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 "visibility.h"
  40 #include "typedefs.h"
  41 #include "pdbio.h"
  42 #include "grompp.h"
  43 #include "gpp_atomtype.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 /* Used for reading .rtp/.tdb */
  50 /* ebtsBONDS must be the first, new types can be added to the end */
  51 /* these *MUST* correspond to the arrays in hackblock.c */
  52 enum { ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR };
  53 extern const char *btsNames[ebtsNR];
  54 extern const int btsNiatoms[ebtsNR];
  55
  56 /* if changing any of these structs, make sure that all of the
  57    free/clear/copy/merge_t_* functions stay updated */
  58
  59 /* BONDEDS */
  60 typedef struct {
  61   char  *a[MAXATOMLIST]; /* atom names */
  62   char  *s;              /* optional define string which gets copied from
  63                             .rtp/.tdb to .top and will be parsed by cpp
  64                             during grompp */
  65 } t_rbonded;
  66
  67 typedef struct {
  68   int       type;        /* The type of bonded interaction */
  69   int       nb;          /* number of bondeds */
  70   t_rbonded *b;          /* bondeds */
  71 } t_rbondeds;
  72
  73 /* RESIDUES (rtp) */
  74 typedef struct {
  75   char   *resname;
  76   /* The base file name this rtp entry was read from */
  77   char   *filebase;
  78   /* atom data */
  79   int    natom;
  80   t_atom *atom;
  81   char   ***atomname;
  82   int    *cgnr;
  83   /* Bonded interaction setup */
  84   gmx_bool      bKeepAllGeneratedDihedrals;
  85   int       nrexcl;
  86   gmx_bool      bGenerateHH14Interactions;
  87   gmx_bool      bRemoveDihedralIfWithImproper;
  88   /* list of bonded interactions to add */
  89   t_rbondeds rb[ebtsNR];
  90 } t_restp;
  91
  92 /* Block to hack residues */
  93 typedef struct {
  94   int     nr;       /* Number of atoms to hack    */
  95   char    *oname;   /* Old name                   */
  96   char    *nname;   /* New name                   */
  97   /* the type of hack depends on the setting of oname and nname:
  98    * if oname==NULL                we're adding, must have tp>0 also!
  99    * if oname!=NULL && nname==NULL we're deleting
 100    * if oname!=NULL && nname!=NULL we're replacing
 101    */
 102   t_atom  *atom;    /* New atom data              */
 103   int     cgnr;     /* chargegroup number. if not read will be NOTSET */
 104   int     tp;       /* Type of attachment (1..11) */
 105   int     nctl;     /* How many control atoms there are */
 106   char    *a[4];    /* Control atoms i,j,k,l      */
 107   gmx_bool    bAlreadyPresent;
 108   gmx_bool    bXSet;
 109   rvec    newx;     /* calculated new position    */
 110   atom_id newi;     /* new atom index number (after additions) */
 111 } t_hack;
 112
 113 typedef struct {
 114   char      *name;  /* Name of hack block (residue or terminus) */
 115   char      *filebase; /* The base file name this entry was read from */
 116   int       nhack;  /* Number of atoms to hack                  */
 117   int       maxhack;/* used for efficient srenew-ing            */
 118   t_hack    *hack;  /* Hack list                                */
 119   /* list of bonded interactions to add */
 120   t_rbondeds rb[ebtsNR];
 121 } t_hackblock;
 122
 123 /* all libraries and other data to protonate a structure or trajectory */
 124 typedef struct {
 125   gmx_bool        bInit; /* true after init; set false by init_t_protonate */
 126   /* force field name: */
 127   char        FF[10];
 128   /* libarary data: */
 129   int         *nab;
 130   t_hack      **ab;
 131   t_hackblock *ah, *ntdb, *ctdb;
 132   t_hackblock **sel_ntdb, **sel_ctdb;
 133   int         nah;
 134   t_symtab    tab;
 135   /* residue indices (not numbers!) of the N and C termini */
 136   int         *rN, *rC;
 137   gpp_atomtype_t atype;
 138   /* protonated topology: */
 139   t_atoms     *patoms;
 140   /* unprotonated topology: */
 141   t_atoms     *upatoms;
 142
 143 } t_protonate;
 144
 145 typedef struct {
 146   char *res1, *res2;
 147   char *atom1,*atom2;
 148   char *newres1,*newres2;
 149   int  nbond1,nbond2;
 150   real length;
 151 } t_specbond;
 152
 153 t_specbond *get_specbonds(int *nspecbond);
 154 void done_specbonds(int nsb,t_specbond sb[]);
 155
 156 void free_t_restp(int nrtp, t_restp **rtp);
 157 void free_t_hack(int nh, t_hack **h);
 158 void free_t_hackblock(int nhb, t_hackblock **hb);
 159 /* free the whole datastructure */
 160
 161 void clear_t_hackblock(t_hackblock *hb);
 162 void clear_t_hack(t_hack *hack);
 163 /* reset struct */
 164
 165 gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
 166                             gmx_bool bMin, gmx_bool bPlus);
 167 /* add s[].b[] to d[].b[]
 168  * If bMin==TRUE, don't copy bondeds with atoms starting with '-'
 169  * If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
 170  * Returns if bonds were removed at the termini.
 171  */
 172
 173 void copy_t_restp(t_restp *s, t_restp *d);
 174 void copy_t_hack(t_hack *s, t_hack *d);
 175 void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
 176 /* make copy of whole datastructure */
 177
 178 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
 179 /* add s[] to *d[] */
 180
 181 void merge_hacks(t_hackblock *s, t_hackblock *d);
 182 /* add s->hacks[] to d->hacks[] */
 183
 184 void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
 185 /* add s->hacks[] and s->rb[] to d*/
 186
 187 void dump_hb(FILE *out, int nres, t_hackblock hb[]);
 188 /* print out whole datastructure */
 189
 190 GMX_LIBGMXPREPROCESS_EXPORT
 191 void init_t_protonate(t_protonate *protonate);
 192 /* initialize t_protein struct */
 193
 194 #ifdef __cplusplus
 195 }
 196 #endif
 197
 198 #endif  /* _hackblock_h */