diff --git a/modules/conop/pymod/CMakeLists.txt b/modules/conop/pymod/CMakeLists.txt
index 3af9287193cc368b673e3279d939793cba5e3f5d..9c09906222fb97e1c935590ec22e81b536c94891 100644
--- a/modules/conop/pymod/CMakeLists.txt
+++ b/modules/conop/pymod/CMakeLists.txt
@@ -1,9 +1,8 @@
set(OST_CONOP_PYMOD_SOURCES
wrap_conop.cc
- export_builder.cc
+ # export_builder.cc
export_compound.cc
export_processor.cc
- export_rule_based.cc
export_heuristic.cc
export_amino_acids.cc
export_conop.cc
diff --git a/modules/conop/pymod/__init__.py b/modules/conop/pymod/__init__.py
index a24f5d2ec21b9333c7548cce372739a3c1753e6d..9f4a7b010deb424af0d570ab30356a8e5d21737d 100644
--- a/modules/conop/pymod/__init__.py
+++ b/modules/conop/pymod/__init__.py
@@ -73,3 +73,17 @@ def SetDefaultBuilder(builder_name):
'''
conop_inst=Conopology.Instance()
conop_inst.SetDefaultBuilder(builder_name)
+
+def SetDefaultLib(compound_lib):
+ '''
+ Set the default compound library. The compound library is used by various
+ functions of the framework that requires knowledge of naming and
+ connectivity of residues.j
+ '''
+ conop_inst=Conopology.Instance()
+ conop_inst.SetDefaultLib(compound_lib)
+
+def GetDefaultLib():
+ conop_inst=Conopology.Instance()
+ return conop_inst.GetDefaultLib()
+
diff --git a/modules/conop/pymod/cleanup.py b/modules/conop/pymod/cleanup.py
index 9ecf9c7ef12b8bb4fce889a5fb8062aab2364eda..1a51673d778e3e51237a3d576db8e67fca75279f 100644
--- a/modules/conop/pymod/cleanup.py
+++ b/modules/conop/pymod/cleanup.py
@@ -16,10 +16,9 @@ def Cleanup(entity, strip_water=True, canonicalize=True, remove_ligands=True):
:return: a cleaned version of the entity
"""
#setup
- builder = conop.GetBuilder()
- if not hasattr(builder, "compound_lib") :
- raise RuntimeError( "Cannot cleanup structure, since the default builder doesn't use the compound library")
- compound_lib = builder.compound_lib
+ lib = conop.GetDefaultLib()
+ if not lib:
+ raise RuntimeError("Cleanup requires a compound library.")
clean_entity = entity.Copy()
ed = clean_entity.EditXCS()
#remove water residues
@@ -27,7 +26,7 @@ def Cleanup(entity, strip_water=True, canonicalize=True, remove_ligands=True):
_StripWater(clean_entity, ed)
#replace modified residues before removing ligands to avoid removing MSE and others
if canonicalize:
- _CanonicalizeResidues(clean_entity, ed, compound_lib)
+ _CanonicalizeResidues(clean_entity, ed, lib)
#remove all hetatoms that are not water
if remove_ligands:
_RemoveLigands(clean_entity, ed)
diff --git a/modules/conop/pymod/export_conop.cc b/modules/conop/pymod/export_conop.cc
index 309ce86b3572987be230a6badeb519a252c073db..f617adaae70babd193888612098d2802f176bb60 100644
--- a/modules/conop/pymod/export_conop.cc
+++ b/modules/conop/pymod/export_conop.cc
@@ -22,20 +22,20 @@
using namespace boost::python;
#include <ost/conop/conop.hh>
#include <ost/mol/mol.hh>
-#include <ost/conop/builder.hh>
using namespace ost::conop;
void export_Conop() {
class_<Conopology, boost::noncopyable>("Conopology", no_init)
.def("Instance", &Conopology::Instance, return_value_policy<reference_existing_object>()).staticmethod("Instance")
- .def("ConnectAll", &Conopology::ConnectAll)
- .def("GetBuilder", &Conopology::GetBuilder)
- .def("ConnectAll", &Conopology::ConnectAll)
- .def("RegisterBuilder", &Conopology::RegisterBuilder)
- .def("SetDefaultBuilder", &Conopology::SetDefaultBuilder)
+ //.def("ConnectAll", &Conopology::ConnectAll)
+ .def("SetDefaultLib", &Conopology::SetDefaultLib)
+ .def("GetDefaultLib", &Conopology::GetDefaultLib)
+ //.def("GetBuilder", &Conopology::GetBuilder)
+ //.def("ConnectAll", &Conopology::ConnectAll)
+ //.def("RegisterBuilder", &Conopology::RegisterBuilder)
+ //.def("SetDefaultBuilder", &Conopology::SetDefaultBuilder)
;
- register_ptr_to_python<BuilderP>();
}
diff --git a/modules/conop/pymod/export_processor.cc b/modules/conop/pymod/export_processor.cc
index b69c0d1d8b800c77620a8031516b0a9acac7f8ac..180da8f48363571c1c8465bb4f8f2b01271f900f 100644
--- a/modules/conop/pymod/export_processor.cc
+++ b/modules/conop/pymod/export_processor.cc
@@ -18,11 +18,11 @@
//------------------------------------------------------------------------------
//
#include <boost/python.hpp>
-using namespace boost::python;
#include <ost/conop/processor.hh>
using namespace ost;
using namespace ost::conop;
+using namespace boost::python;
struct PyProcessor : public Processor {};
struct WrappedProcessor : public PyProcessor, public wrapper<WrappedProcessor> {
@@ -44,10 +44,19 @@ struct WrappedProcessor : public PyProcessor, public wrapper<WrappedProcessor> {
