diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 795d4f96e2613fcb50c66abcde51ffe91075f724..51de4cca63a8b7f794d4a671ca5cff1b779d7cdb 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -685,18 +685,20 @@ Local Distance Test scores (lDDT, DRMSD)
Dictionary-like object containing the list of interatomic distances that
originate from a single residue to be checked during a run of the Local
Distance Difference Test algorithm
- (key = pair of :class:`UniqueAtomIdentifier`, value = pair of floats)
+ (key = pair of :class:`UniqueAtomIdentifier`, value = pair of floats
+ representing min and max distance observed in the structures used to build
+ the map).
.. class:: GlobalRDMap
- Dictionary-like object containing all the :class:`~ost.mol.alg.ResidueRDMap` objects related to residues of a single structure
- (key = :class:`~ost.mol.ResNum`, value = :class:`ResidueRDMap`)
+ Dictionary-like object containing all the :class:`~ost.mol.alg.ResidueRDMap` objects related to all the residues
+ (key = :class:`~ost.mol.ResNum`, value = :class:`ResidueRDMap`).
.. function:: PrintResidueRDMap(residue_distance_list)
Prints to standard output all the distances contained in a
- :class:`~ost.mol.alg.ResidueRDMap` object
+ :class:`~ost.mol.alg.ResidueRDMap` object.
.. function:: PrintGlobalRDMap(global_distance_list)
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index e0d2bee05a80d0959b3528776d501151f2b388c0..8623d8779342b089366d6d43bf835cdc1c51377b 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -404,19 +404,28 @@ std::pair<EntityView,StereoChemistryInfo> CheckStereoChemistry(const EntityView&
}
if (other_atom.GetHashCode() > atom.GetHandle().GetHashCode()) {
Real blength = bond.GetLength();
- String bond_str = bond_string(atom,other_atom);
- std::pair<Real,Real> length_stddev = bond_table.GetParam(bond_str,residue_str);
+ String bond_str = bond_string(atom, other_atom);
+ std::pair<Real,Real> length_stddev = bond_table.GetParam(bond_str, residue_str);
Real ref_length = length_stddev.first;
Real ref_stddev = length_stddev.second;
Real min_length = ref_length - bond_tolerance*ref_stddev;
Real max_length = ref_length + bond_tolerance*ref_stddev;
Real zscore = (blength - ref_length)/ref_stddev;
if (blength < min_length || blength > max_length) {
- LOG_INFO("BOND:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << bond_str << " " << min_length << " " << max_length << " " << blength << " " << zscore << " " << "FAIL")
+ LOG_INFO("BOND:" << " " << res.GetChain() << " "
+ << res.GetName() << " " << res.GetNumber() << " "
+ << bond_str << " " << min_length << " " << max_length
+ << " " << blength << " " << zscore << " " << "FAIL")
bad_bond_count++;
- UniqueAtomIdentifier atom_ui(atom.GetResidue().GetChain().GetName(),atom.GetResidue().GetNumber(),atom.GetResidue().GetName(),atom.GetName());
- UniqueAtomIdentifier other_atom_ui(other_atom.GetResidue().GetChain().GetName(),other_atom.GetResidue().GetNumber(),other_atom.GetResidue().GetName(),other_atom.GetName());
- StereoChemicalBondViolation bond_v(atom_ui,other_atom_ui,blength,std::make_pair(min_length,max_length));
+ UniqueAtomIdentifier atom_ui(atom.GetResidue().GetChain().GetName(),
+ atom.GetResidue().GetNumber(),
+ atom.GetResidue().GetName(), atom.GetName());
+ UniqueAtomIdentifier other_atom_ui(other_atom.GetResidue().GetChain().GetName(),
+ other_atom.GetResidue().GetNumber(),
+ other_atom.GetResidue().GetName(),
+ other_atom.GetName());
+ StereoChemicalBondViolation bond_v(atom_ui, other_atom_ui, blength,
+ std::make_pair(min_length, max_length));
bond_violation_list.push_back(bond_v);
remove_sc=true;
if (always_remove_bb==true) {
@@ -432,7 +441,10 @@ std::pair<EntityView,StereoChemistryInfo> CheckStereoChemistry(const EntityView&
}
}
} else {
- LOG_VERBOSE("BOND:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << bond_str << " " << min_length << " " << max_length << " " << blength << " " << zscore << " " << "PASS")
+ LOG_VERBOSE("BOND:" << " " << res.GetChain() << " "
+ << res.GetName() << " " << res.GetNumber() << " "
