src/tools/edittop.c

   1 /*
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "smalloc.h"
  40 #include "string2.h"
  41 #include "gmx_fatal.h"
  42 #include "symtab.h"
  43
  44 void replace_atom(t_topology *top,int inr,char *anm,char *resnm,
  45                   real q,real m,int type)
  46 {
  47   t_atoms *atoms;
  48
  49   atoms = &(top->atoms);
  50
  51   /* Replace important properties of an atom by other properties */
  52   if ((inr < 0) || (inr > atoms->nr))
  53     gmx_fatal(FARGS,"Replace_atom: inr (%d) not in %d .. %d",inr,0,atoms->nr);
  54   if (debug)
  55     fprintf(debug,"Replacing atom %d ... ",inr);
  56   /* Charge, mass and type */
  57   atoms->atom[inr].q    = atoms->atom[inr].qB    = q;
  58   atoms->atom[inr].m    = atoms->atom[inr].mB    = m;
  59   atoms->atom[inr].type = atoms->atom[inr].typeB = type;
  60
  61   /* Residue name */
  62   atoms->resinfo[atoms->atom[inr].resind].name = put_symtab(&top->symtab,resnm);
  63   /* Atom name */
  64   atoms->atomname[inr] = put_symtab(&top->symtab,anm);
  65   if (debug)
  66     fprintf(debug," done\n");
  67 }
  68
  69 static void delete_from_interactions(t_idef *idef,int inr)
  70 {
  71   int  i,j,k,nra,nnr;
  72   t_iatom *niatoms;
  73   bool bDel;
  74
  75   /* Delete interactions including atom inr from lists */
  76   for(i=0; (i<F_NRE); i++) {
  77     nra = interaction_function[i].nratoms;
  78     nnr = 0;
  79     snew(niatoms,idef->il[i].nr);
  80     for(j=0; (j<idef->il[i].nr); j+=nra+1) {
  81       bDel = FALSE;
  82       for(k=0; (k<nra); k++)
  83         if (idef->il[i].iatoms[j+k+1] == inr)
  84           bDel = TRUE;
  85       if (!bDel) {
  86         /* If this does not need to be deleted, then copy it to temp array */
  87         for(k=0; (k<nra+1); k++)
  88           niatoms[nnr+k] = idef->il[i].iatoms[j+k];
  89         nnr+=nra+1;
  90       }
  91     }
  92     /* Copy temp array back */
  93     for(j=0; (j<nnr); j++)
  94       idef->il[i].iatoms[j] = niatoms[j];
  95     idef->il[i].nr = nnr;
  96     sfree(niatoms);
  97   }
  98 }
  99
 100 static void delete_from_block(t_block *block,int inr)
 101 {
 102   /* Update block data structure */
 103   int i,i1,j1,j,k;
 104
 105   for(i=0; (i<block->nr); i++) {
 106     for(j=block->index[i]; (j<block->index[i+1]); j++) {
 107       if (j == inr) {
 108         /* This atom has to go */
 109         /* Change indices too */
 110         for(i1=i+1; (i1<=block->nr); i1++)
 111           block->index[i1]--;
 112       }
 113     }
 114   }
 115 }
 116
 117 static void delete_from_blocka(t_blocka *block,int inr)
 118 {
 119   /* Update block data structure */
 120   int i,i1,j1,j,k;
 121
 122   for(i=0; (i<block->nr); i++) {
 123     for(j=block->index[i]; (j<block->index[i+1]); j++) {
 124       k = block->a[j];
 125       if (k == inr) {
 126         /* This atom has to go */
 127         for(j1=j; (j1<block->nra-1); j1++)
 128           block->a[j1] = block->a[j1+1];
 129         block->nra--;
 130         /* Change indices too */
 131         for(i1=i+1; (i1<=block->nr); i1++)
 132           block->index[i1]--;
 133       }
 134     }
 135   }
 136 }
 137
 138 static void delete_from_atoms(t_atoms *atoms,int inr)
 139 {
 140   int i;
 141
 142   /* Shift the atomnames down */
 143   for(i=inr; (i<atoms->nr-1); i++)
 144     atoms->atomname[i] = atoms->atomname[i+1];
 145
 146   /* Shift the atom struct down */
 147   for(i=inr; (i<atoms->nr-1); i++)
 148     atoms->atom[i] = atoms->atom[i+1];
 149
 150   if (atoms->pdbinfo) {
 151     /* Shift the pdbatom struct down */
 152     for(i=inr; (i<atoms->nr-1); i++)
 153       atoms->pdbinfo[i] = atoms->pdbinfo[i+1];
 154   }
 155   atoms->nr--;
 156 }
 157
 158 void delete_atom(t_topology *top,int inr)
 159 {
 160   int k;
 161
 162   if ((inr < 0) || (inr >= top->atoms.nr))
 163     gmx_fatal(FARGS,"Delete_atom: inr (%d) not in %d .. %d",inr,0,
 164                 top->atoms.nr);
 165   if (debug)
 166     fprintf(debug,"Deleting atom %d ...",inr);
 167
 168   /* First remove bonds etc. */
 169   delete_from_interactions(&top->idef,inr);
 170   /* Now charge groups etc. */
 171   delete_from_block(&(top->cgs),inr);
 172   delete_from_block(&(top->mols),inr);
 173   delete_from_blocka(&(top->excls),inr);
 174   /* Now from the atoms struct */
 175   delete_from_atoms(&top->atoms,inr);
 176   if (debug)
 177     fprintf(debug," done\n");
 178 }