PyObject* self_;
};
+
void export_processor() {
+ enum_<Dialect>("Dialect")
+ .value("PDB_DIALECT", PDB_DIALECT)
+ .value("CHARMM_DIALECT", CHARMM_DIALECT)
+ .export_values()
+ ;
class_<Processor, ProcessorPtr, boost::noncopyable>("_Processor", no_init)
.def("Copy", &Processor::Copy)
+ .add_property("check_bond_feasibility",
+ &Processor::GetCheckBondFeasibility,
+ &Processor::SetCheckBondFeasibility)
.add_property("strict_hydrogens", &Processor::GetStrictHydrogens,
&Processor::SetStrictHydrogens)
.add_property("connect", &Processor::GetConnect,
diff --git a/modules/conop/pymod/wrap_conop.cc b/modules/conop/pymod/wrap_conop.cc
index fc19e341c89673dcd72d2eff2b143df3da10fb2e..b76739548e84353e4c8db1c03d38b9714cd77108 100644
--- a/modules/conop/pymod/wrap_conop.cc
+++ b/modules/conop/pymod/wrap_conop.cc
@@ -19,7 +19,7 @@
#include <boost/python.hpp>
using namespace boost::python;
-void export_Builder();
+//void export_Builder();
void export_Compound();
void export_Sanitizer();
void export_Conop();
@@ -31,7 +31,7 @@ void export_rule_based();
void export_diag();
BOOST_PYTHON_MODULE(_ost_conop)
{
- export_Builder();
+ // export_Builder();
export_Conop();
export_processor();
export_rule_based();
diff --git a/modules/conop/src/CMakeLists.txt b/modules/conop/src/CMakeLists.txt
index dfa77f4490545802c73b5cfa1ebd14a5fa511601..28cf8368ef52c223b4827046e03bf0635ce4b44f 100644
--- a/modules/conop/src/CMakeLists.txt
+++ b/modules/conop/src/CMakeLists.txt
@@ -1,34 +1,36 @@
set(OST_CONOP_HEADERS
-builder.hh
-builder_fw.hh
+#builder.hh
+#builder_fw.hh
conop.hh
processor.hh
-heuristic_builder.hh
+#heuristic_builder.hh
amino_acids.hh
diag.hh
model_check.hh
+heuristic.hh
compound.hh
compound_lib.hh
module_config.hh
rule_based.hh
nonstandard.hh
-rule_based_builder.hh
+#rule_based_builder.hh
ring_finder.hh
)
set(OST_CONOP_SOURCES
-builder.cc
+# builder.cc
processor.cc
amino_acids.cc
conop.cc
+heuristic.cc
diag.cc
rule_based.cc
model_check.cc
-heuristic_builder.cc
+#heuristic_builder.cc
compound.cc
compound_lib.cc
nonstandard.cc
-rule_based_builder.cc
+#rule_based_builder.cc
ring_finder.cc
)
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index e48b3444e16c4ac7bf1ba5ef70ea28ff8341f93a..ee9cbea237b0e95563208a774858650aef880b77 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -21,7 +21,6 @@
#include <ost/log.hh>
#include "conop.hh"
-#include "heuristic_builder.hh"
#include <ost/profile.hh>
namespace ost { namespace conop {
@@ -33,11 +32,10 @@ Conopology& Conopology::Instance()
return impl;
}
-Conopology::Conopology():
- builder_map_()
+Conopology::Conopology()//:builder_map_()
{
- builder_map_["HEURISTIC"]=BuilderP(new HeuristicBuilder());
- builder_map_["DEFAULT"]=builder_map_["HEURISTIC"];
+ //builder_map_["HEURISTIC"]=BuilderP(new HeuristicBuilder());
+ //builder_map_["DEFAULT"]=builder_map_["HEURISTIC"];
known_elements_.insert("AC");
known_elements_.insert("AG");
@@ -151,7 +149,7 @@ Conopology::Conopology():
known_elements_.insert("ZN");
known_elements_.insert("ZR");
}
-
+#if 0
void Conopology::RegisterBuilder(const BuilderP& b, const String& name) {
if (!GetBuilder(name))
builder_map_[name]=b;
@@ -292,6 +290,7 @@ void Conopology::ConnectAll(const BuilderP& b, mol::EntityHandle eh, int flags)
eh.Apply(tmaker);
}
+#endif
bool Conopology::IsValidElement(const String& ele) const
{
String upper_ele=ele;
diff --git a/modules/conop/src/conop.hh b/modules/conop/src/conop.hh
index 1234a30fd0ae024a69eeeb0d2a4fa9227bdcb73a..4c7d4633c557794e41157af1ede50152134a8cf3 100644
--- a/modules/conop/src/conop.hh
+++ b/modules/conop/src/conop.hh
@@ -22,8 +22,8 @@
#include <map>
#include <ost/conop/module_config.hh>
#include <ost/mol/entity_handle.hh>
-#include "builder_fw.hh"
-
+#include "processor.hh"
+#include "compound_lib.hh"
namespace ost { namespace conop {
@@ -33,14 +33,19 @@ typedef enum {
class DLLEXPORT_OST_CONOP Conopology {
- typedef std::map<String,BuilderP> BuilderMap;
+ //typedef std::map<String,BuilderP> BuilderMap;
+ typedef std::map<String,ProcessorPtr> ProcessorMap;
public:
// singleton
static Conopology& Instance();
+ // returns the default compound library (if any)
+ CompoundLibPtr GetDefaultLib() const { return lib_; }
+ void SetDefaultLib(const CompoundLibPtr& lib) { lib_ = lib; }
+
// retrieve a builder by name
- BuilderP GetBuilder(const String& name="DEFAULT");
+ //BuilderP GetBuilder(const String& name="DEFAULT");
/*
convenience function, connect all atoms with given coordinates,
@@ -48,20 +53,35 @@ public:
does this need to live within Conopology ?
