From 34c84be97051c68b232707d91225af12609dd937 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Thu, 26 Apr 2018 14:26:50 +0200
Subject: [PATCH] fix: SCHWED-3121 Remove StereoChemicalProps from lDDTScorer
---
modules/mol/alg/pymod/wrap_mol_alg.cc | 13 ++-------
modules/mol/alg/src/local_dist_diff_test.cc | 31 ++++++---------------
modules/mol/alg/src/local_dist_diff_test.hh | 8 ------
3 files changed, 11 insertions(+), 41 deletions(-)
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 59cb8b2e2..1c42af212 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -205,24 +205,17 @@ object lDDTScorerInitWrapper(tuple args, dict kwargs){
throw std::invalid_argument("'settings' argument is required");
}
- ost::mol::alg::StereoChemicalProps stereochemical_params;
- if(kwargs.contains("stereochemical_params")){
- stereochemical_params = extract<ost::mol::alg::StereoChemicalProps>(kwargs["stereochemical_params"]);
- kwargs["stereochemical_params"].del();
- }
-
if(len(kwargs) > 0){
std::stringstream ss;
ss << "Invalid keywords observed when setting up lDDTScorer! ";
ss << "Or did you pass the same keyword twice? ";
- ss << "Valid keywords are: settings and stereochemical_params!";
+ ss << "Valid keywords are: references, model and settings!";
throw std::invalid_argument(ss.str());
}
return self.attr("__init__")(reference_list_vector,
model,
- settings,
- stereochemical_params);
+ settings);
}
@@ -396,7 +389,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
class_<mol::alg::lDDTScorer>("lDDTScorer", no_init)
.def("__init__", raw_function(lDDTScorerInitWrapper))
- .def(init<std::vector<mol::EntityView>&, mol::EntityView&, mol::alg::lDDTSettings&, mol::alg::StereoChemicalProps&>())
+ .def(init<std::vector<mol::EntityView>&, mol::EntityView&, mol::alg::lDDTSettings&>())
.add_property("global_score", &mol::alg::lDDTScorer::GetGlobalScore)
.add_property("conserved_contacts", &mol::alg::lDDTScorer::GetNumConservedContacts)
.add_property("total_contacts", &mol::alg::lDDTScorer::GetNumTotalContacts)
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index bc7b18ab8..fa4eededf 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -498,31 +498,16 @@ lDDTScorer::lDDTScorer(std::vector<EntityView>& init_references,
references_view(init_references),
model_view(init_model)
{
- _Init();
- }
-
-lDDTScorer::lDDTScorer(std::vector<EntityView>& init_references,
- ost::mol::EntityView& init_model,
- lDDTSettings& init_settings,
- StereoChemicalProps& init_stereochemical_params):
- settings(init_settings),
- references_view(init_references),
- model_view(init_model),
- stereochemical_params(init_stereochemical_params) {
- _Init();
+ _score_calculated = false;
+ _score_valid = false;
+ _has_local_scores = false;
+ _num_cons_con = -1;
+ _num_tot_con = -1;
+ _global_score = -1.0;
+ CleanlDDTReferences(references_view);
+ _PrepareGlobalRDMap();
}
-void lDDTScorer::_Init(){
- _score_calculated = false;
- _score_valid = false;
- _has_local_scores = false;
- _num_cons_con = -1;
- _num_tot_con = -1;
- _global_score = -1.0;
- CleanlDDTReferences(references_view);
- _PrepareGlobalRDMap();
-}
-
Real lDDTScorer::GetGlobalScore(){
if (!_score_calculated) {
_ComputelDDT();
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 8c9aa5f59..b32d66301 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -89,15 +89,10 @@ class lDDTScorer
EntityView model_view;
std::vector<EntityView> references_view;
GlobalRDMap glob_dist_list;
- StereoChemicalProps stereochemical_params;
lDDTScorer(std::vector<EntityView>& init_references,
ost::mol::EntityView& init_model,
lDDTSettings& init_settings);
- lDDTScorer(std::vector<EntityView>& init_references,
- ost::mol::EntityView& init_model,
- lDDTSettings& init_settings,
- StereoChemicalProps& init_stereochemical_params);
Real GetGlobalScore();
std::vector<lDDTLocalScore> GetLocalScores();
int GetNumConservedContacts(); // number of conserved distances in the model
@@ -116,7 +111,6 @@ class lDDTScorer
int _num_tot_con;
Real _global_score;
std::vector<lDDTLocalScore> _local_scores;
- void _Init();
void _ComputelDDT();
void _GetLocallDDT();
void _PrepareGlobalRDMap();
@@ -270,5 +264,3 @@ void DLLEXPORT_OST_MOL_ALG PrintlDDTPerResidueStats(std::vector<lDDTLocalScore>&
}}}
#endif
-
-
--
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