diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index 3e0e70d41bc5484965f7e2e0fed8e9870c6e7186..bf14500361e7aafcb2060df321e8592fd8054fff 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -6,7 +6,7 @@ The compound library
Compound libraries contain information on chemical compounds, such as their
connectivity, chemical class and one-letter-code. The compound library has
several uses, but the most important one is to provide the connectivy
-information for the :class:`rule-based builder <RuleBasedBuilder>`.
+information for the :class:`rule-based processor <RuleBasedBuilder>`.
The compound definitions for standard PDB files are taken from the
components.cif dictionary provided by the PDB. The dictionary is updated with
diff --git a/modules/conop/doc/connectivity.rst b/modules/conop/doc/connectivity.rst
index 9df7cc40b1fc59b603751f24cd460b8a68717fdc..64a43bfd2e4060b6e8ce731242b5dbfcda484fd1 100644
--- a/modules/conop/doc/connectivity.rst
+++ b/modules/conop/doc/connectivity.rst
@@ -36,30 +36,6 @@ of erroneous structures. The clients of the conop module can specify how the
Processor should treat unknown amino acids, missing atoms and chemically
infeasible bonds.
-The high-level interface
---------------------------------------------------------------------------------
-
-
-.. autofunction:: ConnectAll()
-
-
-
-A call to :func:`ConnectAll` is sufficient to assign residue and atoms
-properties as well as to connect atoms with bonds.
-
-
-.. code-block:: python
-
- # Suppose that BuildRawModel is a function that returns a protein structure
- # with no atom properties assigned and no bonds formed.
- ent=BuildRawModel(...)
- print ent.bonds # will return an empty list
- # Call ConnectAll() to assign properties/connect atoms
- conop.ConnectAll(ent)
- print ent.bonds # will print a list containing many bonds
-
-For a more fine-grained control, consider using the :class:`Processor` interface.
-
Processors
--------------------------------------------------------------------------------
diff --git a/modules/conop/doc/conop.dox b/modules/conop/doc/conop.dox
index c59b5a5b1a78ec2a90b48bdda556c29dd8042e27..ee071624521fdfb5a308abcf38001fd3fca7226c 100644
--- a/modules/conop/doc/conop.dox
+++ b/modules/conop/doc/conop.dox
@@ -40,7 +40,7 @@ Builder should treat unknown amino acids, missing atoms and chemically
infeasible bonds.
So far, two classes implement the Builder interface: A heuristic and a
-rule-based builder. The builders mainly differ in the source of their
+rule-based processor. The builders mainly differ in the source of their
connectivity information. The HeuristicBuilder uses a hard-coded heuristic
connectivity table for the 20 standard amino acids as well as nucleotides.
For other compounds such as ligands the HeuristicBuilder runs a distance-based
@@ -63,7 +63,7 @@ conop.Conopology.Instance().SetDefaultBuilder('rbb')
All subsequent calls to io::LoadEntity will make use of the RuleBasedBuilder
instead of the heuristic builder. See \ref convert_mmcif "here" for more
-information on how to create the neccessary files to use the rule-based builder.
+information on how to create the neccessary files to use the rule-based processor.
\subsection connecting_atoms Connecting atoms
diff --git a/modules/conop/pymod/__init__.py b/modules/conop/pymod/__init__.py
index 9f4a7b010deb424af0d570ab30356a8e5d21737d..3b7856fe1634cd5d9ec3dfb7e22218618ae2655e 100644
--- a/modules/conop/pymod/__init__.py
+++ b/modules/conop/pymod/__init__.py
@@ -29,56 +29,11 @@ STANDARD_AMINOACIDS=(
'HIS', 'PHE',
)
-def ConnectAll(ent):
- '''
- Uses the current default builder to connect the atoms of the entity, assign
- torsions, and fill in missing or correct erroneous information such as the
- chemical class of the residues and the atom's element.
