diff --git a/modules/mol/alg/doc/lddt_deprecated.rst b/modules/mol/alg/doc/lddt_deprecated.rst
index c0228cbb3ad6cfb3a42259ea26a04ca56d084e02..4293046fd7e9359808d394a815366b1696277453 100644
--- a/modules/mol/alg/doc/lddt_deprecated.rst
+++ b/modules/mol/alg/doc/lddt_deprecated.rst
@@ -444,104 +444,104 @@ lDDT (deprecated)
:type cutoffs_length: int
-
-
-
-.. class:: lDDTScorer(reference, model, settings)
-
- Object to compute lDDT scores using :func:`LocalDistDiffTest` as in
- `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_.
-
- Example usage.
-
- .. code:: python
-
- #! /bin/env python
- """Run lDDT from within script."""
- from ost.io import LoadPDB
- from ost.mol.alg import (CleanlDDTReferences,
- lDDTSettings, lDDTScorer)
-
- ent_full = LoadPDB('3ia3', remote=True)
- model_view = ent_full.Select('cname=A')
- references = [ent_full.Select('cname=C')]
-
- #
- # Initialize settings with default parameters and print them
- settings = lDDTSettings()
- settings.PrintParameters()
-
- # Clean up references
- CleanlDDTReferences(references)
- #
- # Calculate lDDT
- scorer = lDDTScorer(references=references, model=model_view, settings=settings)
- print("Global score:", scorer.global_score)
- scorer.PrintPerResidueStats()
-
- :param references: Sets :attr:`references`
- :param model: Sets :attr:`model`
- :param settings: Sets :attr:`settings`
-
- .. attribute:: references
-
- A list of reference structures.
-
- :type: list(:class:`~ost.mol.EntityView`)
-
- .. attribute:: model
-
- A model structure.
-
- :type: :class:`~ost.mol.EntityView`
-
- .. attribute:: settings
-
- Settings used to calculate lDDT.
-
- :type: :class:`~ost.mol.alg.lDDTSettings`
-
- .. attribute:: global_dist_list
-
- Global map of residue properties.
-
- :type: :class:`~ost.mol.alg.GlobalRDMap`
-
- .. attribute:: global_score
-
- Global lDDT score. It is calculated as :attr:`conserved_contacts` divided
- by :attr:`total_contacts`.
-
- :type: float
-
- .. attribute:: conserved_contacts
-
- Number of conserved distances.
-
- :type: int
-
- .. attribute:: total_contacts
-
- Number of total distances.
-
- :type:
-
- .. attribute:: local_scores
-
- Local scores. For each of the residue lDDT is it is calculated as residue
- conserved contacts divided by residue total contacts.
-
- :type: list(:class:`~ost.mol.alg.lDDTLocalScore`)
-
- .. attribute:: is_valid
-
- Is the calculated score valid?
-
- :type: bool
-
- .. method:: PrintPerResidueStats
-
- Print per-residue statistics.
+.. The deprecated lDDTScorer is commented out to not collide with the new
+.. and shiny lDDTScorer class
+..
+.. .. class:: lDDTScorer(reference, model, settings)
+..
+.. Object to compute lDDT scores using :func:`LocalDistDiffTest` as in
+.. `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_.
+..
+.. Example usage.
+..
+.. .. code:: python
+..
+.. #! /bin/env python
+.. """Run lDDT from within script."""
+.. from ost.io import LoadPDB
+.. from ost.mol.alg import (CleanlDDTReferences,
+.. lDDTSettings, lDDTScorer)
+..
+.. ent_full = LoadPDB('3ia3', remote=True)
+.. model_view = ent_full.Select('cname=A')
+.. references = [ent_full.Select('cname=C')]
+..
+.. #
+.. # Initialize settings with default parameters and print them
+.. settings = lDDTSettings()
+.. settings.PrintParameters()
+..
+.. # Clean up references
+.. CleanlDDTReferences(references)
+.. #
+.. # Calculate lDDT
+.. scorer = lDDTScorer(references=references, model=model_view, settings=settings)
+.. print("Global score:", scorer.global_score)
+.. scorer.PrintPerResidueStats()
+..