*/
- void ConnectAll(const BuilderP& b, mol::EntityHandle eh,
- int flags=0);
+ //void ConnectAll(const BuilderP& b, mol::EntityHandle eh,
+ // int flags=0);
- void RegisterBuilder(const BuilderP& b, const String& name);
- void SetDefaultBuilder(const String& default_name);
+ //void RegisterBuilder(const BuilderP& b, const String& name);
+ //void SetDefaultBuilder(const String& default_name);
bool IsValidElement(const String& element) const;
+
+ void RegisterProcessor(const String& name,
+ const ProcessorPtr& processor) {
+ proc_map_[name] = processor;
+ }
+
+ ProcessorPtr GetProcessor(const String& name) const {
+ ProcessorMap::const_iterator i = proc_map_.find(name);
+ if (i != proc_map_.end() ) {
+ return i->second;
+ }
+ return ProcessorPtr();
+ }
private:
Conopology();
Conopology(const Conopology&) {}
Conopology& operator=(const Conopology&) {return *this;}
- BuilderMap builder_map_;
+ //BuilderMap builder_map_;
+ ProcessorMap proc_map_;;
std::set<String> known_elements_;
+ CompoundLibPtr lib_;
};
}} //
diff --git a/modules/conop/src/heuristic.cc b/modules/conop/src/heuristic.cc
new file mode 100644
index 0000000000000000000000000000000000000000..11070fd7d71402ec78644cf0b2b9510ceecc5260
--- /dev/null
+++ b/modules/conop/src/heuristic.cc
@@ -0,0 +1,36 @@
+//------------------------------------------------------------------------------
+// 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 <ost/log.hh>
+#include <ost/profile.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/mol/torsion_handle.hh>
+#include <ost/mol/impl/residue_impl.hh>
+#include <ost/mol/impl/atom_impl.hh>
+#include <ost/mol/residue_handle.hh>
+#include "heuristic.hh"
+
+namespace ost { namespace conop {
+
+
+void HeuristicProcessor::DoProcess(DiagnosticsPtr diags,
+ mol::EntityHandle ent) const {
+}
+
+}}
diff --git a/modules/conop/src/heuristic.hh b/modules/conop/src/heuristic.hh
new file mode 100644
index 0000000000000000000000000000000000000000..2e5250d26f4c8fd0f3ea515a1b902ebbd437d734
--- /dev/null
+++ b/modules/conop/src/heuristic.hh
@@ -0,0 +1,50 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+#ifndef OST_CONOP_HEURISTIC_HH
+#define OST_CONOP_HEURISTIC_HH
+
+#include <ost/mol/entity_handle.hh>
+#include "compound_lib.hh"
+#include "diag.hh"
+#include "processor.hh"
+
+namespace ost { namespace conop {
+
+
+class HeuristicProcessor;
+
+typedef boost::shared_ptr<HeuristicProcessor> HeuristicProcessorPtr;
+
+class DLLEXPORT_OST_CONOP HeuristicProcessor : public Processor {
+public:
+ HeuristicProcessor() {
+ }
+ virtual ProcessorPtr Copy() const {
+ return ProcessorPtr(new HeuristicProcessor(*this));
+ }
+protected:
+ virtual void DoProcess(DiagnosticsPtr diags,
+ mol::EntityHandle ent) const;
+private:
+};
+
+
+}}
+#endif
+
diff --git a/modules/conop/src/nonstandard.cc b/modules/conop/src/nonstandard.cc
index eeccdb60d16425dd1107629e41fb075100a7c0c3..eaf06680d087c05080f0e578828c7bad3fd68c66 100644
--- a/modules/conop/src/nonstandard.cc
+++ b/modules/conop/src/nonstandard.cc
@@ -26,7 +26,6 @@
#include <ost/conop/conop.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/alg/construct_cbeta.hh>
-#include <ost/conop/rule_based_builder.hh>
#include <ost/conop/compound_lib.hh>
#include "nonstandard.hh"
using namespace ost::mol;
@@ -39,18 +38,19 @@ namespace ost { namespace conop {
bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res, XCSEditor& edi)
{
// first let's get our hands on the component library
- conop::BuilderP builder=conop::Conopology::Instance().GetBuilder("DEFAULT");
- conop::RuleBasedBuilderPtr rbb=dyn_cast<conop::RuleBasedBuilder>(builder);
- conop::CompoundLibPtr comp_lib=rbb->GetCompoundLib();
+ conop::CompoundLibPtr comp_lib=conop::Conopology::Instance().GetDefaultLib();
return CopyResidue(src_res, dst_res, edi, comp_lib);
}
-bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res, XCSEditor& edi, CompoundLibPtr comp_lib)
+bool CopyResidue(ResidueHandle src_res, ResidueHandle dst_res,
+ XCSEditor& edi, CompoundLibPtr comp_lib)
{
bool has_cbeta = false;
bool ret;
- char parent_src = (comp_lib->FindCompound(src_res.GetName(),Compound::PDB))->GetOneLetterCode ();
- char parent_dst = (comp_lib->FindCompound(dst_res.GetName(),Compound::PDB))->GetOneLetterCode ();
+ char parent_src = (comp_lib->FindCompound(src_res.GetName(),
+ Compound::PDB))->GetOneLetterCode ();
+ char parent_dst = (comp_lib->FindCompound(dst_res.GetName(),
+ Compound::PDB))->GetOneLetterCode ();
if (parent_src==parent_dst) {
ret = CopyConserved(src_res, dst_res, edi, has_cbeta, comp_lib);
} else {
@@ -69,9 +69,7 @@ bool CopyConserved(ResidueHandle src_res, ResidueHandle dst_res, XCSEditor& edi,
bool& has_cbeta)
{
// first let's get our hands on the component library
- conop::BuilderP builder=conop::Conopology::Instance().GetBuilder("DEFAULT");
- conop::RuleBasedBuilderPtr rbb=dyn_cast<conop::RuleBasedBuilder>(builder);
- conop::CompoundLibPtr comp_lib=rbb->GetCompoundLib();
+ conop::CompoundLibPtr comp_lib=conop::Conopology::Instance().GetDefaultLib();
return CopyConserved(src_res,dst_res,edi,has_cbeta,comp_lib);
}
diff --git a/modules/conop/src/processor.hh b/modules/conop/src/processor.hh
index d8e3e6bf6e371a5325e4fb7b37543cf674fef31b..0fdaee40dba0ce591e445f6882ee10004e7b7005 100644
--- a/modules/conop/src/processor.hh
+++ b/modules/conop/src/processor.hh
@@ -25,6 +25,11 @@
namespace ost { namespace conop {
+typedef enum {
+ PDB_DIALECT,
+ CHARMM_DIALECT
+} Dialect;
+
enum ConopAction {
CONOP_WARN = 0,
CONOP_SILENT,
@@ -114,6 +119,8 @@ private:
ConopAction zero_occ_treatment_;
};
+ConopAction DLLEXPORT_OST_CONOP ConopActionFromString(const String& name);
+
/// \brief assigns phi/psi/omega to all residues marked peptide-linking of
/// the chain
diff --git a/modules/conop/tests/CMakeLists.txt b/modules/conop/tests/CMakeLists.txt
index ebc0be35c585e31c4698e4a83d05779f1c2f9d58..d65212779729e7e12c306c30ee5084d67923a526 100644
--- a/modules/conop/tests/CMakeLists.txt
+++ b/modules/conop/tests/CMakeLists.txt
@@ -1,8 +1,8 @@
set(OST_CONOP_UNIT_TESTS
- test_heuristic_builder.cc
+ # test_heuristic_builder.cc
tests.cc
test_rule_based_conop.cc
- test_builder.cc
+ # test_builder.cc
helper.cc
test_compound.py
test_cleanup.py
diff --git a/modules/conop/tests/test_cleanup.py b/modules/conop/tests/test_cleanup.py
index 1dc280f4fbaac9867c7f7a1063217bb4527cfbd0..c2b3b2b0e1614ae50f195d433b62e36034f5e971 100644
--- a/modules/conop/tests/test_cleanup.py
+++ b/modules/conop/tests/test_cleanup.py
@@ -5,7 +5,7 @@ from ost.conop import cleanup
class TestCleanUp(unittest.TestCase):
def setUp(self):
- self.comp_lib=conop.GetBuilder().compound_lib
+ self.comp_lib=conop.GetDefaultLib()
