From 62feb1dae3b595d6d01d4eb153729aae7a0d3d04 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Wed, 25 Apr 2018 15:36:06 +0200
Subject: [PATCH] fix: SCHWED-3121 Remove structural checks from lDDTScorer
---
actions/ost-compare-structures | 12 ++---
modules/mol/alg/pymod/wrap_mol_alg.cc | 32 ++------------
modules/mol/alg/src/lddt.cc | 24 +++++-----
modules/mol/alg/src/local_dist_diff_test.cc | 49 +++------------------
modules/mol/alg/src/local_dist_diff_test.hh | 8 +---
5 files changed, 29 insertions(+), 96 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index b12ceedf5..405e8e208 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -740,12 +740,9 @@ def _Main():
"single_chain_lddt": list()
}
lddt_settings = lDDTSettings(
- bond_tolerance=opts.bond_tolerance,
- angle_tolerance=opts.angle_tolerance,
radius=opts.inclusion_radius,
sequence_separation=opts.sequence_separation,
sel="",
- structural_checks=False, # These are performed elsewhere
consistency_checks=False, # These are performed elsewhere
label="lddt")
ost.LogInfo("lDDT settings: ")
@@ -760,7 +757,8 @@ def _Main():
lddt_scorer.references[0].chains[0].GetName()
if skip_score:
ost.LogInfo(
- " --> Skipping single chain lDDT because consistency check failed")
+ " --> Skipping single chain lDDT because "
+ "consistency check failed")
lddt_results["single_chain_lddt"].append({
"status": "FAILURE",
"error": "Consistency check failed.",
@@ -824,7 +822,8 @@ def _Main():
# perform oligo lddt scoring
if skip_score:
ost.LogInfo(
- " --> Skipping oligomeric lDDT because consistency check failed")
+ " --> Skipping oligomeric lDDT because consistency "
+ "check failed")
lddt_results["oligo_lddt"] = {
"status": "FAILURE",
"error": "Consistency check failed.",
@@ -847,7 +846,8 @@ def _Main():
"global_score": 0.0}
if skip_score:
ost.LogInfo(
- " --> Skipping weighted lDDT because consistency check failed")
+ " --> Skipping weighted lDDT because consistency "
+ "check failed")
lddt_results["weighted_lddt"] = {
"status": "FAILURE",
"error": "Consistency check failed.",
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 419dc0427..449a03543 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -123,18 +123,6 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
object self = args[0];
args = tuple(args.slice(1,_));
- Real bond_tolerance = 12.0;
- if(kwargs.contains("bond_tolerance")){
- bond_tolerance = extract<Real>(kwargs["bond_tolerance"]);
- kwargs["bond_tolerance"].del();
- }
-
- Real angle_tolerance = 12.0;
- if(kwargs.contains("angle_tolerance")){
- angle_tolerance = extract<Real>(kwargs["angle_tolerance"]);
- kwargs["angle_tolerance"].del();
- }
-
Real radius = 15.0;
if(kwargs.contains("radius")){
radius = extract<Real>(kwargs["radius"]);
@@ -153,12 +141,6 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
kwargs["sel"].del();
}
- bool structural_checks = true;
- if(kwargs.contains("structural_checks")){
- structural_checks = extract<bool>(kwargs["structural_checks"]);
- kwargs["structural_checks"].del();
- }
-
bool consistency_checks = true;
if(kwargs.contains("consistency_checks")){
consistency_checks = extract<bool>(kwargs["consistency_checks"]);
@@ -190,18 +172,15 @@ object lDDTSettingsInitWrapper(tuple args, dict kwargs){
std::stringstream ss;
ss << "Invalid keywords observed when setting up lDDTSettings! ";
ss << "Or did you pass the same keyword twice? ";
- ss << "Valid keywords are: bond_tolerance, angle_tolerance, radius, ";
- ss << "sequence_separation, sel, parameter_file_path, structural_checks, ";
+ ss << "Valid keywords are: radius, ";
+ ss << "sequence_separation, sel, parameter_file_path, ";
ss << "consistency_checks, cutoffs, label!";
throw std::invalid_argument(ss.str());
}
- return self.attr("__init__")(bond_tolerance,
- angle_tolerance,
- radius,
+ return self.attr("__init__")(radius,
sequence_separation,
sel,
- structural_checks,
consistency_checks,