-
- :param ent: A valid entity
- :type ent: :class:`~ost.mol.EntityHandle`
- '''
- conop_inst=Conopology.Instance()
- conop_inst.ConnectAll(conop_inst.GetBuilder("DEFAULT"), ent, 0)
-
-def GetBuilder(name='DEFAULT'):
- '''
- Get registered builder by name
-
- :param name: The name of the builder
-
- :returns: The builder or None, if the builder doesn't exist
- '''
- return Conopology.Instance().GetBuilder(name)
-
-def RegisterBuilder(builder, name):
- '''
- Register builder to OpenStructure
-
- :param builder: A instance of :class:`Builder`
-
- :param name: The name of the builder
- '''
- conop_inst=Conopology.Instance()
- conop_inst.RegisterBuilder(builder, name)
-
-def SetDefaultBuilder(builder_name):
- '''
- Set the builder with the given name as the default. You will have to register
- a builder with :func:`RegisterBuilder` before you will be able to set it as
- the default.
-
- :raises: :exc:`RuntimeError` when trying to set a builder as the default that
- has not been registered yet.
- '''
- 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
+ connectivity of residues.
'''
conop_inst=Conopology.Instance()
conop_inst.SetDefaultLib(compound_lib)
diff --git a/modules/conop/pymod/export_conop.cc b/modules/conop/pymod/export_conop.cc
index f617adaae70babd193888612098d2802f176bb60..39f006b45f96fc41a83403ab9363c7e5568cbd20 100644
--- a/modules/conop/pymod/export_conop.cc
+++ b/modules/conop/pymod/export_conop.cc
@@ -28,13 +28,8 @@ 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("SetDefaultLib", &Conopology::SetDefaultLib)
.def("GetDefaultLib", &Conopology::GetDefaultLib)
- //.def("GetBuilder", &Conopology::GetBuilder)
- //.def("ConnectAll", &Conopology::ConnectAll)
- //.def("RegisterBuilder", &Conopology::RegisterBuilder)
- //.def("SetDefaultBuilder", &Conopology::SetDefaultBuilder)
;
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index ee9cbea237b0e95563208a774858650aef880b77..58fc349b6df596e1bfc3de56396169ce2649eeef 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -32,10 +32,8 @@ Conopology& Conopology::Instance()
return impl;
}
-Conopology::Conopology()//:builder_map_()
+Conopology::Conopology()
{
- //builder_map_["HEURISTIC"]=BuilderP(new HeuristicBuilder());
- //builder_map_["DEFAULT"]=builder_map_["HEURISTIC"];
known_elements_.insert("AC");
known_elements_.insert("AG");
@@ -149,148 +147,7 @@ Conopology::Conopology()//:builder_map_()
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;
-}
-
-void Conopology::SetDefaultBuilder(const String& default_name) {
- BuilderP builder=GetBuilder(default_name);
- if (builder)
- builder_map_["DEFAULT"]=builder;
- else
- throw ost::Error("trying to set unknown builder '"+
- default_name+"' as the default");
-}
-
-BuilderP Conopology::GetBuilder(const String& name)
-{
- BuilderMap::iterator it=builder_map_.find(name);
- if (it!=builder_map_.end()){
- return (*it).second;
- }
- return BuilderP();
-}
-
-namespace {
-
-class PropAssigner: public mol::EntityVisitor {
-public:
- PropAssigner(const BuilderP& builder): builder_(builder) {}
-
- virtual bool VisitResidue(const mol::ResidueHandle& res)
- {
- String key=builder_->IdentifyResidue(res);
- if (key=="UNK" && res.GetKey()!="UNK" && res.GetKey()!="UNL") {