self.ent = io.LoadPDB("sample_test_cleanup.pdb")
self.ent_no_wat = io.LoadPDB("sample_nowater.pdb")
self.ent_no_lig = io.LoadPDB("sample_noligands.pdb")
@@ -155,8 +155,8 @@ class TestCleanUp(unittest.TestCase):
self.assertFalse(self.new_ent.residues[6].IsPeptideLinking()) # here assertFalse instead of assertTrue
self.assertTrue(self.new_ent.residues[6].atoms[0].is_hetatom)
-if not hasattr(conop.GetBuilder(), 'compound_lib'):
- print 'Default builder without compound lib. Ignoring test_cleanup.py tests'
+if not conop.GetDefaultLib():
+ print 'No compound library available. Ignoring test_cleanup.py tests'
sys.exit()
if __name__== '__main__':
diff --git a/modules/conop/tests/test_compound.py b/modules/conop/tests/test_compound.py
index a215a78f7a5dd966c2619346aaabf0f084b7bbd7..700f52b286d6e7f842cd004c2dffff6006603436 100644
--- a/modules/conop/tests/test_compound.py
+++ b/modules/conop/tests/test_compound.py
@@ -5,7 +5,7 @@ from ost import conop
class TestCompound(unittest.TestCase):
def setUp(self):
- self.compound_lib=conop.GetBuilder().compound_lib
+ self.compound_lib=conop.GetDefaultLib()
def testFindCompound(self):
compound=self.compound_lib.FindCompound('***')
@@ -22,9 +22,8 @@ class TestCompound(unittest.TestCase):
if __name__=='__main__':
- builder=conop.GetBuilder()
- if not hasattr(builder, 'compound_lib'):
- print 'default builder does not use compound library. ignoring unit tests'
+ if not conop.GetDefaultLib():
+ print 'No compound library available. ignoring compound unit tests'
else:
from ost import testutils
testutils.RunTests()
diff --git a/modules/conop/tests/test_nonstandard.py b/modules/conop/tests/test_nonstandard.py
index 170749c6eacd73bc64f4b6826e4df5d80f104512..f10b7d9d0324b5783a8ad6b0e0c162c8b818c828 100644
--- a/modules/conop/tests/test_nonstandard.py
+++ b/modules/conop/tests/test_nonstandard.py
@@ -117,9 +117,8 @@ class TestNonStandard(unittest.TestCase):
if __name__ == "__main__":
- builder=conop.GetBuilder()
- if not hasattr(builder, 'compound_lib'):
- print 'default builder does not use compound library. ignoring unit tests'
+ if not conop.GetDefaultLib():
+ print 'No compound library available. Ignoring unit tests'
else:
from ost import testutils
testutils.RunTests()
diff --git a/modules/gui/pymod/dng/init.py b/modules/gui/pymod/dng/init.py
index d46af73d8e1a93678a576698e06bdd69b552b84c..5468b7cd9b358f5a5ec7e08ed89b8ed48dd59386 100644
--- a/modules/gui/pymod/dng/init.py
+++ b/modules/gui/pymod/dng/init.py
@@ -37,8 +37,8 @@ def _InitRuleBasedBuilder():
if os.path.exists(compound_lib_path):
conop_inst=conop.Conopology.Instance()
compound_lib=conop.CompoundLib.Load(compound_lib_path)
- conop_inst.RegisterBuilder(conop.RuleBasedBuilder(compound_lib), 'RBB')
- conop_inst.SetDefaultBuilder('RBB')
+ conop_inst.SetDefaultLib(compound_lib)
+ io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(compound_lib)
# switch to rule-based builder for high fidelity if compounds.chemlib is
# available
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 0d6d0e142147cfc499b279610081f5a0fba28610..6df260a86ccd23e4a9b2b77094cef6ae85379c6d 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -148,9 +148,12 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
prof.no_hetatms=_override(prof.no_hetatms, no_hetatms)
prof.dialect=_override(prof.dialect, dialect)
prof.quack_mode=_override(prof.quack_mode, quack_mode)
- prof.strict_hydrogens=_override(prof.strict_hydrogens, strict_hydrogens)
+ if prof.processor:
+ prof.processor.strict_hydrogens=_override(prof.processor.strict_hydrogens,
+ strict_hydrogens)
+ prof.processor.check_bond_feasibilityk=_override(prof.processor.check_bond_feasibility,
+ bond_feasibility_check)
prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
- prof.bond_feasibility_check=_override(prof.bond_feasibility_check, bond_feasibility_check)
prof.join_spread_atom_records=_override(prof.join_spread_atom_records,
join_spread_atom_records)
@@ -162,13 +165,11 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
raise IOError('Can not load PDB %s from www.pdb.org'%filename)
conop_inst=conop.Conopology.Instance()
- builder=conop_inst.GetBuilder("DEFAULT")
- if prof.dialect=='PDB':
- builder.dialect=conop.PDB_DIALECT
- elif prof.dialect=='CHARMM':
- builder.dialect=conop.CHARMM_DIALECT
- builder.strict_hydrogens=prof.strict_hydrogens
- builder.bond_feasibility_check=prof.bond_feasibility_check
+ if prof.processor:
+ if prof.dialect=='PDB':
+ prof.processor.dialect=conop.PDB_DIALECT
+ elif prof.dialect=='CHARMM':
+ prof.processor.dialect=conop.CHARMM_DIALECT
reader=PDBReader(filename, prof)
reader.read_seqres=seqres
try:
@@ -177,7 +178,8 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
while reader.HasNext():
ent=mol.CreateEntity()
reader.Import(ent, restrict_chains)
- conop_inst.ConnectAll(builder, ent, 0)
+ if prof.processor:
+ prof.processor.Process(ent)
ent_list.append(ent)
if len(ent_list)==0:
raise IOError("File '%s' doesn't contain any entities" % filename)
@@ -186,7 +188,8 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
ent=mol.CreateEntity()
if reader.HasNext():
reader.Import(ent, restrict_chains)
- conop_inst.ConnectAll(builder, ent, 0)
+ if prof.processor:
+ prof.processor.Process(ent)
else:
raise IOError("File '%s' doesn't contain any entities" % filename)
if seqres:
@@ -321,7 +324,9 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
prof = profile.Copy()
prof.calpha_only=_override(prof.calpha_only, calpha_only)
- prof.strict_hydrogens=_override(prof.strict_hydrogens, strict_hydrogens)
+ if prof.processor:
+ proc = prof.processor
+ proc.strict_hydrogens=_override(proc.strict_hydrogens, strict_hydrogens)
prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
if remote:
@@ -331,18 +336,14 @@ def LoadMMCIF(filename, restrict_chains="", fault_tolerant=None, calpha_only=Non
else:
raise IOError('Can not load PDB %s from www.pdb.org'%filename)
- conop_inst = conop.Conopology.Instance()
- builder = conop_inst.GetBuilder("DEFAULT")
-
- builder.strict_hydrogens = prof.strict_hydrogens
-
try:
ent = mol.CreateEntity()
reader = MMCifReader(filename, ent, prof)
reader.read_seqres = seqres
#if reader.HasNext():
reader.Parse()
- conop_inst.ConnectAll(builder, ent, 0)
+ if prof.processor:
+ prof.processor.Process(ent)
#else:
# raise IOError("File doesn't contain any entities")
if seqres and info:
@@ -457,7 +458,8 @@ def _PDBize(biounit, asu, seqres=None, min_polymer_size=10):
new_res.SetStringProp('type', mol.StringFromChainType(chain.type))
ins_code = chr(ord(ins_code)+1)
_CopyAtoms(res, new_res, edi, tr)
- conop.ConnectAll(pdb_bu)
+ # FIXME: get rid of connect all call...
