src/gromacs/gmxana/edittop.cpp

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