src/tools/edittop.c

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * GRowing Old MAkes el Chrono Sweat
  28  */
  29 static char *SRCID_edittop_c = "$Id$";
  30
  31 #include "smalloc.h"
  32 #include "string2.h"
  33 #include "fatal.h"
  34 #include "assert.h"
  35 #include "symtab.h"
  36
  37 void replace_atom(t_topology *top,int inr,char *anm,char *resnm,
  38                   real q,real m,int type)
  39 {
  40   t_atoms *atoms;
  41
  42   atoms = &(top->atoms);
  43
  44   /* Replace important properties of an atom by other properties */
  45   if ((inr < 0) || (inr > atoms->nr))
  46     fatal_error(0,"Replace_atom: inr (%d) not in %d .. %d",inr,0,atoms->nr);
  47   if (debug)
  48     fprintf(debug,"Replacing atom %d ... ",inr);
  49   /* Charge, mass and type */
  50   atoms->atom[inr].q    = atoms->atom[inr].qB    = q;
  51   atoms->atom[inr].m    = atoms->atom[inr].mB    = m;
  52   atoms->atom[inr].type = atoms->atom[inr].typeB = type;
  53
  54   /* Residue name */
  55   atoms->resname[atoms->atom[inr].resnr] = put_symtab(&top->symtab,resnm);
  56   /* Atom name */
  57   atoms->atomname[inr] = put_symtab(&top->symtab,anm);
  58   if (debug)
  59     fprintf(debug," done\n");
  60 }
  61
  62 static void delete_from_interactions(t_idef *idef,int inr)
  63 {
  64   int  i,j,k,nra,nnr;
  65   t_iatom *niatoms;
  66   bool bDel;
  67
  68   /* Delete interactions including atom inr from lists */
  69   for(i=0; (i<F_NRE); i++) {
  70     nra = interaction_function[i].nratoms;
  71     nnr = 0;
  72     snew(niatoms,idef->il[i].nr);
  73     for(j=0; (j<idef->il[i].nr); j+=nra+1) {
  74       bDel = FALSE;
  75       for(k=0; (k<nra); k++)
  76         if (idef->il[i].iatoms[j+k+1] == inr)
  77           bDel = TRUE;
  78       if (!bDel) {
  79         /* If this does not need to be deleted, then copy it to temp array */
  80         for(k=0; (k<nra+1); k++)
  81           niatoms[nnr+k] = idef->il[i].iatoms[j+k];
  82         nnr+=nra+1;
  83       }
  84     }
  85     /* Copy temp array back */
  86     for(j=0; (j<nnr); j++)
  87       idef->il[i].iatoms[j] = niatoms[j];
  88     idef->il[i].nr = nnr;
  89     sfree(niatoms);
  90
  91     /* Reduce multinr if necessary */
  92     for(j=0; (j<MAXPROC); j++)
  93       if (idef->il[i].multinr[j] >= nnr)
  94         idef->il[i].multinr[j] = nnr;
  95   }
  96 }
  97
  98 static void delete_from_block(t_block *block,int inr)
  99 {
 100   /* Update block data structure */
 101   int i,i1,j1,j,k;
 102
 103   for(i=0; (i<block->nr); i++) {
 104     for(j=block->index[i]; (j<block->index[i+1]); j++) {
 105       k = block->a[j];
 106       if (k == inr) {
 107         /* This atom has to go */
 108         for(j1=j; (j1<block->nra-1); j1++)
 109           block->a[j1] = block->a[j1+1];
 110         block->nra--;
 111         /* Change indices too */
 112         for(i1=i+1; (i1<=block->nr); i1++)
 113           block->index[i1]--;
 114       }
 115     }
 116   }
 117 }
 118
 119 static void delete_from_atoms(t_atoms *atoms,int inr)
 120 {
 121   int i,nrei,ind0;
 122
 123   /* Delete inr as an exclusion from other atoms */
 124   delete_from_block(&(atoms->excl),inr);
 125   /* Now delete the exclusions with inr as i atom */
 126   ind0 = atoms->excl.index[inr];
 127   nrei = atoms->excl.index[inr+1]-ind0;
 128   for(i=ind0+nrei; (i<atoms->excl.nra); i++)
 129     atoms->excl.a[i-nrei] = atoms->excl.a[i];
 130   atoms->excl.nra -= nrei;
 131   for(i=inr; (i<atoms->excl.nr); i++)
 132     atoms->excl.index[i] = atoms->excl.index[i+1] - nrei;
 133   atoms->excl.nr--;
 134   assert(atoms->excl.index[atoms->excl.nr] == atoms->excl.nra);
 135
 136   /* Shift the atomnames down */
 137   for(i=inr; (i<atoms->nr-1); i++)
 138     atoms->atomname[i] = atoms->atomname[i+1];
 139
 140   /* Shift the atom struct down */
 141   for(i=inr; (i<atoms->nr-1); i++)
 142     atoms->atom[i] = atoms->atom[i+1];
 143
 144   if (atoms->pdbinfo) {
 145     /* Shift the pdbatom struct down */
 146     for(i=inr; (i<atoms->nr-1); i++)
 147       atoms->pdbinfo[i] = atoms->pdbinfo[i+1];
 148   }
 149   atoms->nr--;
 150 }
 151
 152 void delete_atom(t_topology *top,int inr)
 153 {
 154   int k;
 155
 156   if ((inr < 0) || (inr >= top->atoms.nr))
 157     fatal_error(0,"Delete_atom: inr (%d) not in %d .. %d",inr,0,
 158                 top->atoms.nr);
 159   if (debug)
 160     fprintf(debug,"Deleting atom %d ...",inr);
 161
 162   /* First remove bonds etc. */
 163   delete_from_interactions(&top->idef,inr);
 164   /* Now charge groups etc. */
 165   for(k=0; (k<ebNR); k++)
 166     delete_from_block(&(top->blocks[k]),inr);
 167   /* Now from the atoms struct */
 168   delete_from_atoms(&top->atoms,inr);
 169   if (debug)
 170     fprintf(debug," done\n");
 171 }