+ # conop.ConnectAll(pdb_bu)
return pdb_bu
MMCifInfoBioUnit.PDBize = _PDBize
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index c5abad5d434ddbdf1285c854cf4a427a8d0f34b9..55c842c875415c8d81c412ac8431b53105c50ced 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -36,22 +36,25 @@ void (PDBWriter::*write_b)(const mol::EntityView&)=&PDBWriter::Write;
void export_pdb_io()
{
class_<IOProfile>("IOProfile",
- init<String,bool,bool,bool,bool,bool,bool,bool>((arg("dialect")="PDB",
- arg("strict_hydrogens")=false,
- arg("quack_mode")=false,
- arg("fault_tolerant")=false,
- arg("join_spread_atom_records")=false,
- arg("no_hetatms")=false,
- arg("calpha_only")=false,
- arg("bond_feasibility_check")=true)))
+ init<String,bool,bool,bool,bool,bool,bool,bool,
+ conop::ProcessorPtr>((arg("dialect")="PDB",
+ arg("strict_hydrogens")=false,
+ arg("quack_mode")=false,
+ arg("fault_tolerant")=false,
+ arg("join_spread_atom_records")=false,
+ arg("no_hetatms")=false,
+ arg("calpha_only")=false,
+ arg("bond_feasibility_check")=true,
+ arg("processor")=conop::ProcessorPtr())))
.def_readwrite("dialect", &IOProfile::dialect)
.def_readwrite("fault_tolerant", &IOProfile::fault_tolerant)
.def_readwrite("quack_mode", &IOProfile::quack_mode)
- .def_readwrite("strict_hydrogens", &IOProfile::strict_hydrogens)
+ //.def_readwrite("strict_hydrogens", &IOProfile::strict_hydrogens)
.def_readwrite("no_hetatms", &IOProfile::no_hetatms)
.def_readwrite("calpha_only", &IOProfile::calpha_only)
.def_readwrite("join_spread_atom_records", &IOProfile::join_spread_atom_records)
- .def_readwrite("bond_feasibility_check", &IOProfile::bond_feasibility_check)
+ .def_readwrite("processor", &IOProfile::processor)
+ //.def_readwrite("bond_feasibility_check", &IOProfile::bond_feasibility_check)
.def("Copy", &IOProfile::Copy)
.def(self_ns::str(self))
;
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index 0f08c72e08ab95460e5552770706bd3c54d3a002..7820aba23f6715da589a4987475e0f5f9601e75c 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -35,6 +35,7 @@
#include <ost/profile.hh>
#include <ost/io/io_exception.hh>
+#include <ost/io/mol/io_profile.hh>
#include <ost/io/swap_util.hh>
#include "entity_io_crd_handler.hh"
@@ -409,12 +410,14 @@ bool EntityIOCRDHandler::ProvidesExport(const boost::filesystem::path& loc,
mol::EntityHandle LoadCRD(const String& file_name)
{
Profile profile_load("LoadCRD");
- conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
CRDReader reader(file_name);
mol::EntityHandle ent=mol::CreateEntity();
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
reader.Import(ent);
- conop::Conopology::Instance().ConnectAll(builder,ent);
+ IOProfile& prof = IOProfileRegistry::Instance().GetDefault();
+ if (prof.processor) {
+ prof.processor->Process(ent);
+ }
return ent;
}
diff --git a/modules/io/src/mol/entity_io_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
index 6a5306b055c44f7d6c6ccc82f5defa8c1acd1d35..b21407458c4422f105834152444f91215f6e2060 100644
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ b/modules/io/src/mol/entity_io_mae_handler.cc
@@ -36,10 +36,9 @@
#include <ost/log.hh>
#include <ost/conop/conop.hh>
-#include <ost/conop/heuristic_builder.hh>
#include <ost/mol/xcs_editor.hh>
#include <ost/profile.hh>
-
+#include <ost/io/mol/io_profile.hh>
#include <ost/io/io_exception.hh>
#include <ost/io/swap_util.hh>
@@ -366,12 +365,14 @@ bool EntityIOMAEHandler::ProvidesExport(const boost::filesystem::path& loc,
mol::EntityHandle LoadMAE(const String& file_name)
{
//conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
- conop::BuilderP builder(new conop::HeuristicBuilder);
MAEReader reader(file_name);
mol::EntityHandle ent=mol::CreateEntity();
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
reader.Import(ent);
- conop::Conopology::Instance().ConnectAll(builder,ent);
+ IOProfile& prof = IOProfileRegistry::Instance().GetDefault();
+ if (prof.processor) {
+ prof.processor->Process(ent);
+ }
return ent;
}
diff --git a/modules/io/src/mol/io_profile.hh b/modules/io/src/mol/io_profile.hh
index b4802583a838156ef5aac62048c158b50bff65d3..0bec6ba70c81a7935cac2bd226db36a57116603e 100644
--- a/modules/io/src/mol/io_profile.hh
+++ b/modules/io/src/mol/io_profile.hh
@@ -23,39 +23,50 @@
#include <map>
#include <ost/mol/entity_handle.hh>
#include <ost/io/module_config.hh>
+#include <ost/conop/processor.hh>
+
namespace ost { namespace io {
+
struct DLLEXPORT IOProfile {
public:
- IOProfile(String d, bool sh, bool qm, bool ft, bool js, bool nh, bool co, bool bf):
- dialect(d), strict_hydrogens(sh), quack_mode(qm), fault_tolerant(ft),
- join_spread_atom_records(js), no_hetatms(nh), calpha_only(co), bond_feasibility_check(bf)
- { }
- IOProfile(): dialect("PDB"), strict_hydrogens(true), quack_mode(false),
- fault_tolerant(false), join_spread_atom_records(false), no_hetatms(false),
- calpha_only(false), bond_feasibility_check(true)
+ IOProfile(String d, bool sh, bool qm, bool ft, bool js, bool nh,
+ bool co, bool bf, conop::ProcessorPtr proc=conop::ProcessorPtr()):
