Merge "Fixed trjconv -sub" into release-4-5-patches

diff --git a/src/kernel/pgutil.c b/src/kernel/pgutil.c
index 404f9ed5fca73b090deb0829d57229d592ba23ef..7a3e7d86818beb272b4a08cd946016726a58bdb6 100644 (file)
--- a/src/kernel/pgutil.c
+++ b/src/kernel/pgutil.c
@@ -42,29 +42,43 @@
 #include "string.h"
 #include "gmx_fatal.h"
 
+#define BUFSIZE 1024
 static void atom_not_found(int fatal_errno,const char *file,int line,
                           const char *atomname,int resind,
-                          const char *bondtype,gmx_bool bDontQuit)
+                          const char *bondtype,gmx_bool bAllowMissing)
 {
-  if (strcmp(bondtype,"check") != 0) {
-    if (bDontQuit) {
-      gmx_warning("WARNING: Atom %s is used in an interaction of type %s in the\n"
-                 "topology database, but an atom of that name was not found in\n"
-                 "residue number %d.\n",
-                 atomname,bondtype,resind+1);
-    } else {
-      gmx_fatal(fatal_errno,file,line,
-               "Atom %s is used in an interaction of type %s in the topology\n"
-               "database, but an atom of that name was not found in residue\n"
-               "number %d.\n",
-               atomname,bondtype,resind+1);
+    char message_buffer[BUFSIZE];
+    if (strcmp(bondtype,"check") != 0)
+    {
+        if (0 != strcmp(bondtype, "atom"))
+        {
+            snprintf(message_buffer, 1024,
+                     "Atom %s is used in an interaction of type %s in the topology\n"
+                     "database, but an atom of that name was not found in residue\n"
+                     "number %d.\n",
+                     atomname,bondtype,resind+1);
+        }
+        else
+        {
+            snprintf(message_buffer, 1024,
+                     "Atom %s is used in the topology database, but an atom of that\n"
+                     "name was not found in residue number %d.\n",
+                     atomname,resind+1);
+        }
+        if (bAllowMissing)
+        {
+            gmx_warning("WARNING: %s", message_buffer);
+        }
+        else
+        {
+            gmx_fatal(fatal_errno,file,line,message_buffer);
+        }
     }
-  }
 }
        
 atom_id search_atom(const char *type,int start,int natoms,t_atom at[],
                    char ** const * anm,
-                   const char *bondtype,gmx_bool bDontQuit)
+                   const char *bondtype,gmx_bool bAllowMissing)
 {
   int     i,resind=-1;
   gmx_bool    bPrevious,bNext;
@@ -88,7 +102,7 @@ atom_id search_atom(const char *type,int start,int natoms,t_atom at[],
        return (atom_id) i;
     }
     if (!(bNext && at[start].resind==at[natoms-1].resind))
-      atom_not_found(FARGS,type,at[start].resind,bondtype,bDontQuit);
+      atom_not_found(FARGS,type,at[start].resind,bondtype,bAllowMissing);
   }
   else {
     /* The previous residue */
@@ -99,7 +113,7 @@ atom_id search_atom(const char *type,int start,int natoms,t_atom at[],
       if (gmx_strcasecmp(type,*(anm[i]))==0)
        return (atom_id) i;
     if (start > 0)
-      atom_not_found(FARGS,type,at[start].resind,bondtype,bDontQuit);
+      atom_not_found(FARGS,type,at[start].resind,bondtype,bAllowMissing);
   }
   return NO_ATID;
 }

diff --git a/src/kernel/pgutil.h b/src/kernel/pgutil.h
index 70fe397c62bc9939b0d53c329ab33d21192c555b..b4ac091894b803475b2cecd7e5b82aa8f65967df 100644 (file)
--- a/src/kernel/pgutil.h
+++ b/src/kernel/pgutil.h
@@ -41,12 +41,12 @@
 extern atom_id search_atom(const char *type,int start,
                           int natoms,t_atom at[],
                           char ** const * anm,
-                          const char *bondtype,gmx_bool bDontQuit);
+                          const char *bondtype,gmx_bool bAllowMissing);
 /* Search an atom in array of pointers to strings, starting from start
  * if type starts with '-' then searches backwards from start.
  * bondtype is only used for printing the error/warning string,
  * when bondtype="check" no error/warning is issued.
- * When bDontQuit=FALSE an fatal error is issued, otherwise a warning.
+ * When bAllowMissing=FALSE an fatal error is issued, otherwise a warning.
  */
 
 extern void set_at(t_atom *at,real m,real q,int type,int resind);