cutoffs,
label);
@@ -405,17 +384,14 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
class_<mol::alg::lDDTSettings>("lDDTSettings", no_init)
.def("__init__", raw_function(lDDTSettingsInitWrapper))
- .def(init<Real, Real, Real, int, String, bool, bool, std::vector<Real>&, String>())
+ .def(init<Real, int, String, 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("bond_tolerance", &mol::alg::lDDTSettings::bond_tolerance)
- .def_readwrite("angle_tolerance", &mol::alg::lDDTSettings::angle_tolerance)
.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("structural_checks", &mol::alg::lDDTSettings::structural_checks)
.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 19c24c018..6fb921093 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -158,7 +158,9 @@ int main (int argc, char **argv)
String version = OST_VERSION_STRING;
lDDTSettings settings;
String parameter_file_path;
- settings.structural_checks=false;
+ bool structural_checks = false;
+ Real bond_tolerance = 12.0;
+ Real angle_tolerance = 12.0;
// creates the required loading profile
IOProfile profile;
// parses options
@@ -215,7 +217,7 @@ int main (int argc, char **argv)
profile.calpha_only=true;
}
if (vm.count("structural-checks")) {
- settings.structural_checks=true;
+ structural_checks=true;
}
if (vm.count("ignore-consistency-checks")) {
settings.consistency_checks=false;
@@ -226,7 +228,7 @@ int main (int argc, char **argv)
if (vm.count("parameter-file")) {
parameter_file_path=vm["parameter-file"].as<String>();
- } else if (settings.structural_checks==true) {
+ } else if (structural_checks==true) {
std::cout << "Please specify a stereo-chemical parameter file" << std::endl;
exit(-1);
}
@@ -249,10 +251,10 @@ int main (int argc, char **argv)
Logger::Instance().PushVerbosityLevel(ost_verbosity_level);
if (vm.count("bond_tolerance")) {
- settings.bond_tolerance=vm["bond_tolerance"].as<Real>();
+ bond_tolerance=vm["bond_tolerance"].as<Real>();
}
if (vm.count("angle_tolerance")) {
- settings.angle_tolerance=vm["angle_tolerance"].as<Real>();
+ angle_tolerance=vm["angle_tolerance"].as<Real>();
}
if (vm.count("inclusion_radius")) {
settings.radius=vm["inclusion_radius"].as<Real>();
@@ -305,7 +307,7 @@ int main (int argc, char **argv)
// prints out parameters used in the lddt calculation
std::cout << "Verbosity level: " << verbosity_level << std::endl;
settings.PrintParameters();
- if (settings.structural_checks) {
+ if (structural_checks) {
LOG_INFO("Log entries format:");
LOG_INFO("BOND INFO FORMAT: Chain Residue ResNum Bond Min Max Observed Z-score Status");
LOG_INFO("ANGLE INFO FORMAT: Chain Residue ResNum Angle Min Max Observed Z-score Status");
@@ -334,7 +336,7 @@ int main (int argc, char **argv)
String filestring=BFPathToString(pathstring);
std::cout << "File: " << files[i] << std::endl;
- if (settings.structural_checks) {
+ if (structural_checks) {
StereoChemicalProps stereochemical_params;
try {
stereochemical_params = ost::io::ReadStereoChemicalPropsFile(parameter_file_path, true);
@@ -348,8 +350,8 @@ int main (int argc, char **argv)
stereochemical_params.bond_table,
stereochemical_params.angle_table,
stereochemical_params.nonbonded_table,
- settings.bond_tolerance,
- settings.angle_tolerance);
+ bond_tolerance,
+ angle_tolerance);
} catch (std::exception& e) {
std::cout << e.what() << std::endl;
exit(-1);
@@ -362,8 +364,8 @@ int main (int argc, char **argv)
// prints the residue-by-residue statistics
std::vector<lDDTLocalScore> local_scores;
EntityView outview = model.GetChainList()[0].Select("peptide=true");
- local_scores = GetlDDTPerResidueStats(outview, glob_dist_list, settings.structural_checks, settings.label);
- PrintlDDTPerResidueStats(local_scores, settings.structural_checks, settings.cutoffs.size());
+ local_scores = GetlDDTPerResidueStats(outview, glob_dist_list, structural_checks, settings.label);
+ PrintlDDTPerResidueStats(local_scores, structural_checks, settings.cutoffs.size());
