From 52e9c14891d77fb08f1dc3efbccee9a16705facf Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 13 Aug 2018 20:18:10 +0200
Subject: [PATCH] SCHWED-3566: Fixed inconsistent handling of sidechain and
backbone issues.
---
modules/mol/alg/src/filter_clashes.cc | 17 +++++++++++------
modules/mol/alg/src/lddt.cc | 22 +++++++++++-----------
2 files changed, 22 insertions(+), 17 deletions(-)
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 18ffc17ba..e0d2bee05 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -421,10 +421,15 @@ std::pair<EntityView,StereoChemistryInfo> CheckStereoChemistry(const EntityView&
remove_sc=true;
if (always_remove_bb==true) {
remove_bb=true;
- }
- String name=atom.GetName();
- if (name=="CA" || name=="N" || name=="O" || name=="C") {
- remove_bb=true;
+ } else {
+ // we need to check both atom names since the order is random!
+ // -> for angles and clashes this is not needed
+ String name1 = atom.GetName();
+ String name2 = other_atom.GetName();
+ if (name1=="CA" || name1=="N" || name1=="O" || name1=="C" ||
+ name2=="CA" || name2=="N" || name2=="O" || name2=="C") {
+ remove_bb=true;
+ }
}
} else {
LOG_VERBOSE("BOND:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << bond_str << " " << min_length << " " << max_length << " " << blength << " " << zscore << " " << "PASS")
@@ -629,7 +634,7 @@ std::pair<EntityView,ClashingInfo> FilterClashes(const EntityView& ent, const Cl
if (remove_bb) {
LOG_VERBOSE("ACTION: removing whole residue " << res);
- res.SetBoolProp("steric_clash",true);
+ res.SetBoolProp("steric_clash_backbone", true);
continue;
}
if (remove_sc) {
@@ -642,7 +647,7 @@ std::pair<EntityView,ClashingInfo> FilterClashes(const EntityView& ent, const Cl
filtered.AddAtom(atom);
}
}
- res.SetBoolProp("steric_clash",true);
+ res.SetBoolProp("steric_clash_sidechain", true);
continue;
}
filtered.AddResidue(res, ViewAddFlag::INCLUDE_ATOMS);
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 4a9c095f5..a64f5bb19 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -361,17 +361,17 @@ 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.");
- }
- }
- }
+ 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
LocalDistDiffTest(model_view, ref_list, glob_dist_list, settings);
--
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