diff --git a/modules/conop/pymod/CMakeLists.txt b/modules/conop/pymod/CMakeLists.txt
index 2ceff8be3d91299cbb5562bf446246ec37d01e12..3af9287193cc368b673e3279d939793cba5e3f5d 100644
--- a/modules/conop/pymod/CMakeLists.txt
+++ b/modules/conop/pymod/CMakeLists.txt
@@ -2,8 +2,12 @@ set(OST_CONOP_PYMOD_SOURCES
wrap_conop.cc
export_builder.cc
export_compound.cc
+ export_processor.cc
+ export_rule_based.cc
+ export_heuristic.cc
export_amino_acids.cc
export_conop.cc
+ export_diag.cc
export_rule_based.cc
export_non_standard.cc
export_ring_finder.cc
diff --git a/modules/conop/pymod/export_diag.cc b/modules/conop/pymod/export_diag.cc
new file mode 100644
index 0000000000000000000000000000000000000000..6155d63c71854e76517aa7a1732feb30ce352a72
--- /dev/null
+++ b/modules/conop/pymod/export_diag.cc
@@ -0,0 +1,44 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+//
+#include <boost/python.hpp>
+#include <ost/conop/diag.hh>
+using namespace ost;
+
+using namespace boost::python;
+using namespace ost::conop;
+
+
+void export_diag() {
+
+ enum_<DiagType>("DiagType")
+ .value("DIAG_UNK_ATOM", DIAG_UNK_ATOM)
+ .value("DIAG_UNK_RESIDUE", DIAG_UNK_RESIDUE)
+ .value("(DIAG_MISSING_ATOM", DIAG_MISSING_ATOM)
+ .value("DIAG_NONSTD_RESIDUE", DIAG_NONSTD_RESIDUE)
+ .export_values()
+ ;
+
+ class_<Diag>("Diag", init<DiagType,const char*>())
+ .def("__str__(self)__", &Diag::Format)
+ ;
+ class_<Diagnostics, DiagnosticsPtr>("Diagnostics")
+ ;
+}
+
diff --git a/modules/conop/pymod/export_heuristic.cc b/modules/conop/pymod/export_heuristic.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/modules/conop/pymod/export_processor.cc b/modules/conop/pymod/export_processor.cc
new file mode 100644
index 0000000000000000000000000000000000000000..b69c0d1d8b800c77620a8031516b0a9acac7f8ac
--- /dev/null
+++ b/modules/conop/pymod/export_processor.cc
@@ -0,0 +1,70 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+//
+#include <boost/python.hpp>
+using namespace boost::python;
+#include <ost/conop/processor.hh>
+using namespace ost;
+
+using namespace ost::conop;
+
+struct PyProcessor : public Processor {};
+struct WrappedProcessor : public PyProcessor, public wrapper<WrappedProcessor> {
+ WrappedProcessor(PyObject* self): self_(self)
+ { }
+ virtual void DoProcess(DiagnosticsPtr diag, mol::EntityHandle ent) const
+ {
+ call_method<void>(self_, "DoProcess", diag, ent);
+ }
+ DiagnosticsPtr DoProcessDefault(DiagnosticsPtr diag,
+ mol::EntityHandle ent) const {
+ return DiagnosticsPtr();
+ }
+ ProcessorPtr Copy() const {
+ return call_method<ProcessorPtr>(self_, "Copy");
+ }
+ ProcessorPtr CopyDefault() const { return ProcessorPtr(); }
+
+ PyObject* self_;
+};
+
+void export_processor() {
+
+ class_<Processor, ProcessorPtr, boost::noncopyable>("_Processor", no_init)
+ .def("Copy", &Processor::Copy)
+ .add_property("strict_hydrogens", &Processor::GetStrictHydrogens,
+ &Processor::SetStrictHydrogens)
+ .add_property("connect", &Processor::GetConnect,
+ &Processor::SetConnect)
+ .add_property("assign_torsions", &Processor::GetAssignTorsions,
+ &Processor::SetAssignTorsions)
+ .add_property("unk_res_treatment", &Processor::GetUnkResidueTreatment,
+ &Processor::SetUnkResidueTreatment)
+ .add_property("unk_atom_treatment", &Processor::GetUnkAtomTreatment,
+ &Processor::SetUnkAtomTreatment)
+ .def("Process", &Processor::Process)
+ ;
+ class_<PyProcessor, boost::noncopyable,
+ boost::shared_ptr<WrappedProcessor>,
+ bases<Processor> >("Processor")
