From ee157e4ff10564b9ea78767c766535126d3d11c3 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Wed, 25 Apr 2018 16:39:41 +0200
Subject: [PATCH] fix: SCHWED-3121 Remove selection from lDDTScorer
---
actions/ost-compare-structures | 1 -
modules/mol/alg/pymod/wrap_mol_alg.cc | 12 ++----------
modules/mol/alg/src/lddt.cc | 9 +++++----
modules/mol/alg/src/local_dist_diff_test.cc | 21 ---------------------
modules/mol/alg/src/local_dist_diff_test.hh | 3 ---
5 files changed, 7 insertions(+), 39 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 405e8e208..a23841c4f 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -742,7 +742,6 @@ def _Main():
lddt_settings = lDDTSettings(
radius=opts.inclusion_radius,
sequence_separation=opts.sequence_separation,
- sel="",
consistency_checks=False, # These are performed elsewhere
label="lddt")
ost.LogInfo("lDDT settings: ")
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 449a03543..44a316ea7 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -135,12 +135,6 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
kwargs["sequence_separation"].del();
}
- String sel = "";
- if(kwargs.contains("sel")){
- sel = extract<String>(kwargs["sel"]);
- kwargs["sel"].del();
- }
-
bool consistency_checks = true;
if(kwargs.contains("consistency_checks")){
consistency_checks = extract<bool>(kwargs["consistency_checks"]);
@@ -173,14 +167,13 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
ss << "Invalid keywords observed when setting up lDDTSettings! ";
ss << "Or did you pass the same keyword twice? ";
ss << "Valid keywords are: radius, ";
- ss << "sequence_separation, sel, parameter_file_path, ";
+ ss << "sequence_separation, parameter_file_path, ";
ss << "consistency_checks, cutoffs, label!";
throw std::invalid_argument(ss.str());
}
return self.attr("__init__")(radius,
sequence_separation,
- sel,
consistency_checks,
cutoffs,
label);
@@ -384,14 +377,13 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
class_<mol::alg::lDDTSettings>("lDDTSettings", no_init)
.def("__init__", raw_function(lDDTSettingsInitWrapper))
- .def(init<Real, int, String, bool, std::vector<Real>&, String>())
+ .def(init<Real, int, bool, std::vector<Real>&, String>())
.def("ToString", &mol::alg::lDDTSettings::ToString)
.def("PrintParameters", &mol::alg::lDDTSettings::PrintParameters)
.def("__repr__", &mol::alg::lDDTSettings::ToString)
.def("__str__", &mol::alg::lDDTSettings::ToString)
.def_readwrite("radius", &mol::alg::lDDTSettings::radius)
.def_readwrite("sequence_separation", &mol::alg::lDDTSettings::sequence_separation)
- .def_readwrite("sel", &mol::alg::lDDTSettings::sel)
.def_readwrite("consistency_checks", &mol::alg::lDDTSettings::consistency_checks)
.def_readwrite("cutoffs", &mol::alg::lDDTSettings::cutoffs)
.def_readwrite("label", &mol::alg::lDDTSettings::label);
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 6fb921093..bd592bc12 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -161,6 +161,7 @@ int main (int argc, char **argv)
bool structural_checks = false;
Real bond_tolerance = 12.0;
Real angle_tolerance = 12.0;
+ String sel;
// creates the required loading profile
IOProfile profile;
// parses options
@@ -168,7 +169,7 @@ int main (int argc, char **argv)
po::options_description desc("Options");
desc.add_options()
("calpha,c", "consider only calpha atoms")
- ("sel,s", po::value<String>(&settings.sel)->default_value(""), "selection performed on reference structure")
+ ("sel,s", po::value<String>(&sel)->default_value(""), "selection performed on reference structure")
("tolerant,t", "fault tolerant mode")
("structural-checks,f", "perform stereo-chemical and clash checks")
("ignore-consistency-checks,x", "ignore residue name consistency checks")
@@ -279,10 +280,10 @@ int main (int argc, char **argv)
if (!ref) {
exit(-1);
}
- if (settings.sel != ""){
- std::cout << "Performing \"" << settings.sel << "\" selection on reference " << ref_filename << std::endl;
+ if (sel != ""){
+ std::cout << "Performing \"" << sel << "\" selection on reference " << ref_filename << std::endl;
try {
- ref_list.push_back(ref.Select(settings.sel));
+ ref_list.push_back(ref.Select(sel));
} catch (const ost::mol::QueryError& e) {
std::cerr << "Provided selection argument failed." << std::endl << e.GetFormattedMessage() << std::endl;
exit(-1);
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index 597e84c85..31d198191 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -405,7 +405,6 @@ StereoChemicalProps::StereoChemicalProps(
lDDTSettings::lDDTSettings(): radius(15.0),
sequence_separation(0),
- sel(""),
consistency_checks(true),
label("localldt") {
cutoffs.push_back(0.5);
@@ -416,13 +415,11 @@ lDDTSettings::lDDTSettings(): radius(15.0),
lDDTSettings::lDDTSettings(Real init_radius,
int init_sequence_separation,
- String init_sel,
bool init_consistency_checks,
std::vector<Real>& init_cutoffs,
String init_label):
radius(init_radius),
sequence_separation(init_sequence_separation),
- sel(init_sel),
consistency_checks(init_consistency_checks),
cutoffs(init_cutoffs),
label(init_label) {}
@@ -573,24 +570,6 @@ std::vector<EntityView> lDDTScorer::GetReferences(){
return references_view;
}
-void lDDTScorer::_PrepareReferences(std::vector<EntityHandle>& references){
- for (unsigned int i = 0; i < references.size(); i++) {
- if (settings.sel != ""){
- std::cout << "Performing \"" << settings.sel << "\" selection on reference " << references[i].GetName() << std::endl;
- try {
- references_view.push_back(references[i].Select(settings.sel));
- } catch (const ost::mol::QueryError& e) {
- std::stringstream errstr;
- errstr << "Provided selection argument failed." << std::endl << e.GetFormattedMessage();
- throw std::runtime_error(errstr.str());
- }
- }
- else {
- references_view.push_back(references[i].CreateFullView());
- }
- }
-}
-
void lDDTScorer::_PrepareGlobalRDMap(){
glob_dist_list = PreparelDDTGlobalRDMap(references_view,
settings.cutoffs,
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 5e3a8d4df..364b65951 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -43,7 +43,6 @@ struct StereoChemicalProps
struct lDDTSettings {
Real radius;
int sequence_separation;
- String sel;
bool consistency_checks;
std::vector<Real> cutoffs;
String label;
@@ -51,7 +50,6 @@ struct lDDTSettings {
lDDTSettings();
lDDTSettings(Real init_radius,
int init_sequence_separation,
- String init_sel,
bool init_consistency_checks,
std::vector<Real>& init_cutoffs,
String init_label);
@@ -124,7 +122,6 @@ class lDDTScorer
void _ComputelDDT();
void _GetLocallDDT();
void _CheckConsistency();
- void _PrepareReferences(std::vector<EntityHandle>& references);
void _PrepareGlobalRDMap();
};
--
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