Fix to change sequential numbering in genconf and residue index selection in make_ndx...

diff --git a/src/tools/gmx_genconf.c b/src/tools/gmx_genconf.c
index 3f636cec2c7d94fb50320dba50aa97436e1ebb5f..cf534feeba5b063359affd5fbbaaacae8b9212b1 100644 (file)
--- a/src/tools/gmx_genconf.c
+++ b/src/tools/gmx_genconf.c
@@ -295,7 +295,7 @@ int gmx_genconf(int argc, char *argv[])
   /*depending on how you look at it, this is either a nasty hack or the way it should work*/
   if (bRenum)
     for (i=0;i<atoms->nres;i++)
-         atoms->resinfo[i].nr=i;
+         atoms->resinfo[i].nr=i+1;
   
   
   if (bShuffle)

diff --git a/src/tools/make_ndx.c b/src/tools/make_ndx.c
index 5a7bb9c2e949923fa3d032603205199a8b1e5e12..1d9b7c5ff8e935422fe45af6715e0f36bb6e8160 100644 (file)
--- a/src/tools/make_ndx.c
+++ b/src/tools/make_ndx.c
@@ -351,6 +351,7 @@ static int select_residueindices(char **string,t_atoms *atoms,
                                 atom_id *nr,atom_id *index,char *gname)
 {
   /*this should be similar to select_residuenumbers except select by index (sequential numbering in file)*/
+  /*resind+1 for 1-indexing*/
   char    buf[STRLEN];
   int     i,j,up;
   t_resinfo *ri;
@@ -370,13 +371,13 @@ static int select_residueindices(char **string,t_atoms *atoms,
     for(i=0; i<atoms->nr; i++) {
       ri = &atoms->resinfo[atoms->atom[i].resind];
       for(j=n1; (j<=up); j++) {
-       if (atoms->atom[i].resind == j && (c == ' ' || ri->ic == c)) {
+       if (atoms->atom[i].resind+1 == j && (c == ' ' || ri->ic == c)) {
          index[*nr]=i;
          (*nr)++;
        }
       }
     }
-    printf("Found %u atom%s with resind. in range %u-%d\n",
+    printf("Found %u atom%s with resind.+1 in range %u-%d\n",
           *nr,(*nr==1)?"":"s",n1,up);
     if (n1==up)
       sprintf(buf,"r_%u",n1);
@@ -391,7 +392,7 @@ static int select_residueindices(char **string,t_atoms *atoms,
     do {
       for(i=0; i<atoms->nr; i++) {
        ri = &atoms->resinfo[atoms->atom[i].resind];
-       if (atoms->atom[i].resind == j && ri->ic == c) {
+       if (atoms->atom[i].resind+1 == j && ri->ic == c) {
        index[*nr]=i;
        (*nr)++;
        }
@@ -982,7 +983,7 @@ static void edit_index(int natoms, t_atoms *atoms,rvec *x,t_blocka *block, char
       printf(" 'r' nr1[ic1] [nr2[ic2] ...] : selects residues by number and insertion code.\n");
       printf(" 'r' nr1 - nr2               : selects residues in the range from nr1 to nr2.\n");
       printf(" 'r' name1[*] [name2[*] ...] : as 'a', but for residue names.\n");
-      printf(" 'ri' nr1 - nr2              : selects residue indices (as opposed to numbers) in the range from nr1 to nr2.\n");
+      printf(" 'ri' nr1 - nr2              : selects residue indices, 1-indexed, (as opposed to numbers) in the range from nr1 to nr2.\n");
       printf(" 'chain' ch1 [ch2 ...]       : selects atoms by chain identifier(s),\n");
       printf("                               not available with a .gro file as input.\n");
       printf(" !                 : takes the complement of a group with respect to all\n");