Fix some issues with C++ compatibility of Python3

-Alias('complete-test', testList)

\ No newline at end of file

+Alias('complete-test', testList)

--- a/pdb2pka/substruct/Algorithms.cpp

+++ b/pdb2pka/substruct/Algorithms.cpp

@@ -136,7 +136,7 @@ static PyObject *find_max_clique(PyObjec

   for (int i=0; i<cliq.size; i++) {

     cerr << cliq.vertex[i] << " ";

-    PyList_Append(erg, PyInt_FromLong(cliq.vertex[i]));

+    PyList_Append(erg, PyLong_FromLong(cliq.vertex[i]));

   }

   for(int i = 0; i < n; i++) {

@@ -242,7 +242,7 @@ static PyObject *find_cliques(PyObject *

     PyObject* cli = PyList_New(0);

     for (int j=0; j < collector.cliques[i].size; j++) {

-      PyList_Append(cli, PyInt_FromLong(collector.cliques[i].vertex[j]));

+      PyList_Append(cli, PyLong_FromLong(collector.cliques[i].vertex[j]));

     }

     PyList_Append(result, cli);

@@ -299,10 +299,24 @@ static PyMethodDef ModuleMethods[] =   {

 };

 /*----------------------------------------------------------------------------*/

+

+// Followed

+//   https://stackoverflow.com/questions/28305731/compiler-cant-find-py-initmodule-is-it-deprecated-and-if-so-what-should-i

+// to replace Py_InitModule

+

+static struct PyModuleDef cModMethods =

+{

+    PyModuleDef_HEAD_INIT,

+    MODULE_STR,  /* name of module */

+    "",          /* module documentation, may be NULL */

+    -1,          /* size of per-interpreter state of the module, or -1 if the module keeps state in global variables. */

+    ModuleMethods

+};

+

 PyMODINIT_FUNC MODULE_INIT()

 {

-    PyObject *ThisModule = Py_InitModule( MODULE_STR , ModuleMethods);

+    PyObject *ThisModule = PyModule_Create(&cModMethods);

     PyObject *ModuleDict = PyModule_GetDict(ThisModule);  

     // for correct handling of Numpy