- unk_res_[res.GetKey()]+=1;
- }
- builder_->FillResidueProps(res);
- return true;
- }
-
- virtual bool VisitAtom(const mol::AtomHandle& atom)
- {
- builder_->FillAtomProps(atom);
- return false;
- }
-
- virtual void OnExit()
- {
- for (std::map<String, int>::iterator i=unk_res_.begin(),
- e=unk_res_.end(); i!=e; ++i) {
- if (i->second>1) {
- LOG_WARNING("structure contains unknown residues with name " << i->first
- << " ("<< i->second << "x)");
- } else {
- LOG_WARNING("structure contains unknown residue with name " << i->first);
- }
-
- }
- }
-private:
- BuilderP builder_;
- std::map<String, int> unk_res_;
-};
-
-class ChemClassAssigner : public mol::EntityVisitor {
-public:
- ChemClassAssigner(BuilderP b): builder(b) { }
- virtual bool VisitResidue(const mol::ResidueHandle& res)
- {
- if (res.GetChemClass()==mol::ChemClass()) {
- builder->GuessChemClass(res);
- }
- return false;
- }
-private:
- BuilderP builder;
-};
-class Connector: public mol::EntityVisitor
-{
-public:
- Connector(const BuilderP& b, bool peptide_bonds):
- builder_(b),
- prev_(),
- peptide_bonds_(peptide_bonds)
- {}
-
- virtual bool VisitChain(const mol::ChainHandle& chain) {
- prev_=mol::ResidueHandle(); // reset prev
- return true;
- }
-
- virtual bool VisitResidue(const mol::ResidueHandle& res) {
- builder_->ConnectAtomsOfResidue(res);
- if (peptide_bonds_ && prev_) {
- builder_->ConnectResidueToPrev(res,prev_);
- }
- prev_=res;
- return false;
- }
-
-private:
- BuilderP builder_;
- mol::ResidueHandle prev_;
- bool peptide_bonds_;
-};
-
-class TorsionMaker: public mol::EntityVisitor
-{
-public:
- TorsionMaker(const BuilderP& b):
- builder_(b)
- {}
-
- virtual bool VisitChain(const mol::ChainHandle& chain) {
- builder_->AssignTorsions(chain);
- return false;
- }
-
-private:
- BuilderP builder_;
-};
-} // ns
-
-void Conopology::ConnectAll(const BuilderP& b, mol::EntityHandle eh, int flags)
-{
- Profile profile_connect("ConnectAll");
- LOG_DEBUG("Conopology: ConnectAll: building internal coordinate system");
- mol::XCSEditor xcs_e=eh.EditXCS(mol::BUFFERED_EDIT);
- PropAssigner a(b);
- eh.Apply(a);
- ChemClassAssigner cca(b);
- eh.Apply(cca);
- LOG_DEBUG("Conopology: ConnectAll: connecting all bonds");
- Connector connector(b, !(flags & NO_PEPTIDE_BONDS));
- eh.Apply(connector);
-
- LOG_DEBUG("Conopology: ConnectAll: assigning all torsions");
- TorsionMaker tmaker(b);
- 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 4c7d4633c557794e41157af1ede50152134a8cf3..34f58e080f97384df0bfc9ca7db6ee2ab3f6220c 100644
--- a/modules/conop/src/conop.hh
+++ b/modules/conop/src/conop.hh
@@ -33,9 +33,6 @@ typedef enum {
class DLLEXPORT_OST_CONOP Conopology {
- //typedef std::map<String,BuilderP> BuilderMap;
- typedef std::map<String,ProcessorPtr> ProcessorMap;
-
public:
// singleton
static Conopology& Instance();
@@ -44,42 +41,13 @@ public:
CompoundLibPtr GetDefaultLib() const { return lib_; }
void SetDefaultLib(const CompoundLibPtr& lib) { lib_ = lib; }
- // retrieve a builder by name
- //BuilderP GetBuilder(const String& name="DEFAULT");
-
- /*
- convenience function, connect all atoms with given coordinates,
- such as after coordinate file import, based on a given builder
-
- does this need to live within Conopology ?