+ dialect(d), quack_mode(qm), fault_tolerant(ft), join_spread_atom_records(js),
+ no_hetatms(nh), calpha_only(co), processor(proc)
+ {
+ if (!processor) return;
+ processor->SetCheckBondFeasibility(bf);
+ processor->SetStrictHydrogens(sh);
+ //processor->SetQuackMode(qm);
+ }
+ IOProfile(): dialect("PDB"), quack_mode(false), fault_tolerant(false),
+ join_spread_atom_records(false), no_hetatms(false),
+ calpha_only(false), processor()
{ }
- virtual ~IOProfile() { }
- String dialect;
- bool strict_hydrogens;
- bool quack_mode;
- bool fault_tolerant;
- bool join_spread_atom_records;
- bool no_hetatms;
- bool calpha_only;
- bool bond_feasibility_check;
+ String dialect;
+ bool quack_mode;
+ bool fault_tolerant;
+ bool join_spread_atom_records;
+ bool no_hetatms;
+ bool calpha_only;
+ conop::ProcessorPtr processor;
IOProfile Copy()
{
- return IOProfile(dialect, strict_hydrogens, quack_mode, fault_tolerant,
- join_spread_atom_records, no_hetatms, calpha_only, bond_feasibility_check);
+ return IOProfile(dialect, processor ? processor->GetStrictHydrogens() : false,
+ quack_mode, fault_tolerant, join_spread_atom_records,
+ no_hetatms, calpha_only,
+ processor ? processor->GetCheckBondFeasibility() : false,
+ processor ? processor->Copy() : conop::ProcessorPtr());
}
- virtual void PostImport(mol::EntityHandle ent) { }
};
+
inline std::ostream& operator<<(std::ostream& stream, const IOProfile& p)
{
+#if 0
stream << "IOProfile(dialect='" << p.dialect << "', strict_hydrogens="
<< (p.strict_hydrogens ? "True" : "False") << ", quack_mode="
<< (p.quack_mode ? "True" : "False") << ", join_spread_atom_records="
@@ -64,6 +75,8 @@ inline std::ostream& operator<<(std::ostream& stream, const IOProfile& p)
<< (p.calpha_only ? "True" : "False") << ", fault_tolerant="
<< (p.fault_tolerant ? "True" : "False") << ", bond_feasibility_check="
<< (p.bond_feasibility_check ? "True" : "False") << ")";
+#endif
+#warning implement me
return stream;
}
diff --git a/modules/io/src/mol/load_entity.cc b/modules/io/src/mol/load_entity.cc
index 6fdfa57576b4c655b744955ae02dd30809cd100e..c1322367cc6e188f4a51c4801e0278dc4b37fe95 100644
--- a/modules/io/src/mol/load_entity.cc
+++ b/modules/io/src/mol/load_entity.cc
@@ -22,6 +22,7 @@
#include "load_entity.hh"
#include <ost/mol/xcs_editor.hh>
#include <ost/io/io_manager.hh>
+#include <ost/io/mol/io_profile.hh>
#include <ost/io/mol/entity_io_handler.hh>
#include <ost/profile.hh>
@@ -38,19 +39,15 @@ void Import(mol::EntityHandle& eh, const String& filename, int flag)
// TODO: proper error handling
LOG_DEBUG("calling import on entity io handle");
- /*
- This should probably allow various parameters to be passed
- to adjust the loading behaviour for a particular filter.
- Alternatively, these settings could be done outside via
- the main IOManager interface, as global settings per import plugin
- */
ent_io->Import(eh,filename);
LOG_DEBUG("running conopology");
if(ent_io->RequiresBuilder()) {
- conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
- conop::Conopology::Instance().ConnectAll(builder,eh,flag);
+ IOProfile& prof = IOProfileRegistry::Instance().GetDefault();
+ if (prof.processor) {
+ prof.processor->Process(eh);
+ }
}
}
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 762939ca817800366ee487ffadef9da493f5103a..a9c0ad6bfc87cf72cf56a66dda0193ddd981db6b 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -25,7 +25,6 @@
#include <ost/mol/xcs_editor.hh>
#include <ost/conop/conop.hh>
-#include <ost/conop/rule_based_builder.hh>
#include <ost/io/mol/mmcif_reader.hh>
namespace ost { namespace io {
@@ -670,17 +669,17 @@ void MMCifReader::ParseEntityPoly(const std::vector<StringRef>& columns)
}
} else if (indices_[PDBX_SEQ_ONE_LETTER_CODE] != -1) {
seqres=columns[indices_[PDBX_SEQ_ONE_LETTER_CODE]];
- conop::BuilderP builder=conop::Conopology::Instance().GetBuilder("DEFAULT");
- conop::RuleBasedBuilderPtr rbb=dyn_cast<conop::RuleBasedBuilder>(builder);
- if (!rbb) {
+
+ conop::CompoundLibPtr comp_lib=conop::Conopology::Instance()
+ .GetDefaultLib();
+ if (!comp_lib) {
if (!warned_rule_based_) {
- LOG_WARNING("SEQRES import requires the rule-based builder. Ignoring "
- "SEQRES records");
+ LOG_WARNING("SEQRES import requires a compound library. "
+ "Ignoring SEQRES records");
}
warned_rule_based_=true;
return;
}
- conop::CompoundLibPtr comp_lib=rbb->GetCompoundLib();
edm_it->second.seqres = this->ConvertSEQRES(seqres.str_no_whitespace(),
comp_lib);
} else {
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index b4b097c1b8c8bdffcf29a3ccfac8ee9173a4abf0..739bf6bd34e5363447409c26c0822f09b594403a 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -29,7 +29,6 @@
#include <ost/message.hh>
#include <ost/conop/conop.hh>
-#include <ost/conop/rule_based_builder.hh>
#include <ost/geom/mat3.hh>
#include <ost/io/io_exception.hh>
#include "pdb_reader.hh"
@@ -235,17 +234,17 @@ void PDBReader::ParseCompndEntry (const StringRef& line, int line_num)
void PDBReader::ParseSeqRes(const StringRef& line, int line_num)
{
- conop::BuilderP builder=conop::Conopology::Instance().GetBuilder("DEFAULT");