}
return 0;
}
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index 4e4545f45..597e84c85 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -403,12 +403,9 @@ StereoChemicalProps::StereoChemicalProps(
nonbonded_table(init_nonbonded_table),
is_valid(true) {}
-lDDTSettings::lDDTSettings(): bond_tolerance(12.0),
- angle_tolerance(12.0),
- radius(15.0),
+lDDTSettings::lDDTSettings(): radius(15.0),
sequence_separation(0),
sel(""),
- structural_checks(true),
consistency_checks(true),
label("localldt") {
cutoffs.push_back(0.5);
@@ -417,41 +414,24 @@ lDDTSettings::lDDTSettings(): bond_tolerance(12.0),
cutoffs.push_back(4.0);
}
-lDDTSettings::lDDTSettings(Real init_bond_tolerance,
- Real init_angle_tolerance,
- Real init_radius,
+lDDTSettings::lDDTSettings(Real init_radius,
int init_sequence_separation,
String init_sel,
- bool init_structural_checks,
bool init_consistency_checks,
std::vector<Real>& init_cutoffs,
- String init_label):
- bond_tolerance(init_bond_tolerance),
- angle_tolerance(init_angle_tolerance),
+ String init_label):
radius(init_radius),
sequence_separation(init_sequence_separation),
sel(init_sel),
- structural_checks(init_structural_checks),
consistency_checks(init_consistency_checks),
cutoffs(init_cutoffs),
label(init_label) {}
std::string lDDTSettings::ToString() {
std::ostringstream rep;
- if (structural_checks) {
- rep << "Stereo-chemical and steric clash checks: On \n";
- } else {
- rep << "Stereo-chemical and steric clash checks: Off \n";
- }
-
rep << "Inclusion Radius: " << radius << "\n";
rep << "Sequence separation: " << sequence_separation << "\n";
rep << "Cutoffs: " << vector_to_string(cutoffs) << "\n";
-
- if (structural_checks) {
- rep << "Tolerance in stddevs for bonds: " << bond_tolerance << "\n";
- rep << "Tolerance in stddevs for angles: " << angle_tolerance << "\n";
- }
rep << "Residue properties label: " << label << "\n";
return rep.str();
@@ -547,25 +527,6 @@ void lDDTScorer::_Init(){
_global_score = -1.0;
CleanlDDTReferences(references_view);
_PrepareGlobalRDMap();
- if (settings.structural_checks) {
- if (!stereochemical_params.is_valid) {
- throw std::runtime_error(
- "Please provide stereochemical_params to enable structural_checks.");
- }
- try {
- CheckStructure(model_view,
- stereochemical_params.bond_table,
- stereochemical_params.angle_table,
- stereochemical_params.nonbonded_table,
- settings.bond_tolerance,
- settings.angle_tolerance);
- } catch (std::exception& e) {
- std::cout << e.what() << std::endl;
- std::stringstream errstr;
- errstr << "Structure check failed: " << e.what();
- throw std::runtime_error(errstr.str());
- }
- }
if (settings.consistency_checks) {
_CheckConsistency();
}
@@ -604,7 +565,7 @@ void lDDTScorer::PrintPerResidueStats(){
_GetLocallDDT();
}
PrintlDDTPerResidueStats(_local_scores,
- settings.structural_checks,
+ false,
settings.cutoffs.size());
}
@@ -684,7 +645,7 @@ void lDDTScorer::_GetLocallDDT(){
}
_local_scores = GetlDDTPerResidueStats(model_view,
glob_dist_list,
- settings.structural_checks,
+ false, // do not print structural checks
settings.label);
_has_local_scores = true;
}
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index c48627203..5e3a8d4df 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -41,23 +41,17 @@ struct StereoChemicalProps
};
struct lDDTSettings {
- Real bond_tolerance;
- Real angle_tolerance;
Real radius;
int sequence_separation;
String sel;
- bool structural_checks;
bool consistency_checks;
std::vector<Real> cutoffs;
String label;
lDDTSettings();
- lDDTSettings(Real init_bond_tolerance,
- Real init_angle_tolerance,
- Real init_radius,
+ lDDTSettings(Real init_radius,
int init_sequence_separation,
String init_sel,
- bool init_structural_checks,
bool init_consistency_checks,
std::vector<Real>& init_cutoffs,
String init_label);
--
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