/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
#include "gmx_fatal.h"
#include "symtab.h"
-void replace_atom(t_topology *top,int inr,char *anm,char *resnm,
- real q,real m,int type)
+void replace_atom(t_topology *top, int inr, char *anm, char *resnm,
+ real q, real m, int type)
{
- t_atoms *atoms;
-
- atoms = &(top->atoms);
-
- /* Replace important properties of an atom by other properties */
- if ((inr < 0) || (inr > atoms->nr))
- gmx_fatal(FARGS,"Replace_atom: inr (%d) not in %d .. %d",inr,0,atoms->nr);
- if (debug)
- fprintf(debug,"Replacing atom %d ... ",inr);
- /* Charge, mass and type */
- atoms->atom[inr].q = atoms->atom[inr].qB = q;
- atoms->atom[inr].m = atoms->atom[inr].mB = m;
- atoms->atom[inr].type = atoms->atom[inr].typeB = type;
-
- /* Residue name */
- atoms->resinfo[atoms->atom[inr].resind].name = put_symtab(&top->symtab,resnm);
- /* Atom name */
- atoms->atomname[inr] = put_symtab(&top->symtab,anm);
- if (debug)
- fprintf(debug," done\n");
+ t_atoms *atoms;
+
+ atoms = &(top->atoms);
+
+ /* Replace important properties of an atom by other properties */
+ if ((inr < 0) || (inr > atoms->nr))
+ {
+ gmx_fatal(FARGS, "Replace_atom: inr (%d) not in %d .. %d", inr, 0, atoms->nr);
+ }
+ if (debug)
+ {
+ fprintf(debug, "Replacing atom %d ... ", inr);
+ }
+ /* Charge, mass and type */
+ atoms->atom[inr].q = atoms->atom[inr].qB = q;
+ atoms->atom[inr].m = atoms->atom[inr].mB = m;
+ atoms->atom[inr].type = atoms->atom[inr].typeB = type;
+
+ /* Residue name */
+ atoms->resinfo[atoms->atom[inr].resind].name = put_symtab(&top->symtab, resnm);
+ /* Atom name */
+ atoms->atomname[inr] = put_symtab(&top->symtab, anm);
+ if (debug)
+ {
+ fprintf(debug, " done\n");
+ }
}
-static void delete_from_interactions(t_idef *idef,int inr)
+static void delete_from_interactions(t_idef *idef, int inr)
{
- int i,j,k,nra,nnr;
- t_iatom *niatoms;
- gmx_bool bDel;
-
- /* Delete interactions including atom inr from lists */
- for(i=0; (i<F_NRE); i++) {
- nra = interaction_function[i].nratoms;
- nnr = 0;
- snew(niatoms,idef->il[i].nr);
- for(j=0; (j<idef->il[i].nr); j+=nra+1) {
- bDel = FALSE;
- for(k=0; (k<nra); k++)
- if (idef->il[i].iatoms[j+k+1] == inr)
- bDel = TRUE;
- if (!bDel) {
- /* If this does not need to be deleted, then copy it to temp array */
- for(k=0; (k<nra+1); k++)
- niatoms[nnr+k] = idef->il[i].iatoms[j+k];
- nnr+=nra+1;
- }
+ int i, j, k, nra, nnr;
+ t_iatom *niatoms;
+ gmx_bool bDel;
+
+ /* Delete interactions including atom inr from lists */
+ for (i = 0; (i < F_NRE); i++)
+ {
+ nra = interaction_function[i].nratoms;
+ nnr = 0;
+ snew(niatoms, idef->il[i].nr);
+ for (j = 0; (j < idef->il[i].nr); j += nra+1)
+ {
+ bDel = FALSE;
+ for (k = 0; (k < nra); k++)
+ {
+ if (idef->il[i].iatoms[j+k+1] == inr)
+ {
+ bDel = TRUE;
+ }
+ }
+ if (!bDel)
+ {
+ /* If this does not need to be deleted, then copy it to temp array */
+ for (k = 0; (k < nra+1); k++)
+ {
+ niatoms[nnr+k] = idef->il[i].iatoms[j+k];
+ }
+ nnr += nra+1;
+ }
+ }
+ /* Copy temp array back */
+ for (j = 0; (j < nnr); j++)
+ {
+ idef->il[i].iatoms[j] = niatoms[j];
+ }
+ idef->il[i].nr = nnr;
+ sfree(niatoms);
}
- /* Copy temp array back */
- for(j=0; (j<nnr); j++)
- idef->il[i].iatoms[j] = niatoms[j];
- idef->il[i].nr = nnr;
- sfree(niatoms);
- }
}
-static void delete_from_block(t_block *block,int inr)
+static void delete_from_block(t_block *block, int inr)
{
- /* Update block data structure */
- int i,i1,j1,j,k;
-
- for(i=0; (i<block->nr); i++) {
- for(j=block->index[i]; (j<block->index[i+1]); j++) {
- if (j == inr) {
- /* This atom has to go */
