From aaafb5d273c19377d43d73749fad68df55448220 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Tue, 3 Jan 2012 12:49:55 +0100
Subject: [PATCH] Added logging to the LDT code proper and moved format info to
the beginning of the log
---
modules/mol/alg/src/filter_clashes.cc | 3 ---
modules/mol/alg/src/ldt.cc | 5 +++++
modules/mol/alg/src/local_dist_test.cc | 9 ++++++++-
3 files changed, 13 insertions(+), 4 deletions(-)
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index c3bcc8484..b2bf4fbcf 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -147,8 +147,6 @@ void StereoChemicalParams::PrintAllParameters() const
EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParams& bond_table, const StereoChemicalParams& angle_table, Real bond_tolerance, Real angle_tolerance, bool always_remove_bb)
{
LOG_INFO("Checking stereo-chemistry")
- 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")
EntityView filtered=ent.CreateEmptyView();
ResidueViewList residues=ent.GetResidueList();
for (ResidueViewList::iterator i=residues.begin(), e=residues.end(); i!=e; ++i) {
@@ -289,7 +287,6 @@ EntityView CheckStereoChemistry(const EntityHandle& ent, const StereoChemicalPar
EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_distances, bool always_remove_bb)
{
LOG_INFO("Filtering non-bonded clashes")
- LOG_INFO("CLASH INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "Observed" << " " << "Difference" << " " << "Status")
EntityView filtered=ent.CreateEmptyView();
ResidueViewList residues=ent.GetResidueList();
for (ResidueViewList::iterator
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
index 97b00f21e..abb23ee63 100644
--- a/modules/mol/alg/src/ldt.cc
+++ b/modules/mol/alg/src/ldt.cc
@@ -316,6 +316,11 @@ int main (int argc, char **argv)
std::cout << "Tolerance in stddevs for bonds: " << bond_tolerance << std::endl;
std::cout << "Tolerance in stddevs for angles: " << angle_tolerance << std::endl;
std::cout << "Clashing distance for unknown atom types: " << min_default_distance << std::endl;
+ 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");
+ LOG_INFO("CLASH INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "Observed" << " " << "Difference" << " " << "Status");
+ LOG_INFO("LDT INFO FORMAT:" << " " << "Chain1" << " " << "Residue1" << " " << "ResNum1" << " " << "Atom1" << " " << "Chain2" << " " << "Residue2" << " " << "ResNum2" << " " << "Atom2" << " " << "Min" << " " << "ModelDist" << " " << "TargetDist" << " " << "Difference" << " " << "Tolerance" << " " << "Status");
}
for (size_t i=0; i<files.size(); ++i) {
EntityHandle model=load(files[i], profile);
diff --git a/modules/mol/alg/src/local_dist_test.cc b/modules/mol/alg/src/local_dist_test.cc
index 5441f681b..b77fb9048 100644
--- a/modules/mol/alg/src/local_dist_test.cc
+++ b/modules/mol/alg/src/local_dist_test.cc
@@ -106,10 +106,17 @@ std::pair<Real, Real> calc_overlap1(ResidueView ref_res,
Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
if (std::abs(mdl_dist-ref_dist)<tol) {
+ LOG_VERBOSE("CLASH:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetNumber() << " " << av2.GetResidue().GetName() << " " << av2.GetName() << " "
+ << mdl_dist << " " << ref_dist << " " << mdl_dist-ref_dist << " " << tol << " " << "PASS")
overlap.first+=1;
overlap_list[ref_res.GetIndex()].first+=1.0;
overlap_list[aj->GetResidue().GetIndex()].first+=1.0;
- }
+ } else {
+ LOG_INFO("CLASH:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetNumber() << " " << av2.GetResidue().GetName() << " " << av2.GetName() << " "
+ << mdl_dist << " " << ref_dist << " " << mdl_dist-ref_dist << " " << tol << " " << "FAIL")
+ }
}
}
}
--
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