src/gromacs/gmxana/edittop.c

   1 /*
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  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include "gromacs/legacyheaders/typedefs.h"
  42 #include "gromacs/topology/symtab.h"
  43 #include "gromacs/utility/smalloc.h"
  44 #include "gromacs/utility/fatalerror.h"
  45
  46 void replace_atom(t_topology *top, int inr, char *anm, char *resnm,
  47                   real q, real m, int type)
  48 {
  49     t_atoms *atoms;
  50
  51     atoms = &(top->atoms);
  52
  53     /* Replace important properties of an atom by other properties */
  54     if ((inr < 0) || (inr > atoms->nr))
  55     {
  56         gmx_fatal(FARGS, "Replace_atom: inr (%d) not in %d .. %d", inr, 0, atoms->nr);
  57     }
  58     if (debug)
  59     {
  60         fprintf(debug, "Replacing atom %d ... ", inr);
  61     }
  62     /* Charge, mass and type */
  63     atoms->atom[inr].q    = atoms->atom[inr].qB    = q;
  64     atoms->atom[inr].m    = atoms->atom[inr].mB    = m;
  65     atoms->atom[inr].type = atoms->atom[inr].typeB = type;
  66
  67     /* Residue name */
  68     atoms->resinfo[atoms->atom[inr].resind].name = put_symtab(&top->symtab, resnm);
  69     /* Atom name */
  70     atoms->atomname[inr] = put_symtab(&top->symtab, anm);
  71     if (debug)
  72     {
  73         fprintf(debug, " done\n");
  74     }
  75 }
  76
  77 static void delete_from_interactions(t_idef *idef, int inr)
  78 {
  79     int      i, j, k, nra, nnr;
  80     t_iatom *niatoms;
  81     gmx_bool bDel;
  82
  83     /* Delete interactions including atom inr from lists */
  84     for (i = 0; (i < F_NRE); i++)
  85     {
  86         nra = interaction_function[i].nratoms;
  87         nnr = 0;
  88         snew(niatoms, idef->il[i].nr);
  89         for (j = 0; (j < idef->il[i].nr); j += nra+1)
  90         {
  91             bDel = FALSE;
  92             for (k = 0; (k < nra); k++)
  93             {
  94                 if (idef->il[i].iatoms[j+k+1] == inr)
  95                 {
  96                     bDel = TRUE;
  97                 }
  98             }
  99             if (!bDel)
 100             {
 101                 /* If this does not need to be deleted, then copy it to temp array */
 102                 for (k = 0; (k < nra+1); k++)
 103                 {
 104                     niatoms[nnr+k] = idef->il[i].iatoms[j+k];
 105                 }
 106                 nnr += nra+1;
 107             }
 108         }
 109         /* Copy temp array back */
 110         for (j = 0; (j < nnr); j++)
 111         {
 112             idef->il[i].iatoms[j] = niatoms[j];
 113         }
 114         idef->il[i].nr = nnr;
 115         /* cppcheck-suppress uninitvar Fixed in cppcheck 1.65 */
 116         sfree(niatoms);
 117     }
 118 }
 119
 120 static void delete_from_block(t_block *block, int inr)
 121 {
 122     /* Update block data structure */
 123     int i, i1, j1, j, k;
 124
 125     for (i = 0; (i < block->nr); i++)
 126     {
 127         for (j = block->index[i]; (j < block->index[i+1]); j++)
 128         {
 129             if (j == inr)
 130             {
 131                 /* This atom has to go */
 132                 /* Change indices too */
 133                 for (i1 = i+1; (i1 <= block->nr); i1++)
 134                 {
 135                     block->index[i1]--;
 136                 }
 137             }
 138         }
 139     }
 140 }
 141
 142 static void delete_from_blocka(t_blocka *block, int inr)
 143 {
 144     /* Update block data structure */
 145     int i, i1, j1, j, k;
 146
 147     for (i = 0; (i < block->nr); i++)
 148     {
 149         for (j = block->index[i]; (j < block->index[i+1]); j++)
 150         {
 151             k = block->a[j];
 152             if (k == inr)
 153             {
 154                 /* This atom has to go */
 155                 for (j1 = j; (j1 < block->nra-1); j1++)
 156                 {
 157                     block->a[j1] = block->a[j1+1];
 158                 }
 159                 block->nra--;
 160                 /* Change indices too */
 161                 for (i1 = i+1; (i1 <= block->nr); i1++)
 162                 {
 163                     block->index[i1]--;
 164                 }
 165             }
 166         }
 167     }
 168 }
 169
 170 static void delete_from_atoms(t_atoms *atoms, int inr)
 171 {
 172     int i;
 173
 174     /* Shift the atomnames down */
 175     for (i = inr; (i < atoms->nr-1); i++)
 176     {
 177         atoms->atomname[i] = atoms->atomname[i+1];
 178     }
 179
 180     /* Shift the atom struct down */
 181     for (i = inr; (i < atoms->nr-1); i++)
 182     {
 183         atoms->atom[i] = atoms->atom[i+1];
 184     }
 185
 186     if (atoms->pdbinfo)
 187     {
 188         /* Shift the pdbatom struct down */
 189         for (i = inr; (i < atoms->nr-1); i++)
 190         {
 191             atoms->pdbinfo[i] = atoms->pdbinfo[i+1];
 192         }
 193     }
 194     atoms->nr--;
 195 }
 196
 197 void delete_atom(t_topology *top, int inr)
 198 {
 199     int k;
 200
 201     if ((inr < 0) || (inr >= top->atoms.nr))
 202     {
 203         gmx_fatal(FARGS, "Delete_atom: inr (%d) not in %d .. %d", inr, 0,
 204                   top->atoms.nr);
 205     }
 206     if (debug)
 207     {
 208         fprintf(debug, "Deleting atom %d ...", inr);
 209     }
 210
 211     /* First remove bonds etc. */
 212     delete_from_interactions(&top->idef, inr);
 213     /* Now charge groups etc. */
 214     delete_from_block(&(top->cgs), inr);
 215     delete_from_block(&(top->mols), inr);
 216     delete_from_blocka(&(top->excls), inr);
 217     /* Now from the atoms struct */
 218     delete_from_atoms(&top->atoms, inr);
 219     if (debug)
 220     {
 221         fprintf(debug, " done\n");
 222     }
 223 }