+ << bond_str << " " << min_length << " " << max_length
+ << " " << blength << " " << zscore << " " << "PASS")
}
bond_count++;
running_sum_zscore_bonds+=zscore;
@@ -486,12 +498,25 @@ std::pair<EntityView,StereoChemistryInfo> CheckStereoChemistry(const EntityView&
Real max_width = ref_width + angle_tolerance*ref_stddev;
Real zscore = (awidth - ref_width)/ref_stddev;
if (awidth < min_width || awidth > max_width) {
- LOG_INFO("ANGLE:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << angle_str << " " << min_width << " " << max_width << " " << awidth << " " << zscore << " " << "FAIL")
+ LOG_INFO("ANGLE:" << " " << res.GetChain() << " "
+ << res.GetName() << " " << res.GetNumber() << " "
+ << angle_str << " " << min_width << " " << max_width
+ << " " << awidth << " " << zscore << " " << "FAIL")
bad_angle_count++;
- UniqueAtomIdentifier atom1_ui(atom1.GetResidue().GetChain().GetName(),atom1.GetResidue().GetNumber(),atom1.GetResidue().GetName(),atom1.GetName());
- UniqueAtomIdentifier atom_ui(atom.GetResidue().GetChain().GetName(),atom.GetResidue().GetNumber(),atom.GetResidue().GetName(),atom.GetName());
- UniqueAtomIdentifier atom2_ui(atom2.GetResidue().GetChain().GetName(),atom2.GetResidue().GetNumber(),atom2.GetResidue().GetName(),atom2.GetName());
- StereoChemicalAngleViolation angle_v(atom1_ui,atom_ui,atom2_ui,awidth,std::make_pair(min_width,max_width));
+ UniqueAtomIdentifier atom1_ui(atom1.GetResidue().GetChain().GetName(),
+ atom1.GetResidue().GetNumber(),
+ atom1.GetResidue().GetName(),
+ atom1.GetName());
+ UniqueAtomIdentifier atom_ui(atom.GetResidue().GetChain().GetName(),
+ atom.GetResidue().GetNumber(),
+ atom.GetResidue().GetName(),
+ atom.GetName());
+ UniqueAtomIdentifier atom2_ui(atom2.GetResidue().GetChain().GetName(),
+ atom2.GetResidue().GetNumber(),
+ atom2.GetResidue().GetName(),
+ atom2.GetName());
+ StereoChemicalAngleViolation angle_v(atom1_ui,atom_ui,atom2_ui,awidth,
+ std::make_pair(min_width,max_width));
angle_violation_list.push_back(angle_v);
remove_sc=true;
if (always_remove_bb==true) {
@@ -502,7 +527,10 @@ std::pair<EntityView,StereoChemistryInfo> CheckStereoChemistry(const EntityView&
remove_bb=true;
}
} else {
- LOG_VERBOSE("ANGLE:" << " " << res.GetChain() << " " << res.GetName() << " " << res.GetNumber() << " " << angle_str << " " << min_width << " " << max_width << " " << awidth << " " << zscore << " " << "PASS")
+ LOG_VERBOSE("ANGLE:" << " " << res.GetChain() << " "
+ << res.GetName() << " " << res.GetNumber() << " "
+ << angle_str << " " << min_width << " " << max_width
+ << " " << awidth << " " << zscore << " " << "PASS")
}
angle_count++;
running_sum_zscore_angles+=zscore;
@@ -610,7 +638,14 @@ std::pair<EntityView,ClashingInfo> FilterClashes(const EntityView& ent, const Cl
Real threshold=distance-tolerance;
if (d<threshold*threshold) {
- LOG_INFO(atom.GetResidue().GetChain() << " " << atom.GetResidue().GetName() << " " << atom.GetResidue().GetNumber() << " " << atom.GetName() << " " << atom2.GetResidue().GetChain() << " " << atom2.GetResidue().GetName() << " " << atom2.GetResidue().GetNumber() << " " << atom2.GetName() << " " << threshold << " " << sqrt(d) << " " << sqrt(d)-threshold << " " << "FAIL")
+ LOG_INFO("CLASH:" << " " << atom.GetResidue().GetChain() << " "
+ << atom.GetResidue().GetName() << " "
+ << atom.GetResidue().GetNumber() << " " << atom.GetName()
+ << " " << atom2.GetResidue().GetChain() << " "
+ << atom2.GetResidue().GetName() << " "
+ << atom2.GetResidue().GetNumber() << " " << atom2.GetName()
+ << " " << threshold << " " << sqrt(d) << " "
+ << sqrt(d)-threshold << " " << "FAIL")
bad_distance_count++;
UniqueAtomIdentifier atom_ui(atom.GetResidue().GetChain().GetName(),atom.GetResidue().GetNumber(),atom.GetResidue().GetName(),atom.GetName());
UniqueAtomIdentifier atom2_ui(atom2.GetResidue().GetChain().GetName(),atom2.GetResidue().GetNumber(),atom2.GetResidue().GetName(),atom2.GetName());
@@ -626,7 +661,14 @@ std::pair<EntityView,ClashingInfo> FilterClashes(const EntityView& ent, const Cl
remove_bb=true;
}
} else {