- /* Change indices too */
- for(i1=i+1; (i1<=block->nr); i1++)
- block->index[i1]--;
- }
+ /* Update block data structure */
+ int i, i1, j1, j, k;
+
+ for (i = 0; (i < block->nr); i++)
+ {
+ for (j = block->index[i]; (j < block->index[i+1]); j++)
+ {
+ if (j == inr)
+ {
+ /* This atom has to go */
+ /* Change indices too */
+ for (i1 = i+1; (i1 <= block->nr); i1++)
+ {
+ block->index[i1]--;
+ }
+ }
+ }
}
- }
}
-static void delete_from_blocka(t_blocka *block,int inr)
+static void delete_from_blocka(t_blocka *block, int inr)
{
- /* Update block data structure */
- int i,i1,j1,j,k;
-
- for(i=0; (i<block->nr); i++) {
- for(j=block->index[i]; (j<block->index[i+1]); j++) {
- k = block->a[j];
- if (k == inr) {
- /* This atom has to go */
- for(j1=j; (j1<block->nra-1); j1++)
- block->a[j1] = block->a[j1+1];
- block->nra--;
- /* Change indices too */
- for(i1=i+1; (i1<=block->nr); i1++)
- block->index[i1]--;
- }
+ /* Update block data structure */
+ int i, i1, j1, j, k;
+
+ for (i = 0; (i < block->nr); i++)
+ {
+ for (j = block->index[i]; (j < block->index[i+1]); j++)
+ {
+ k = block->a[j];
+ if (k == inr)
+ {
+ /* This atom has to go */
+ for (j1 = j; (j1 < block->nra-1); j1++)
+ {
+ block->a[j1] = block->a[j1+1];
+ }
+ block->nra--;
+ /* Change indices too */
+ for (i1 = i+1; (i1 <= block->nr); i1++)
+ {
+ block->index[i1]--;
+ }
+ }
+ }
}
- }
}
-static void delete_from_atoms(t_atoms *atoms,int inr)
+static void delete_from_atoms(t_atoms *atoms, int inr)
{
- int i;
-
- /* Shift the atomnames down */
- for(i=inr; (i<atoms->nr-1); i++)
- atoms->atomname[i] = atoms->atomname[i+1];
-
- /* Shift the atom struct down */
- for(i=inr; (i<atoms->nr-1); i++)
- atoms->atom[i] = atoms->atom[i+1];
-
- if (atoms->pdbinfo) {
- /* Shift the pdbatom struct down */
- for(i=inr; (i<atoms->nr-1); i++)
- atoms->pdbinfo[i] = atoms->pdbinfo[i+1];
- }
- atoms->nr--;
+ int i;
+
+ /* Shift the atomnames down */
+ for (i = inr; (i < atoms->nr-1); i++)
+ {
+ atoms->atomname[i] = atoms->atomname[i+1];
+ }
+
+ /* Shift the atom struct down */
+ for (i = inr; (i < atoms->nr-1); i++)
+ {
+ atoms->atom[i] = atoms->atom[i+1];
+ }
+
+ if (atoms->pdbinfo)
+ {
+ /* Shift the pdbatom struct down */
+ for (i = inr; (i < atoms->nr-1); i++)
+ {
+ atoms->pdbinfo[i] = atoms->pdbinfo[i+1];
+ }
+ }
+ atoms->nr--;
}
-void delete_atom(t_topology *top,int inr)
+void delete_atom(t_topology *top, int inr)
{
- int k;
-
- if ((inr < 0) || (inr >= top->atoms.nr))
- gmx_fatal(FARGS,"Delete_atom: inr (%d) not in %d .. %d",inr,0,
- top->atoms.nr);
- if (debug)
- fprintf(debug,"Deleting atom %d ...",inr);
-
- /* First remove bonds etc. */
- delete_from_interactions(&top->idef,inr);
- /* Now charge groups etc. */
- delete_from_block(&(top->cgs),inr);
- delete_from_block(&(top->mols),inr);
- delete_from_blocka(&(top->excls),inr);
- /* Now from the atoms struct */
- delete_from_atoms(&top->atoms,inr);
- if (debug)
- fprintf(debug," done\n");
+ int k;
+
+ if ((inr < 0) || (inr >= top->atoms.nr))
+ {
+ gmx_fatal(FARGS, "Delete_atom: inr (%d) not in %d .. %d", inr, 0,
+ top->atoms.nr);
+ }
+ if (debug)
+ {
+ fprintf(debug, "Deleting atom %d ...", inr);
+ }
+
+ /* First remove bonds etc. */
+ delete_from_interactions(&top->idef, inr);
+ /* Now charge groups etc. */
+ delete_from_block(&(top->cgs), inr);
+ delete_from_block(&(top->mols), inr);
+ delete_from_blocka(&(top->excls), inr);
+ /* Now from the atoms struct */
+ delete_from_atoms(&top->atoms, inr);
+ if (debug)
+ {
+ fprintf(debug, " done\n");
+ }
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff