From 91f2c7eeb35755150a77f4603adc4e11d316077f Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Tue, 12 Jun 2012 11:27:52 +0200
Subject: [PATCH] Removed default clashing distances
---
modules/mol/alg/pymod/wrap_mol_alg.cc | 4 ++--
modules/mol/alg/src/filter_clashes.cc | 18 ++++++++++--------
modules/mol/alg/src/filter_clashes.hh | 4 ++--
modules/mol/alg/src/ldt.cc | 11 ++---------
4 files changed, 16 insertions(+), 21 deletions(-)
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 9d3877de7..2ea296b6e 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -67,7 +67,7 @@ ost::mol::alg::ClashingDistances fill_clashing_distances_wrapper (const list& st
stereo_chemical_props_file_vector[i] = boost::python::extract<char const*>(stereo_chemical_props_file[i]);
}
- return ost::mol::alg::FillClashingDistances(stereo_chemical_props_file_vector,min_default_distance,min_distance_tolerance);
+ return ost::mol::alg::FillClashingDistances(stereo_chemical_props_file_vector);
}
ost::mol::alg::GlobalRDMap create_distance_list_from_multiple_references(const list& ref_list, const list& cutoff_list, Real max_dist)
@@ -118,7 +118,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
(arg("source"), arg("sel"), arg("ref_view"),arg("begin")=0, arg("end")=-1));
- class_<mol::alg::ClashingDistances> ("ClashingDistances" ,init<Real,Real>())
+ class_<mol::alg::ClashingDistances> ("ClashingDistances",init<>())
.def("SetClashingDistance",&mol::alg::ClashingDistances::SetClashingDistance)
.def("GetClashingDistance",&mol::alg::ClashingDistances::GetClashingDistance)
.def("GetMaxAdjustedDistance",&mol::alg::ClashingDistances::GetMaxAdjustedDistance)
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 0d3a8f809..e4758a86d 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -98,7 +98,9 @@ std::pair<Real,Real> ClashingDistances::GetClashingDistance(const String& ele1,c
String key=stkey.str();
std::map <String,std::pair<float,float> >::const_iterator find_ci= min_distance_.find(key);
if (find_ci == min_distance_.end()) {
- return std::make_pair<Real,Real> (default_min_distance_,default_min_distance_tolerance_);
+ std::stringstream serr;
+ serr << "Entry for distance " << stkey << " not found in the parameter table";
+ throw Error(serr.str());
}
return find_ci->second;
}
@@ -253,9 +255,9 @@ StereoChemicalParams FillStereoChemicalParams(const String& header, std::vector<
return table;
};
-ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_props_file, Real min_default_distance, Real min_distance_tolerance)
+ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_props_file)
{
- ClashingDistances table(min_default_distance,min_distance_tolerance);
+ ClashingDistances table;
bool found=false;
std::vector<String>::const_iterator line_iter=stereo_chemical_props_file.begin();
while (line_iter!=stereo_chemical_props_file.end()) {
@@ -271,7 +273,7 @@ ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_pro
std::vector<StringRef> second_line_str_vec = second_line_string_ref.split();
if (second_line_str_vec.size()!=3) {
std::cout << "The number of elements in one of the lines is wrong" << std::endl;
- return ClashingDistances(min_default_distance,min_distance_tolerance);
+ return ClashingDistances();
}
String item = second_line_str_vec[0].str();
@@ -282,19 +284,19 @@ ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_pro
value=static_cast<Real>(parse_value.second);
} else {
std::cout << "One of the distance values is not a number" << std::endl;
- return ClashingDistances(min_default_distance,min_distance_tolerance);
+ return ClashingDistances();
};
if (parse_stddev.first==true) {
stddev=static_cast<Real>(parse_stddev.second);
} else {
