diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc index c3bcc8484adaee9ec3068b34945d6f2cc3915b94..b2bf4fbcf16b2efa35b33a0c998f859a16aa5301 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 97b00f21ef3b80d24382c4875cef72f1b167a683..abb23ee6317d4c38d998d479aba38fbc518ca7a8 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 5441f681b2349797eb6b0a38266d63285dbe7616..b77fb904899896d1d26e122de5b43d7a52d1e779 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") + } } } }