+.. :param references: Sets :attr:`references`
+.. :param model: Sets :attr:`model`
+.. :param settings: Sets :attr:`settings`
+..
+.. .. attribute:: references
+..
+.. A list of reference structures.
+..
+.. :type: list(:class:`~ost.mol.EntityView`)
+..
+.. .. attribute:: model
+..
+.. A model structure.
+..
+.. :type: :class:`~ost.mol.EntityView`
+..
+.. .. attribute:: settings
+..
+.. Settings used to calculate lDDT.
+..
+.. :type: :class:`~ost.mol.alg.lDDTSettings`
+..
+.. .. attribute:: global_dist_list
+..
+.. Global map of residue properties.
+..
+.. :type: :class:`~ost.mol.alg.GlobalRDMap`
+..
+.. .. attribute:: global_score
+..
+.. Global lDDT score. It is calculated as :attr:`conserved_contacts` divided
+.. by :attr:`total_contacts`.
+..
+.. :type: float
+..
+.. .. attribute:: conserved_contacts
+..
+.. Number of conserved distances.
+..
+.. :type: int
+..
+.. .. attribute:: total_contacts
+..
+.. Number of total distances.
+..
+.. :type:
+..
+.. .. attribute:: local_scores
+..
+.. Local scores. For each of the residue lDDT is it is calculated as residue
+.. conserved contacts divided by residue total contacts.
+..
+.. :type: list(:class:`~ost.mol.alg.lDDTLocalScore`)
+..
+.. .. attribute:: is_valid
+..
+.. Is the calculated score valid?
+..
+.. :type: bool
+..
+.. .. method:: PrintPerResidueStats
+..
+.. Print per-residue statistics.
.. class:: UniqueAtomIdentifier(chain, residue_number, residue_name, atom_name)
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index e1b80398615764e98b67b912ae0e75758b24c136..8d57c57dfc06b634d82705c4a879085c89edc3a9 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -172,6 +172,9 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
label);
}
+/*
+lDDTScorer is commented out to not collide with the new lDDTScorer class
+that lives in Python
object lDDTScorerInitWrapper(tuple args, dict kwargs){
object self = args[0];
@@ -217,7 +220,7 @@ object lDDTScorerInitWrapper(tuple args, dict kwargs){
model,
settings);
}
-
+*/
void clean_lddt_references_wrapper(const list& reference_list)
{
@@ -265,6 +268,10 @@ list get_lddt_per_residue_stats_wrapper(mol::EntityView& model,
return local_scores_list;
}
+/*
+lDDTScorer is commented out to not collide with the new lDDTScorer class
+that lives in Python
+
list get_local_scores_wrapper(mol::alg::lDDTScorer& scorer) {
std::vector<mol::alg::lDDTLocalScore> scores = scorer.GetLocalScores();
list local_scores_list;
@@ -282,7 +289,7 @@ list get_references_wrapper(mol::alg::lDDTScorer& scorer) {
}
return local_references_list;
}
-
+*/
void print_lddt_per_residue_stats_wrapper(list& scores, bool structural_checks, int cutoffs_size){
int scores_length = boost::python::extract<int>(scores.attr("__len__")());
@@ -395,6 +402,9 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
.def_readwrite("conserved_dist", &mol::alg::lDDTLocalScore::conserved_dist)
.def_readwrite("total_dist", &mol::alg::lDDTLocalScore::total_dist);
+ /*
+ lDDTScorer is commented out to not collide with the new lDDTScorer class
+ that lives in Python
class_<mol::alg::lDDTScorer>("lDDTScorer", no_init)
.def("__init__", raw_function(lDDTScorerInitWrapper))
.def(init<std::vector<mol::EntityView>&, mol::EntityView&, mol::alg::lDDTSettings&>())
@@ -406,6 +416,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
.def_readonly("model", &mol::alg::lDDTScorer::model_view)
.add_property("references", &get_references_wrapper)
.add_property("is_valid", &mol::alg::lDDTScorer::IsValid);
+ */
class_<mol::alg::StereoChemicalProps>("StereoChemicalProps",
init<mol::alg::StereoChemicalParams&,