From 336f5a660aa0ec51dcddeee317c803854bcce860 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Thu, 26 Apr 2018 09:11:16 +0200
Subject: [PATCH] fix: SCHWED-3121 Remove consistency check from scorer
---
actions/ost-compare-structures | 1 -
modules/mol/alg/pymod/wrap_mol_alg.cc | 12 ++-------
modules/mol/alg/src/lddt.cc | 16 +++++++++++-
modules/mol/alg/src/local_dist_diff_test.cc | 29 +--------------------
modules/mol/alg/src/local_dist_diff_test.hh | 3 ---
5 files changed, 18 insertions(+), 43 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index a23841c4f..554c24a8b 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,
- consistency_checks=False, # These are performed elsewhere
label="lddt")
ost.LogInfo("lDDT settings: ")
ost.LogInfo(str(lddt_settings).rstrip())
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 44a316ea7..59cb8b2e2 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();
}
- bool consistency_checks = true;
- if(kwargs.contains("consistency_checks")){
- consistency_checks = extract<bool>(kwargs["consistency_checks"]);
- kwargs["consistency_checks"].del();
- }
-
std::vector<Real> cutoffs;
if(kwargs.contains("cutoffs")){
list cutoff_list = extract<list>(kwargs["cutoffs"]);
@@ -168,13 +162,12 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
ss << "Or did you pass the same keyword twice? ";
ss << "Valid keywords are: radius, ";
ss << "sequence_separation, parameter_file_path, ";
- ss << "consistency_checks, cutoffs, label!";
+ ss << "cutoffs, label!";
throw std::invalid_argument(ss.str());
}
return self.attr("__init__")(radius,
sequence_separation,
- consistency_checks,
cutoffs,
label);
}
@@ -377,14 +370,13 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
class_<mol::alg::lDDTSettings>("lDDTSettings", no_init)
.def("__init__", raw_function(lDDTSettingsInitWrapper))
- .def(init<Real, int, bool, std::vector<Real>&, String>())
+ .def(init<Real, int, 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("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 bd592bc12..dfb239ed7 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -159,6 +159,7 @@ int main (int argc, char **argv)
lDDTSettings settings;
String parameter_file_path;
bool structural_checks = false;
+ bool ignore_consistency_checks = false;
Real bond_tolerance = 12.0;
Real angle_tolerance = 12.0;
String sel;
@@ -221,7 +222,7 @@ int main (int argc, char **argv)
structural_checks=true;
}
if (vm.count("ignore-consistency-checks")) {
- settings.consistency_checks=false;
+ ignore_consistency_checks=true;
}
if (vm.count("tolerant")) {
profile.fault_tolerant=true;
@@ -359,6 +360,19 @@ int main (int argc, char **argv)
}
}
+ // Check consistency
+ for (std::vector<EntityView>::const_iterator ref_list_it = ref_list.begin();
+ ref_list_it != ref_list.end(); ++ref_list_it) {
+ bool cons_check = ResidueNamesMatch(model_view,*ref_list_it, ignore_consistency_checks);
+ if (cons_check==false) {
+ if (ignore_consistency_checks==false) {
+ throw std::runtime_error("Residue names in model and in reference structure(s) are inconsistent.");
+ } else {
+ LOG_WARNING("Residue names in model and in reference structure(s) are inconsistent.");
+ }
+ }
+ }
+
// computes the lddt score
Real lddt = LocalDistDiffTest(model_view, ref_list, glob_dist_list, settings);
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index 31d198191..bc7b18ab8 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),
- consistency_checks(true),
label("localldt") {
cutoffs.push_back(0.5);
cutoffs.push_back(1.0);
@@ -415,12 +414,10 @@ lDDTSettings::lDDTSettings(): radius(15.0),
lDDTSettings::lDDTSettings(Real init_radius,
int init_sequence_separation,
- bool init_consistency_checks,
std::vector<Real>& init_cutoffs,
String init_label):
radius(init_radius),
sequence_separation(init_sequence_separation),
- consistency_checks(init_consistency_checks),
cutoffs(init_cutoffs),
label(init_label) {}
@@ -524,9 +521,6 @@ void lDDTScorer::_Init(){
_global_score = -1.0;
CleanlDDTReferences(references_view);
_PrepareGlobalRDMap();
- if (settings.consistency_checks) {
- _CheckConsistency();
- }
}
Real lDDTScorer::GetGlobalScore(){
@@ -581,16 +575,6 @@ bool lDDTScorer::IsValid(){
return _score_valid;
}
-void lDDTScorer::_CheckConsistency(){
- for (std::vector<EntityView>::const_iterator ref_list_it = references_view.begin();
- ref_list_it != references_view.end(); ++ref_list_it) {
- bool cons_check = ResidueNamesMatch(model_view, *ref_list_it, true);
- if (cons_check == false) {
- throw std::runtime_error("Residue names in model and in reference structure(s) are inconsistent.");
- }
- }
-}
-
void lDDTScorer::_ComputelDDT(){
std::pair<int,int> cov = ComputeCoverage(model_view,glob_dist_list);
if (cov.second == -1) {
@@ -769,17 +753,6 @@ Real LocalDistDiffTest(const EntityView& v,
std::vector<EntityView>& ref_list,
const GlobalRDMap& glob_dist_list,
lDDTSettings& settings) {
- for (std::vector<EntityView>::const_iterator ref_list_it = ref_list.begin();
- ref_list_it != ref_list.end(); ++ref_list_it) {
- bool cons_check = ResidueNamesMatch(v,*ref_list_it,settings.consistency_checks);
- if (cons_check==false) {
- if (settings.consistency_checks==true) {
- throw std::runtime_error("Residue names in model and in reference structure(s) are inconsistent.");
- } else {
- LOG_WARNING("Residue names in model and in reference structure(s) are inconsistent.");
- }
- }
- }
std::pair<int,int> cov = ComputeCoverage(v,glob_dist_list);
if (cov.second == -1) {
@@ -981,7 +954,7 @@ std::vector<lDDTLocalScore> GetlDDTPerResidueStats(EntityView& model,
conserved_dist=ritv.GetIntProp(label+"_conserved");
total_dist=ritv.GetIntProp(label+"_total");
} else {
- std::cout << label << std::endl;
+ //std::cout << label << std::endl;
lddt_local = 0;
lddt_local_string="0.0000";
conserved_dist = 0;
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 364b65951..8c9aa5f59 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -43,14 +43,12 @@ struct StereoChemicalProps
struct lDDTSettings {
Real radius;
int sequence_separation;
- bool consistency_checks;
std::vector<Real> cutoffs;
String label;
lDDTSettings();
lDDTSettings(Real init_radius,
int init_sequence_separation,
- bool init_consistency_checks,
std::vector<Real>& init_cutoffs,
String init_label);
void PrintParameters();
@@ -121,7 +119,6 @@ class lDDTScorer
void _Init();
void _ComputelDDT();
void _GetLocallDDT();
- void _CheckConsistency();
void _PrepareGlobalRDMap();
};
--
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