- */
- //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);
-
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_;
- ProcessorMap proc_map_;;
std::set<String> known_elements_;
CompoundLibPtr lib_;
};
diff --git a/modules/gui/pymod/dng/init.py b/modules/gui/pymod/dng/init.py
index 5468b7cd9b358f5a5ec7e08ed89b8ed48dd59386..1b7ed8043bdce2c426565f1a4dee2435a163a218 100644
--- a/modules/gui/pymod/dng/init.py
+++ b/modules/gui/pymod/dng/init.py
@@ -32,7 +32,7 @@ def _my_exit(code):
sys._exit=sys.exit
sys.exit=_my_exit
-def _InitRuleBasedBuilder():
+def _InitRuleBasedProcessor():
compound_lib_path=os.path.join(ost.GetSharedDataPath(), 'compounds.chemlib')
if os.path.exists(compound_lib_path):
conop_inst=conop.Conopology.Instance()
@@ -40,9 +40,9 @@ def _InitRuleBasedBuilder():
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
+# switch to rule-based processor for high fidelity if compounds.chemlib is
# available
-_InitRuleBasedBuilder()
+_InitRuleBasedProcessor()
def _CheckRestore():
settings = QtCore.QSettings()
@@ -165,8 +165,8 @@ parser.add_option("-v", "--verbosity_level", action="store", type="int", dest="v
help="sets the verbosity level [default: %default]")
parser.add_option("-s", "--script", action="callback", default=[], dest="script", type="string", callback=parse_script_option, help="executes a script (syntax: -s SCRIPT [options] [args]) Anything that follows this option is passed to the script")
parser.add_option("-p", "--pdb_id", dest="pdb_ids", default=[],action="append", help="PDB file ID. The file will be retrieved from PDB")
-parser.add_option("-b", "--builder", dest="builder", default="HEURISTIC", help="Type of builder used by the progam (either RULE_BASED or HEURISTIC) [default: %default]")
-parser.add_option("-c", "--compound_library", dest="complib", default="compounds.chemlib", help="Compound library for the RULE_BASED builder (only used if --builder option is set to RULE_BASED, otherwise ignored [default: %default]")
+parser.add_option("-b", "--processor", dest="processor", default="HEURISTIC", help="Type of processor used by the progam (either RULE_BASED or HEURISTIC) [default: %default]")
+parser.add_option("-c", "--compound_library", dest="complib", default="compounds.chemlib", help="Compound library for the RULE_BASED processor (only used if --processor option is set to RULE_BASED, otherwise ignored [default: %default]")
parser.add_option("-q", "--query", dest="query", default="", help="Selection query to be highlighted automatically upon loading (only used together with -p option or when a PDB file is loaded, otherwise ignored [default: None]")
parser.add_option("-S","--stereo", dest="try_stereo", default=False, action="store_true",help="try to get a quad-buffer stereo visual")
parser.disable_interspersed_args()
@@ -184,12 +184,12 @@ if len(parser.rargs)!=0:
if len(options.script)!=0:
script_argv=options.script
-if options.builder=="RULE_BASED":
+if options.processor=="RULE_BASED":
from ost import conop
- compound_lib=conop.CompoundLib.Load(options.complib)
- rbb=conop.RuleBasedBuilder(compound_lib)
- conop.Conopology.Instance().RegisterBuilder(rbb,'rbb')
- conop.Conopology.Instance().SetDefaultBuilder('rbb')
+ if os.path.exists(options.complib):
+ compound_lib=conop.CompoundLib.Load(options.complib)
+ conop.SetDefaultLib(compound_lib)
+ io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(compound_lib)
home = os.getenv('HOME') or os.getenv('USERPROFILE')
_ostrc=os.path.join(home, '.ostrc')
diff --git a/modules/gui/src/file_loader.cc b/modules/gui/src/file_loader.cc
index 890dec0beeeb85f7e025229334435850a6d2b6ab..0c84be5731aa00e420ceac34a951997c0c8dc6af 100644
--- a/modules/gui/src/file_loader.cc
+++ b/modules/gui/src/file_loader.cc
@@ -252,7 +252,7 @@ gfx::GfxObjP FileLoader::TryLoadEntity(const QString& filename, io::EntityIOHand
mol::EntityHandle eh=mol::CreateEntity();
mol::XCSEditor xcs_lock=eh.EditXCS(mol::BUFFERED_EDIT);
handler->Import(eh,filename.toStdString());
- if(handler->RequiresBuilder()) {
+ if(handler->RequiresProcessor()) {
io::IOProfile& prof = io::IOProfileRegistry::Instance().GetDefault();
if (prof.processor) {
prof.processor->Process(eh);
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 38934cc7943df2c6d1cec5f40dd43c34485368e6..0db17e2cf70cd825732b2f0103a7f430859e9554 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -528,8 +528,7 @@ of the annotation available.
Since this function is at the moment mainly used to create biounits from
mmCIF files to be saved as PDBs, the function assumes that the
- :ref:`ChainType` properties are set correctly. :func:`ost.conop.ConnectAll`
- is used to derive connectivity.
+ :ref:`ChainType` properties are set correctly.
:param asu: Asymmetric unit to work on. Should be created from a mmCIF
file.
@@ -828,7 +827,7 @@ of the annotation available.