- conop::RuleBasedBuilderPtr rbb=dyn_cast<conop::RuleBasedBuilder>(builder);
- if (!rbb) {
+ conop::CompoundLibPtr comp_lib;
+ comp_lib = conop::Conopology::Instance().GetDefaultLib();
+
+ if (!comp_lib) {
if (!warned_rule_based_) {
- LOG_WARNING("SEQRES import requires the rule-based builder. Ignoring "
+ LOG_WARNING("SEQRES import requires a compound library. Ignoring"
"SEQRES records");
}
warned_rule_based_=true;
return;
}
- conop::CompoundLibPtr comp_lib=rbb->GetCompoundLib();
if (!seqres_.IsValid()) {
seqres_=seq::CreateSequenceList();
}
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index b0e54cdc37dacf167da076cc78b813c2ee7b4fab..561e91576b565d77dc6e9701bbc803f225167f56 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -23,7 +23,7 @@
#include <ost/dyn_cast.hh>
#include <ost/mol/mol.hh>
#include <ost/conop/conop.hh>
-#include <ost/conop/rule_based_builder.hh>
+#include <ost/conop/heuristic.hh>
#include <ost/io/mol/entity_io_pdb_handler.hh>
#include <ost/io/pdb_reader.hh>
@@ -425,8 +425,8 @@ BOOST_AUTO_TEST_CASE(deuterium_import)
mol::EntityHandle ent=mol::CreateEntity();
reader.Import(ent);
// we use conopology to mark amino acids as peptide-linking.
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
// this check makes sure that we correctly detect deal with the deuterium
// atoms in the residue.
BOOST_CHECK(ent.FindResidue("A", 297).IsPeptideLinking());
@@ -439,8 +439,8 @@ BOOST_AUTO_TEST_CASE(bzdng_318)
mol::EntityHandle ent=mol::CreateEntity();
reader.Import(ent);
// we use conopology to mark amino acids as peptide-linking.
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
{
PDBWriter writer(std::string("testfiles/pdb/bzdng-318-out.pdb"),
IOProfile());
@@ -613,8 +613,9 @@ BOOST_AUTO_TEST_CASE(write_ter)
reader.Import(ent);
// we use conopology to mark amino acids as peptide-linking. this is require
// for proper TER output
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+
+ heu_proc.Process(ent);
writer.Write(ent);
}
BOOST_CHECK(compare_files("testfiles/pdb/ter.pdb",
@@ -634,8 +635,8 @@ BOOST_AUTO_TEST_CASE(write_ter2)
reader.Import(ent);
// we use conopology to mark amino acids as peptide-linking. this is
// require for proper TER output
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
writer.Write(ent);
}
BOOST_CHECK(compare_files("testfiles/pdb/ter2.pdb",
@@ -655,8 +656,8 @@ BOOST_AUTO_TEST_CASE(write_ter3)
reader.Import(ent);
// we use conopology to mark amino acids as peptide-linking. this is
// require for proper TER output
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
writer.Write(ent);
}
BOOST_CHECK(compare_files("testfiles/pdb/ter3.pdb",
@@ -676,8 +677,8 @@ BOOST_AUTO_TEST_CASE(write_ter4)
mol::ResidueHandle r2=edi.AppendResidue(ch, "GLY");
mol::AtomHandle a2=edi.InsertAtom(r2, "N", geom::Vec3(35.0, -99.0, -10.5));
mol::ChainHandle ch2=edi.InsertChain("B");
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
writer.Write(ent);
}
BOOST_CHECK(compare_files("testfiles/pdb/ter_emptychain.pdb",
@@ -697,8 +698,8 @@ BOOST_AUTO_TEST_CASE(write_ter5)
mol::ResidueHandle r2=edi.AppendResidue(ch, "GLY");
mol::AtomHandle a2=edi.InsertAtom(r2, "N", geom::Vec3(35.0, -99.0, -10.5));
mol::ChainHandle ch2=edi.InsertChain("B");
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
writer.Write(ent.Select(""));
}
BOOST_CHECK(compare_files("testfiles/pdb/ter_view-emptychain.pdb",
@@ -716,8 +717,8 @@ BOOST_AUTO_TEST_CASE(write_ter6)
mol::EntityHandle ent=mol::CreateEntity();
reader.Import(ent);
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
writer.Write(ent);
}
BOOST_CHECK(compare_files("testfiles/pdb/ter4.pdb",
@@ -733,8 +734,8 @@ BOOST_AUTO_TEST_CASE(write_conect)
PDBWriter writer(String("testfiles/pdb/conect-out.pdb"), IOProfile());
mol::EntityHandle ent=mol::CreateEntity();
reader.Import(ent);
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
writer.Write(ent);
}
BOOST_CHECK(compare_files("testfiles/pdb/conect.pdb",
@@ -855,14 +856,11 @@ BOOST_AUTO_TEST_CASE(seqres_import)
String lib_path=GetSharedDataPath()+"/compounds.chemlib";
conop::CompoundLibPtr compound_lib=conop::CompoundLib::Load(lib_path);
if (!compound_lib) {
- std::cout << "WARNING: skipping SEQRES import unit test. "
- << "Rule-based builder is required" << std::endl;
+ std::cout << "WARNING: skipping SEQRES import unit test. Compound lib is "
+ << "required" << std::endl;
return;
}
- conop::RuleBasedBuilderPtr rbb(new conop::RuleBasedBuilder(compound_lib));
- conop::Conopology::Instance().RegisterBuilder(rbb, "RBB");
- conop::Conopology::Instance().SetDefaultBuilder("RBB");
-
+ conop::Conopology::Instance().SetDefaultLib(compound_lib);
String fname("testfiles/pdb/seqres.pdb");
IOProfile profile;
PDBReader reader(fname, profile);
@@ -970,8 +968,8 @@ BOOST_AUTO_TEST_CASE(write_charmm_ter)
mol::AtomHandle a=edi.InsertAtom(r, "N", geom::Vec3(32.0, -128.0, -2.5));
mol::ResidueHandle r2=edi.AppendResidue(ch, "GLY");
mol::AtomHandle a2=edi.InsertAtom(r2, "N", geom::Vec3(35.0, -99.0, -10.5));
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(ent);
writer.Write(ent);
}
