src/tools/edittop.c

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  36 #include "smalloc.h"
  37 #include "string2.h"
  38 #include "fatal.h"
  39 #include "assert.h"
  40 #include "symtab.h"
  41
  42 void replace_atom(t_topology *top,int inr,char *anm,char *resnm,
  43                   real q,real m,int type)
  44 {
  45   t_atoms *atoms;
  46
  47   atoms = &(top->atoms);
  48
  49   /* Replace important properties of an atom by other properties */
  50   if ((inr < 0) || (inr > atoms->nr))
  51     fatal_error(0,"Replace_atom: inr (%d) not in %d .. %d",inr,0,atoms->nr);
  52   if (debug)
  53     fprintf(debug,"Replacing atom %d ... ",inr);
  54   /* Charge, mass and type */
  55   atoms->atom[inr].q    = atoms->atom[inr].qB    = q;
  56   atoms->atom[inr].m    = atoms->atom[inr].mB    = m;
  57   atoms->atom[inr].type = atoms->atom[inr].typeB = type;
  58
  59   /* Residue name */
  60   atoms->resname[atoms->atom[inr].resnr] = put_symtab(&top->symtab,resnm);
  61   /* Atom name */
  62   atoms->atomname[inr] = put_symtab(&top->symtab,anm);
  63   if (debug)
  64     fprintf(debug," done\n");
  65 }
  66
  67 static void delete_from_interactions(t_idef *idef,int inr)
  68 {
  69   int  i,j,k,nra,nnr;
  70   t_iatom *niatoms;
  71   bool bDel;
  72
  73   /* Delete interactions including atom inr from lists */
  74   for(i=0; (i<F_NRE); i++) {
  75     nra = interaction_function[i].nratoms;
  76     nnr = 0;
  77     snew(niatoms,idef->il[i].nr);
  78     for(j=0; (j<idef->il[i].nr); j+=nra+1) {
  79       bDel = FALSE;
  80       for(k=0; (k<nra); k++)
  81         if (idef->il[i].iatoms[j+k+1] == inr)
  82           bDel = TRUE;
  83       if (!bDel) {
  84         /* If this does not need to be deleted, then copy it to temp array */
  85         for(k=0; (k<nra+1); k++)
  86           niatoms[nnr+k] = idef->il[i].iatoms[j+k];
  87         nnr+=nra+1;
  88       }
  89     }
  90     /* Copy temp array back */
  91     for(j=0; (j<nnr); j++)
  92       idef->il[i].iatoms[j] = niatoms[j];
  93     idef->il[i].nr = nnr;
  94     sfree(niatoms);
  95
  96     /* Reduce multinr if necessary */
  97     for(j=0; (j<MAXNODES); j++)
  98       if (idef->il[i].multinr[j] >= nnr)
  99         idef->il[i].multinr[j] = nnr;
 100   }
 101 }
 102
 103 static void delete_from_block(t_block *block,int inr)
 104 {
 105   /* Update block data structure */
 106   int i,i1,j1,j,k;
 107
 108   for(i=0; (i<block->nr); i++) {
 109     for(j=block->index[i]; (j<block->index[i+1]); j++) {
 110       k = block->a[j];
 111       if (k == inr) {
 112         /* This atom has to go */
 113         for(j1=j; (j1<block->nra-1); j1++)
 114           block->a[j1] = block->a[j1+1];
 115         block->nra--;
 116         /* Change indices too */
 117         for(i1=i+1; (i1<=block->nr); i1++)
 118           block->index[i1]--;
 119       }
 120     }
 121   }
 122 }
 123
 124 static void delete_from_atoms(t_atoms *atoms,int inr)
 125 {
 126   int i,nrei,ind0;
 127
 128   /* Delete inr as an exclusion from other atoms */
 129   delete_from_block(&(atoms->excl),inr);
 130   /* Now delete the exclusions with inr as i atom */
 131   ind0 = atoms->excl.index[inr];
 132   nrei = atoms->excl.index[inr+1]-ind0;
 133   for(i=ind0+nrei; (i<atoms->excl.nra); i++)
 134     atoms->excl.a[i-nrei] = atoms->excl.a[i];
 135   atoms->excl.nra -= nrei;
 136   for(i=inr; (i<atoms->excl.nr); i++)
 137     atoms->excl.index[i] = atoms->excl.index[i+1] - nrei;
 138   atoms->excl.nr--;
 139   assert(atoms->excl.index[atoms->excl.nr] == atoms->excl.nra);
 140
 141   /* Shift the atomnames down */
 142   for(i=inr; (i<atoms->nr-1); i++)
 143     atoms->atomname[i] = atoms->atomname[i+1];
 144
 145   /* Shift the atom struct down */
 146   for(i=inr; (i<atoms->nr-1); i++)
 147     atoms->atom[i] = atoms->atom[i+1];
 148
 149   if (atoms->pdbinfo) {
 150     /* Shift the pdbatom struct down */
 151     for(i=inr; (i<atoms->nr-1); i++)
 152       atoms->pdbinfo[i] = atoms->pdbinfo[i+1];
 153   }
 154   atoms->nr--;
 155 }
 156
 157 void delete_atom(t_topology *top,int inr)
 158 {
 159   int k;
 160
 161   if ((inr < 0) || (inr >= top->atoms.nr))
 162     fatal_error(0,"Delete_atom: inr (%d) not in %d .. %d",inr,0,
 163                 top->atoms.nr);
 164   if (debug)
 165     fprintf(debug,"Deleting atom %d ...",inr);
 166
 167   /* First remove bonds etc. */
 168   delete_from_interactions(&top->idef,inr);
 169   /* Now charge groups etc. */
 170   for(k=0; (k<ebNR); k++)
 171     delete_from_block(&(top->blocks[k]),inr);
 172   /* Now from the atoms struct */
 173   delete_from_atoms(&top->atoms,inr);
 174   if (debug)
 175     fprintf(debug," done\n");
 176 }