:type: :class:`str`
-.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
+.. LocalWords: cas isbn pubmed asu seqres conop casp COMPND OBSLTE
.. LocalWords: SPRSDE pdb func autofunction exptl attr pdbx oper conf spr dif
.. LocalWords: biounits biounit uniprot UNP seqs AddMMCifPDBChainTr cif asym
.. LocalWords: auth GetMMCifPDBChainTr AddPDBCMMCifhainTr GetPDBMMCifChainTr
diff --git a/modules/io/src/mol/entity_io_crd_handler.cc b/modules/io/src/mol/entity_io_crd_handler.cc
index d16358cc8029dd6b9dad17cf5e7beb039d159dd3..3d858fcc6243f21e7125234548e43e297892763c 100644
--- a/modules/io/src/mol/entity_io_crd_handler.cc
+++ b/modules/io/src/mol/entity_io_crd_handler.cc
@@ -346,8 +346,8 @@ bool CRDWriter::VisitAtom(const mol::AtomHandle& atom)
return true;
}
-/// \brief CHARMM file format requires builder
-bool EntityIOCRDHandler::RequiresBuilder() const
+/// \brief CHARMM file format requires processor
+bool EntityIOCRDHandler::RequiresProcessor() const
{
return true;
}
diff --git a/modules/io/src/mol/entity_io_crd_handler.hh b/modules/io/src/mol/entity_io_crd_handler.hh
index c0d625a804258e7bd8b16d547d228bf5589ed6d2..3781fcda4e3305307c7bf61b6fb65f38ed27736a 100644
--- a/modules/io/src/mol/entity_io_crd_handler.hh
+++ b/modules/io/src/mol/entity_io_crd_handler.hh
@@ -99,7 +99,7 @@ public:
const String& format="auto");
static bool ProvidesExport(const boost::filesystem::path& loc,
const String& format="auto");
- virtual bool RequiresBuilder() const;
+ virtual bool RequiresProcessor() const;
static String GetFormatName() { return String("Crd"); }
static String GetFormatDescription() { return String("CARD format file used by the Charmm software package"); }
diff --git a/modules/io/src/mol/entity_io_handler.hh b/modules/io/src/mol/entity_io_handler.hh
index c65137e185e017ad01ec1d629c1b4dd88b453c0c..709b0762317192d4c6488534b1a52d03f3c6fd56 100644
--- a/modules/io/src/mol/entity_io_handler.hh
+++ b/modules/io/src/mol/entity_io_handler.hh
@@ -57,7 +57,7 @@ public:
// export data from entity view to provided stream
virtual void Export(const mol::EntityView& ent,
std::ostream& stream) const=0;
- virtual bool RequiresBuilder() const=0;
+ virtual bool RequiresProcessor() const=0;
};
typedef boost::shared_ptr<EntityIOHandler> EntityIOHandlerP;
diff --git a/modules/io/src/mol/entity_io_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
index 3c68d9964323a2b37df8636320d797f88fb93751..ca9590169c4b69e2399183a6fade389665789184 100644
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ b/modules/io/src/mol/entity_io_mae_handler.cc
@@ -330,7 +330,7 @@ void MAEReader::parse_and_add_atom(mol::EntityHandle ent,
-bool EntityIOMAEHandler::RequiresBuilder() const
+bool EntityIOMAEHandler::RequiresProcessor() const
{
return true;
}
@@ -380,7 +380,6 @@ bool EntityIOMAEHandler::ProvidesExport(const boost::filesystem::path& loc,
mol::EntityHandle LoadMAE(const String& file_name)
{
- //conop::BuilderP builder = conop::Conopology::Instance().GetBuilder();
MAEReader reader(file_name);
mol::EntityHandle ent=mol::CreateEntity();
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
diff --git a/modules/io/src/mol/entity_io_mae_handler.hh b/modules/io/src/mol/entity_io_mae_handler.hh
index 8f09c375e7b3021073cc599ed524bda130c59900..7f923d3453ed60090a615b14fa2d44c20996d817 100644
--- a/modules/io/src/mol/entity_io_mae_handler.hh
+++ b/modules/io/src/mol/entity_io_mae_handler.hh
@@ -73,7 +73,7 @@ public:
const String& format="auto");
static bool ProvidesExport(const boost::filesystem::path& loc,
const String& format="auto");
- virtual bool RequiresBuilder() const;