- LOG_VERBOSE("CLASH:" << " " << atom.GetResidue().GetChain() << " " << atom.GetResidue().GetName() << " " << atom.GetResidue().GetNumber() << " " << atom.GetName() << " " << atom2.GetResidue().GetChain() << " " << atom2.GetResidue().GetNumber() << " " << atom2.GetResidue().GetName() << " " << atom2.GetName() << " " << threshold << " " << sqrt(d) << " " << sqrt(d)-threshold << " " << "PASS")
+ LOG_VERBOSE("CLASH:" << " " << atom.GetResidue().GetChain() << " "
+ << atom.GetResidue().GetName() << " "
+ << atom.GetResidue().GetNumber() << " " << atom.GetName()
+ << " " << atom2.GetResidue().GetChain() << " "
+ << atom2.GetResidue().GetName() << " "
+ << atom2.GetResidue().GetNumber() << " " << atom2.GetName()
+ << " " << threshold << " " << sqrt(d) << " "
+ << sqrt(d)-threshold << " " << "PASS")
}
distance_count++;
}
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index a64f5bb192d5abab6777b750786858d1fd477d16..dbe122d80d0b13e250edaec00291ea268bfa2bc6 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -311,11 +311,14 @@ int main (int argc, char **argv)
settings.PrintParameters();
if (structural_checks) {
LOG_INFO("Log entries format:");
+ // verbosity level/format must match filter_clashes::CheckStereoChemistry
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 Observed Difference Status");
+ // verbosity level/format must match filter_clashes::FilterClashes
+ LOG_INFO("CLASH INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 Threshold Observed Difference Status");
}
- LOG_INFO("LDDT INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 ModelDist TargetDist Difference Tolerance Status");
+ // verbosity level/format must match local_dist_diff_test::calc_overlap1
+ LOG_VERBOSE("LDDT INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 ModelDist TargetDistMin TargetDistMax Tolerance Status");
// error if the reference structure is empty
if (glob_dist_list.size()==0) {
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index c52bf115666962310aef3de44b126eb5dd300e9b..1182dc375e8c44c01685cc55341ea35269c776fd 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -27,7 +27,8 @@ String vector_to_string(std::vector<Real> vec) {
// helper function
bool within_tolerance(Real mdl_dist, const std::pair<Real,Real>& values, Real tol)
{
-
+ // this considers min & max distance observed in all reference structures
+ // -> for single reference case values.first and values.second are the same
return (values.first-tol)<=mdl_dist && (values.second+tol)>=mdl_dist;
}
@@ -82,10 +83,15 @@ std::pair<long int, long int> calc_overlap1(const ResidueRDMap& res_distance_lis
Real tol = * tol_list_it;
if (within_tolerance(mdl_dist,values,tol)) {
if (log) {
- LOG_VERBOSE("lddt:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
- << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
- << mdl_dist << " " << values.first << " " << values.second << " " << tol << " " << "PASS")
- }
+ LOG_VERBOSE("LDDT:" << " " << av1.GetResidue().GetChain() << " "
+ << av1.GetResidue().GetName() << " "
+ << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " "
+ << av2.GetResidue().GetName() << " "
+ << av2.GetResidue().GetNumber() << " " << av2.GetName()
+ << " " << mdl_dist << " " << values.first << " "
+ << values.second << " " << tol << " " << "PASS")
+ }
overlap.first+=1;
if (!only_fixed) {
overlap_list[rindex1].first+=1;
@@ -93,10 +99,15 @@ std::pair<long int, long int> calc_overlap1(const ResidueRDMap& res_distance_lis
}
} else {
if (log) {
- LOG_VERBOSE("lddt:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
- << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
- << mdl_dist << " " << values.first << " " << values.second << " " << tol << " " << "FAIL");
- }
+ LOG_VERBOSE("LDDT:" << " " << av1.GetResidue().GetChain() << " "
+ << av1.GetResidue().GetName() << " "
+ << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " "
+ << av2.GetResidue().GetName() << " "
+ << av2.GetResidue().GetNumber() << " " << av2.GetName()
+ << " " << mdl_dist << " " << values.first << " "
+ << values.second << " " << tol << " " << "FAIL");
+ }
break;
}
}