Added a few comments to gmx_membed

diff --git a/src/tools/gmx_membed.c b/src/tools/gmx_membed.c
index e187accd45c553199061ca4eabc698c813a5d62e..c8c4a735431b3870b6ede8dc88233b787b69daf8 100644 (file)
--- a/src/tools/gmx_membed.c
+++ b/src/tools/gmx_membed.c
@@ -800,6 +800,7 @@ int rm_bonded(t_block *ins_at, gmx_mtop_t *mtop)
        int i,j,m;
        int type,natom,nmol,at,atom1=0,rm_at=0;
        bool *bRM,bINS;
+       /*this routine lives dangerously by assuming that all molecules of a given type are in order in the structure*/
 
 
        snew(bRM,mtop->nmoltype);
@@ -808,31 +809,33 @@ int rm_bonded(t_block *ins_at, gmx_mtop_t *mtop)
                bRM[i]=TRUE;
        }
 
-       for (i=0;i<mtop->nmolblock;i++)
+       for (i=0;i<mtop->nmolblock;i++) 
        {
+           /*loop over molecule blocks*/
                type        =mtop->molblock[i].type;
                natom       =mtop->molblock[i].natoms_mol;
                nmol            =mtop->molblock[i].nmol;
 
-               for(j=0;j<natom*nmol && bRM[type]==TRUE;j++)
+               for(j=0;j<natom*nmol && bRM[type]==TRUE;j++) 
                {
-                       at=j+atom1;
-                       m=0;
+                   /*loop over atoms in the block*/
+                       at=j+atom1; /*atom index = block index + offset*/
                        bINS=FALSE;
-                       do
+
+                       for (m=0;(m<ins_at->nr) && (bINS==FALSE);m++)
                        {
+                           /*loop over atoms in insertion index group to determine if we're inserting one*/
                                if(at==ins_at->index[m])
                                {
                                        bINS=TRUE;
                                }
-                               m++;
-                       } while ( (m<ins_at->nr) && bINS==FALSE);
+                       }
                        bRM[type]=bINS;
                }
-               atom1+=natom*nmol;
+               atom1+=natom*nmol; /*update offset*/
                if(bRM[type])
                {
-                       rm_at+=natom*nmol;
+                       rm_at+=natom*nmol; /*increment bonded removal counter by # atoms in block*/
                }
        }