+ virtual bool RequiresProcessor() const;
static String GetFormatName() { return String("Mae"); }
static String GetFormatDescription() { return String("MAEstro coordinate file format"); }
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.cc b/modules/io/src/mol/entity_io_mmcif_handler.cc
index 23e9ff3c52a1fd2652b1bbf7c1b7995eac487a11..a86d1dcebda7cc5ec73791d706b482bd6ecdb9e7 100644
--- a/modules/io/src/mol/entity_io_mmcif_handler.cc
+++ b/modules/io/src/mol/entity_io_mmcif_handler.cc
@@ -38,7 +38,7 @@ namespace ost { namespace io {
using boost::format;
-bool EntityIOMMCIFHandler::RequiresBuilder() const
+bool EntityIOMMCIFHandler::RequiresProcessor() const
{
return true;
}
diff --git a/modules/io/src/mol/entity_io_mmcif_handler.hh b/modules/io/src/mol/entity_io_mmcif_handler.hh
index 2fa262156d4867f665a8fc3f4d5ea8e71877f16f..e55a409b850f5ceae92f3b62830a8e895c0f4930 100644
--- a/modules/io/src/mol/entity_io_mmcif_handler.hh
+++ b/modules/io/src/mol/entity_io_mmcif_handler.hh
@@ -42,7 +42,7 @@ public:
const String& format="auto");
static bool ProvidesExport(const boost::filesystem::path& loc,
const String& format="auto");
- virtual bool RequiresBuilder() const;
+ virtual bool RequiresProcessor() const;
static String GetFormatName() { return String("mmCIF"); }
static String GetFormatDescription() {
diff --git a/modules/io/src/mol/entity_io_pdb_handler.cc b/modules/io/src/mol/entity_io_pdb_handler.cc
index fe70388346cf08c24c84bdb705774ec2cf4420b7..69e466a23b0c092aef483c7e1c62e18b719d2a2b 100644
--- a/modules/io/src/mol/entity_io_pdb_handler.cc
+++ b/modules/io/src/mol/entity_io_pdb_handler.cc
@@ -39,7 +39,7 @@ namespace ost { namespace io {
using boost::format;
-bool EntityIOPDBHandler::RequiresBuilder() const
+bool EntityIOPDBHandler::RequiresProcessor() const
{
return true;
}
diff --git a/modules/io/src/mol/entity_io_pdb_handler.hh b/modules/io/src/mol/entity_io_pdb_handler.hh
index 3ceea37f79a88fc7eac60a31e06e28adbcf93b4c..07bfca81e49714d6aaa5b5440820b30815baf1f0 100644
--- a/modules/io/src/mol/entity_io_pdb_handler.hh
+++ b/modules/io/src/mol/entity_io_pdb_handler.hh
@@ -45,7 +45,7 @@ public:
const String& format="auto");
static bool ProvidesExport(const boost::filesystem::path& loc,
const String& format="auto");
- virtual bool RequiresBuilder() const;
+ virtual bool RequiresProcessor() const;
static String GetFormatName() { return String("Pdb"); }
static String GetFormatDescription() { return String("Protein Data Bank file format"); }
diff --git a/modules/io/src/mol/entity_io_sdf_handler.cc b/modules/io/src/mol/entity_io_sdf_handler.cc
index 5a81405682952a05dd5452ddbae1c11e13af2fc7..31ba544b0214906993ae1fced35ebf1cbd6feffb 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.cc
+++ b/modules/io/src/mol/entity_io_sdf_handler.cc
@@ -29,7 +29,7 @@
namespace ost { namespace io {
-bool EntityIOSDFHandler::RequiresBuilder() const
+bool EntityIOSDFHandler::RequiresProcessor() const
{
return false;
}
diff --git a/modules/io/src/mol/entity_io_sdf_handler.hh b/modules/io/src/mol/entity_io_sdf_handler.hh
index 66333e8d3c687fea30ad870ae7218e01ec40a9ec..55c20fc9675ed0df36494b11c456e7e8e4b49e0b 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.hh
+++ b/modules/io/src/mol/entity_io_sdf_handler.hh
@@ -40,7 +40,7 @@ public:
static bool ProvidesExport(const boost::filesystem::path& loc,
const String& format="auto");
- virtual bool RequiresBuilder() const;
+ virtual bool RequiresProcessor() const;
static String GetFormatName() { return String("Sdf"); }
static String GetFormatDescription() { return String("Structure-data format from Molecular Design Limited"); }
