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