculated new position    */
 109   atom_id newi;     /* new atom index number (after additions) */
 110 } t_hack;
 111
 112 typedef struct {
 113   char      *name;  /* Name of hack block (residue or terminus) */
 114   char      *filebase; /* The base file name this entry was read from */
 115   int       nhack;  /* Number of atoms to hack                  */
 116   int       maxhack;/* used for efficient srenew-ing            */
 117   t_hack    *hack;  /* Hack list                                */
 118   /* list of bonded interactions to add */
 119   t_rbondeds rb[ebtsNR];
 120 } t_hackblock;
 121
 122 /* all libraries and other data to protonate a structure or trajectory */
 123 typedef struct {
 124   gmx_bool        bInit; /* true after init; set false by init_t_protonate */
 125   /* force field name: */
 126   char        FF[10];
 127   /* libarary data: */
 128   int         *nab;
 129   t_hack      **ab;
 130   t_hackblock *ah, *ntdb, *ctdb;
 131   t_hackblock **sel_ntdb, **sel_ctdb;
 132   int         nah;
 133   t_symtab    tab;
 134   /* residue indices (not numbers!) of the N and C termini */
 135   int         *rN, *rC;
 136   gpp_atomtype_t atype;
 137   /* protonated topology: */
 138   t_atoms     *patoms;
 139   /* unprotonated topology: */
 140   t_atoms     *upatoms;
 141
 142 } t_protonate;
 143
 144 typedef struct {
 145   char *res1, *res2;
 146   char *atom1,*atom2;
 147   char *newres1,*newres2;
 148   int  nbond1,nbond2;
 149   real length;
 150 } t_specbond;
 151
 152 t_specbond *get_specbonds(int *nspecbond);
 153 void done_specbonds(int nsb,t_specbond sb[]);
 154
 155 void free_t_restp(int nrtp, t_restp **rtp);
 156 void free_t_hack(int nh, t_hack **h);
 157 void free_t_hackblock(int nhb, t_hackblock **hb);
 158 /* free the whole datastructure */
 159
 160 void clear_t_hackblock(t_hackblock *hb);
 161 void clear_t_hack(t_hack *hack);
 162 /* reset struct */
 163
 164 gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
 165                             gmx_bool bMin, gmx_bool bPlus);
 166 /* add s[].b[] to d[].b[]
 167  * If bMin==TRUE, don't copy bondeds with atoms starting with '-'
 168  * If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
 169  * Returns if bonds were removed at the termini.
 170  */
 171
 172 void copy_t_restp(t_restp *s, t_restp *d);
 173 void copy_t_hack(t_hack *s, t_hack *d);
 174 void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
 175 /* make copy of whole datastructure */
 176
 177 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
 178 /* add s[] to *d[] */
 179
 180 void merge_hacks(t_hackblock *s, t_hackblock *d);
 181 /* add s->hacks[] to d->hacks[] */
 182
 183 void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
 184 /* add s->hacks[] and s->rb[] to d*/
 185
 186 void dump_hb(FILE *out, int nres, t_hackblock hb[]);
 187 /* print out whole datastructure */
 188
 189 void init_t_protonate(t_protonate *protonate);
 190 /* initialize t_protein struct */
 191
 192 #ifdef __cplusplus
 193 }
 194 #endif
 195
 196 #endif  /* _hackblock_h */