Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / topology / index.cpp

diff --git a/src/gromacs/topology/index.cpp b/src/gromacs/topology/index.cpp
index 34201277c9ffa5c30c91aeed4faaad1fe1c399b5..153554d9009fab4e086fdfa0b3157bcd9366675a 100644 (file)
--- a/src/gromacs/topology/index.cpp
+++ b/src/gromacs/topology/index.cpp
@@ -34,9 +34,9 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#include "gromacs/topology/index.h"
+#include "gmxpre.h"
 
-#include "config.h"
+#include "index.h"
 
 #include <assert.h>
 #include <ctype.h>
@@ -45,11 +45,10 @@
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/txtdump.h"
-
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/invblock.h"
@@ -127,7 +126,7 @@ void add_grp(t_blocka *b, char ***gnames, int nra, atom_id a[], const char *name
 
     srenew(b->index, b->nr+2);
     srenew(*gnames, b->nr+1);
-    (*gnames)[b->nr] = strdup(name);
+    (*gnames)[b->nr] = gmx_strdup(name);
 
     srenew(b->a, b->nra+nra);
     for (i = 0; (i < nra); i++)
@@ -275,9 +274,9 @@ static void analyse_other(const char ** restype, t_atoms *atoms,
                 if (l == nrestp)
                 {
                     srenew(restp, nrestp+1);
-                    restp[nrestp].rname = strdup(rname);
+                    restp[nrestp].rname = gmx_strdup(rname);
                     restp[nrestp].bNeg  = FALSE;
-                    restp[nrestp].gname = strdup(rname);
+                    restp[nrestp].gname = gmx_strdup(rname);
                     nrestp++;
 
                 }
@@ -624,7 +623,7 @@ void analyse(t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool b
         if (!found)
         {
             srenew(p_typename, ntypes+1);
-            p_typename[ntypes++] = strdup(restype[i]);
+            p_typename[ntypes++] = gmx_strdup(restype[i]);
         }
     }
 
@@ -706,7 +705,7 @@ void analyse(t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool b
     {
         srenew(gb->index, gb->nr+2);
         srenew(*gn, gb->nr+1);
-        (*gn)[gb->nr] = strdup("Water_and_ions");
+        (*gn)[gb->nr] = gmx_strdup("Water_and_ions");
         srenew(gb->a, gb->nra+nwater+nion);
         if (nwater > 0)
         {
@@ -776,7 +775,7 @@ t_blocka *init_index(const char *gfile, char ***grpname)
                 b->index[0] = 0;
             }
             b->index[b->nr]     = b->index[b->nr-1];
-            (*grpname)[b->nr-1] = strdup(str);
+            (*grpname)[b->nr-1] = gmx_strdup(str);
         }
         else
         {
@@ -968,7 +967,7 @@ static void rd_groups(t_blocka *grps, char **grpname, char *gnames[],
             fprintf(stderr, "There is one group in the index\n");
             gnr1 = 0;
         }
-        gnames[i] = strdup(grpname[gnr1]);
+        gnames[i] = gmx_strdup(grpname[gnr1]);
         isize[i]  = grps->index[gnr1+1]-grps->index[gnr1];
         snew(index[i], isize[i]);
         for (j = 0; (j < isize[i]); j++)