BOOST_CHECK(compare_files("testfiles/pdb/charmm_ter.pdb",
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index eb9c852b521990d2195cabc379a82b5d4673dd31..b66b9edde259be5d00a70e27bea0d8e4c982edce 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -22,7 +22,6 @@
#include <ost/io/io_exception.hh>
#include <ost/io/mol/mmcif_reader.hh>
#include <ost/conop/conop.hh>
-#include <ost/conop/rule_based_builder.hh>
#define BOOST_AUTO_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
@@ -143,13 +142,11 @@ BOOST_AUTO_TEST_CASE(mmcif_convert_seqres)
String lib_path=GetSharedDataPath()+"/compounds.chemlib";
conop::CompoundLibPtr compound_lib=conop::CompoundLib::Load(lib_path);
if (!compound_lib) {
- std::cout << "WARNING: skipping SEQRES import unit test. "
- << "Rule-based builder is required" << std::endl;
+ std::cout << "WARNING: skipping SEQRES import unit test. Compound "
+ << "library is required" << std::endl;
return;
}
- conop::RuleBasedBuilderPtr rbb(new conop::RuleBasedBuilder(compound_lib));
- conop::Conopology::Instance().RegisterBuilder(rbb, "RBB");
- conop::Conopology::Instance().SetDefaultBuilder("RBB");
+ conop::Conopology::Instance().SetDefaultLib(compound_lib);
mol::EntityHandle eh=mol::CreateEntity();
TestMMCifReaderProtected tmmcif_p("testfiles/mmcif/atom_site.mmcif", eh);
@@ -158,7 +155,6 @@ BOOST_AUTO_TEST_CASE(mmcif_convert_seqres)
BOOST_CHECK_EQUAL(tmmcif_p.ConvertSEQRES("A(MSE)Y", compound_lib), "AMY");
BOOST_CHECK_THROW(tmmcif_p.ConvertSEQRES("A(MSEY", compound_lib),
IOException);
- conop::Conopology::Instance().SetDefaultBuilder("HEURISTIC");
}
BOOST_AUTO_TEST_CASE(mmcif_onbeginloop)
@@ -403,11 +399,11 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_poly_tests)
String lib_path=GetSharedDataPath()+"/compounds.chemlib";
conop::CompoundLibPtr compound_lib=conop::CompoundLib::Load(lib_path);
if (!compound_lib) {
- std::cout << "WARNING: skipping SEQRES import unit test. "
- << "Rule-based builder is required" << std::endl;
+ std::cout << "WARNING: skipping SEQRES import unit test. Compound "
+ << "lib is required" << std::endl;
return;
}
- conop::Conopology::Instance().SetDefaultBuilder("RBB");
+ conop::Conopology::Instance().SetDefaultLib(compound_lib);
BOOST_MESSAGE(" Running mmcif_entity_poly_tests...");
mol::ChainHandle ch;
IOProfile profile;
@@ -562,7 +558,6 @@ columns.push_back(StringRef("polydeoxyribonucleotide/polyribonucleotide hybrid",
BOOST_MESSAGE(" done.");
BOOST_MESSAGE(" done.");
- conop::Conopology::Instance().SetDefaultBuilder("HEURISTIC");
}
BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index fdd70d953c802f7319611071b57ca1e30a2b5c32..75eec8005263a6854319a158d10be07648cee03b 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -34,7 +34,6 @@
#include <ost/platform.hh>
#include <ost/log.hh>
-#include <ost/conop/rule_based_builder.hh>
#include <ost/dyn_cast.hh>
using namespace ost;
@@ -51,8 +50,10 @@ EntityHandle load(const String& file, const IOProfile& profile)
if (reader.HasNext()) {
EntityHandle ent=CreateEntity();
reader.Import(ent);
- conop::Conopology& conop_inst=conop::Conopology::Instance();
- conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
+ if (profile.processor) {
+ profile.processor->Process(ent);
+ }
+
if (ent.GetChainList().size()!=1) {
std::cout << "WARNING: File " << file << "has more than one chain" << std::endl;
}
@@ -116,7 +117,8 @@ int main (int argc, char **argv)
// creates the required loading profile
IOProfile profile;
- profile.bond_feasibility_check=false;
+#warning implement me
+ //profile.bond_feasibility_check=false;
// parses options
String sel;
diff --git a/modules/seq/alg/tests/test_aligntoseqres.py b/modules/seq/alg/tests/test_aligntoseqres.py
index 6c390008e69d81d2613337a863503769b6da1872..126c7f0471b43b1898f0b010d73847a00aed7f92 100644
--- a/modules/seq/alg/tests/test_aligntoseqres.py
+++ b/modules/seq/alg/tests/test_aligntoseqres.py
@@ -68,9 +68,8 @@ class TestAlignToSeqRes(unittest.TestCase):
self.assertEqual(seq.alg.ValidateSEQRESAlignment(seqres_aln, chain), False)
if __name__ == "__main__":
- builder=conop.GetBuilder()
- if not hasattr(builder, 'compound_lib'):
- print 'default builder does not use compound library. ignoring unit tests'
+ if not conop.GetDefaultLib():
+ print 'No compound library available. Ignoring unit tests'
else:
from ost import testutils
testutils.RunTests()
diff --git a/scripts/init_cl.py b/scripts/init_cl.py
index d4a14df4cd339872dc62c2de5898b04f07e75c76..88068214d34d73573a89e1ed1808e9602187867b 100644
--- a/scripts/init_cl.py
+++ b/scripts/init_cl.py
@@ -40,8 +40,8 @@ def _InitRuleBasedBuilder():
compound_lib_path=os.path.join(ost.GetSharedDataPath(), 'compounds.chemlib')
if os.path.exists(compound_lib_path):
compound_lib=conop.CompoundLib.Load(compound_lib_path)
- conop.RegisterBuilder(conop.RuleBasedBuilder(compound_lib), 'RBB')
- conop.SetDefaultBuilder('RBB')
+ conop.SetDefaultLib(compound_lib)
+ io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(compound_lib)
# switch to rule-based builder for high fidelity if compounds.chemlib is
# available