+ .def("Copy", &WrappedProcessor::CopyDefault)
+ .def("DoProcess", &WrappedProcessor::DoProcessDefault)
+ ;
+}
+
diff --git a/modules/conop/pymod/export_rule_based.cc b/modules/conop/pymod/export_rule_based.cc
index 06b0e7b26d344f0d46755f39a775d42907838001..ab3aefa415aa9323f2da3bcef6dd21d9acb8bf7a 100644
--- a/modules/conop/pymod/export_rule_based.cc
+++ b/modules/conop/pymod/export_rule_based.cc
@@ -1,12 +1,35 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
#include <boost/python.hpp>
+using namespace boost::python;
#include <ost/conop/rule_based.hh>
-using namespace boost::python;
using namespace ost::conop;
-void export_rule_based()
-{
- class_<RuleBasedProcessor>("RuleBasedProcessor", init<CompoundLibPtr>())
- .def("Process", &RuleBasedProcessor::Process)
+void export_rule_based() {
+
+ class_<RuleBasedProcessor, RuleBasedProcessorPtr,
+ boost::noncopyable, bases<Processor> >("RuleBasedProcessor",
+ init<CompoundLibPtr>())
+ .add_property("fix_element", &RuleBasedProcessor::GetFixElement,
+ &RuleBasedProcessor::SetFixElement)
;
}
+
diff --git a/modules/conop/pymod/wrap_conop.cc b/modules/conop/pymod/wrap_conop.cc
index 99ceec31604df60d6b4eac4df826155f2fdcbcf9..fc19e341c89673dcd72d2eff2b143df3da10fb2e 100644
--- a/modules/conop/pymod/wrap_conop.cc
+++ b/modules/conop/pymod/wrap_conop.cc
@@ -26,15 +26,18 @@ void export_Conop();
void export_RingFinder();
void export_AminoAcids();
void export_NonStandard();
-
+void export_processor();
void export_rule_based();
+void export_diag();
BOOST_PYTHON_MODULE(_ost_conop)
{
export_Builder();
export_Conop();
+ export_processor();
export_rule_based();
export_Compound();
export_RingFinder();
export_AminoAcids();
export_NonStandard();
+ export_diag();
}
diff --git a/modules/conop/src/rule_based.hh b/modules/conop/src/rule_based.hh
index 4ea5246a61eb8ee3f88f74a9d3b9d5327f0d606f..f014fe9d5fd6b9d4b9e02a050d3405bc688b9ec0 100644
--- a/modules/conop/src/rule_based.hh
+++ b/modules/conop/src/rule_based.hh
@@ -30,6 +30,10 @@ namespace ost { namespace conop {
mol::AtomHandleList DLLEXPORT_OST_CONOP GetUnknownAtoms(mol::ResidueHandle res,
CompoundPtr compound);
+class RuleBasedProcessor;
+
+typedef boost::shared_ptr<RuleBasedProcessor> RuleBasedProcessorPtr;
+
class DLLEXPORT_OST_CONOP RuleBasedProcessor : public Processor {
public:
RuleBasedProcessor(CompoundLibPtr compound_lib):
diff --git a/modules/conop/tests/CMakeLists.txt b/modules/conop/tests/CMakeLists.txt
index a318766e1c6355c55063b487c1a9c6c5b1a51e95..ebc0be35c585e31c4698e4a83d05779f1c2f9d58 100644
--- a/modules/conop/tests/CMakeLists.txt
+++ b/modules/conop/tests/CMakeLists.txt
@@ -6,6 +6,7 @@ set(OST_CONOP_UNIT_TESTS
helper.cc
test_compound.py
test_cleanup.py
+ test_processor.py
test_nonstandard.py
)
diff --git a/modules/conop/tests/test_processor.py b/modules/conop/tests/test_processor.py
new file mode 100644
index 0000000000000000000000000000000000000000..b8662c44283a2e4298d50281d88724e5295a8b5a
--- /dev/null
+++ b/modules/conop/tests/test_processor.py
@@ -0,0 +1,21 @@
+import unittest
+from ost import conop
+
+
+class TestProcessor(unittest.TestCase):
+ def testPyWrap(self):
+ class MyProc(conop.Processor):
+ def __init__(self):
+ conop.Processor.__init__(self)
+ self.count =0
+ def DoProcess(self, diag, ent):
+ self.count+=1
+ p = MyProc()
+ ent = mol.CreateEntity()
+ p.Process(ent)
+ self.assertEqual(p.count, 1)
+if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
+
+