diff --git a/modules/io/src/mol/load_entity.cc b/modules/io/src/mol/load_entity.cc
index c1322367cc6e188f4a51c4801e0278dc4b37fe95..98eea40f861a728340b8ad97b79997800bbd6119 100644
--- a/modules/io/src/mol/load_entity.cc
+++ b/modules/io/src/mol/load_entity.cc
@@ -43,7 +43,7 @@ void Import(mol::EntityHandle& eh, const String& filename, int flag)
LOG_DEBUG("running conopology");
- if(ent_io->RequiresBuilder()) {
+ if(ent_io->RequiresProcessor()) {
IOProfile& prof = IOProfileRegistry::Instance().GetDefault();
if (prof.processor) {
prof.processor->Process(eh);
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 111d797981ad92135fd7ac4d3320113e4d496f63..33e08b19af7b3ac3fd08eae0f6705c32c8b2d8f6 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -855,7 +855,7 @@ BOOST_AUTO_TEST_CASE(seqres_import)
char * ost_root=getenv("OST_ROOT");
if(!ost_root){
std::cout << "WARNING: skipping SEQRES import unit test. "
- << "Rule-based builder is required" << std::endl;
+ << "Rule-based processor is required" << std::endl;
return;
}
SetPrefixPath(ost_root);
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 9ae371699a9dba2da8da18ae5bca795951def935..4c4c7cf2c572a2cafa4318b55b827b4fe3827ed1 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -141,7 +141,7 @@ BOOST_AUTO_TEST_CASE(mmcif_convert_seqres)
char * ost_root=getenv("OST_ROOT");
if(!ost_root){
std::cout << "WARNING: skipping SEQRES import unit test. "
- << "Rule-based builder is required" << std::endl;
+ << "Rule-based processor is required" << std::endl;
return;
}
SetPrefixPath(ost_root);
@@ -404,7 +404,7 @@ BOOST_AUTO_TEST_CASE(mmcif_entity_poly_tests)
char * ost_root=getenv("OST_ROOT");
if(!ost_root){
std::cout << "WARNING: skipping SEQRES import unit test. "
- << "Rule-based builder is required" << std::endl;
+ << "Rule-based processor is required" << std::endl;
return;
}
SetPrefixPath(ost_root);
diff --git a/modules/seq/alg/pymod/renumber.py b/modules/seq/alg/pymod/renumber.py
index f715f0bd6f1ef9dbbc60b3afc316502a9d462398..092850f2a356c4b240f3afe9f42ebab730c60b70 100644
--- a/modules/seq/alg/pymod/renumber.py
+++ b/modules/seq/alg/pymod/renumber.py
@@ -45,7 +45,9 @@ def Renumber(seq_handle, sequence_number_with_attached_view=1):
if renumberingFlag == True:
err = 'Warning: %s residues have been renumbered!' %changed_residue_count
LogInfo(err)
- conop.ConnectAll(ent_n)
+
+ # FIXME: BZDNG-416
+ #conop.ConnectAll(ent_n)
return ent_n
elif isinstance(seq_handle, seq.AlignmentHandle):
@@ -80,6 +82,7 @@ def Renumber(seq_handle, sequence_number_with_attached_view=1):
if renumberingFlag == True:
err = 'Warning: %s residues have been renumbered!' %changed_residue_count
LogInfo(err)
- conop.ConnectAll(ent_n)
+ # FIXME: BZDNG-416
+ #conop.ConnectAll(ent_n)
return ent_n
diff --git a/scripts/init_cl.py b/scripts/init_cl.py
index 88068214d34d73573a89e1ed1808e9602187867b..e9251dc9b0363710c25f77606e737ae8979d1ff1 100644
--- a/scripts/init_cl.py
+++ b/scripts/init_cl.py
@@ -36,16 +36,16 @@ from ost import *
import ost
ost.SetPrefixPath(os.getenv('DNG_ROOT'))
-def _InitRuleBasedBuilder():
+
+def _InitRuleBasedProcessor():
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.SetDefaultLib(compound_lib)
io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(compound_lib)
-# switch to rule-based builder for high fidelity if compounds.chemlib is
-# available
-_InitRuleBasedBuilder()
+# switch to rule-based processor, if compound library is available
+_InitRuleBasedProcessor()
import os.path
HistoryFile=os.path.expanduser('~/.ost_history')