Bundle commit of all recent changes on pygmx.

pygmx/utility.pxd

@@ -1,7 +1,7 @@
 # C-API in gromacs/utility
 
 #cdef extern from "inttypes.h":
-ctypedef int __int64
+ctypedef unsigned long __int64
 
 cdef extern from "gromacs/utility/basedefinitions.h":
     ctypedef int gmx_bool
@@ -12,3 +12,12 @@ cdef extern from "gromacs/utility/real.h":
 
 cdef extern from "gromacs/utility/futil.h":
     ctypedef gmx_int64_t    gmx_off_t
+
+cdef extern from "gromacs/utility/smalloc.h":
+    void snew(void *ptr, int nelem)
+
+
+cdef inline cstr(instr):
+    if isinstance(instr, str):
+        instr = instr.encode()
+    return instr