std::cout << "One of the tolerance values is not a number" << std::endl;
- return ClashingDistances(min_default_distance,min_distance_tolerance);
+ return ClashingDistances();
}
StringRef itemsr(item.data(),item.length());
std::vector<StringRef> eles = itemsr.split('-');
if (itemsr.size() != 3) {
std::cout << "One of the strings describing the interacting atoms has the wrong format" << std::endl;
- return ClashingDistances(min_default_distance,min_distance_tolerance);
+ return ClashingDistances();
}
String ele1=eles[0].str();
String ele2=eles[1].str();
@@ -312,7 +314,7 @@ ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_pro
}
if (found==false) {
std::cout << "Could not find the relevant section in the stereo-chemical parameter file" << std::endl;
- return ClashingDistances(min_default_distance,min_distance_tolerance);
+ return ClashingDistances();
}
return table;
}
diff --git a/modules/mol/alg/src/filter_clashes.hh b/modules/mol/alg/src/filter_clashes.hh
index 5d64fc230..5984a05f5 100644
--- a/modules/mol/alg/src/filter_clashes.hh
+++ b/modules/mol/alg/src/filter_clashes.hh
@@ -28,7 +28,7 @@ class ClashingDistances
{
public:
- ClashingDistances(Real default_dist, Real tolerance): default_min_distance_(default_dist), default_min_distance_tolerance_(tolerance), valid_flag_(true) {}
+ ClashingDistances(): valid_flag_(true) {}
void SetClashingDistance(const String& ele1,const String& ele2, Real min_distance, Real tolerance);
std::pair<Real,Real> GetClashingDistance(const String& ele1,const String& ele2) const;
Real GetMaxAdjustedDistance() const;
@@ -64,7 +64,7 @@ private:
};
-ClashingDistances DLLEXPORT_OST_MOL_ALG FillClashingDistances(std::vector<String>& stereo_chemical_props_file, Real min_default_distance, Real min_distance_tolerance);
+ClashingDistances DLLEXPORT_OST_MOL_ALG FillClashingDistances(std::vector<String>& stereo_chemical_props_file);
StereoChemicalParams DLLEXPORT_OST_MOL_ALG FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file);
EntityView DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityView& ent,
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
index 23f11fd5f..a4e5f15e6 100644
--- a/modules/mol/alg/src/ldt.cc
+++ b/modules/mol/alg/src/ldt.cc
@@ -98,9 +98,7 @@ std::pair<int,int> compute_coverage (const EntityView& v,const GlobalRDMap& glob
int main (int argc, char **argv)
{
- String version = "Beta - 2012-01-17";
- Real min_default_distance = 1.5;
- Real min_distance_tolerance = 0.0;
+ String version = "Beta - 2012-05-21";
Real bond_tolerance = 8.0;
Real angle_tolerance = 8.0;
Real radius=15.0;
@@ -121,7 +119,6 @@ int main (int argc, char **argv)
("verbosity,v", po::value<int>(), "verbosity level")
("bond_tolerance,b", po::value<Real>(), "tolerance in stddev for bonds")
("angle_tolerance,a", po::value<Real>(), "tolerance in stddev for angles")
- ("default_clash,m", po::value<Real>(), "clashing distance for unknown atom types")
("inclusion_radius,r", po::value<Real>(), "distance inclusion radius")
("files", po::value< std::vector<String> >(), "input file(s)")
("reference",po::value<String>(),"reference(s)")
@@ -184,9 +181,6 @@ int main (int argc, char **argv)
if (vm.count("angle_tolerance")) {
angle_tolerance=vm["angle_tolerance"].as<Real>();
}
- if (vm.count("default_clash")) {
- min_default_distance=vm["default_clash"].as<Real>();
- }
if (vm.count("inclusion_radius")) {
radius=vm["inclusion_radius"].as<Real>();
}
@@ -209,7 +203,6 @@ int main (int argc, char **argv)
std::cout << "Parameter filename: " << parameter_filename << std::endl;
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");
@@ -276,7 +269,7 @@ int main (int argc, char **argv)
exit(-1);
}
- ClashingDistances nonbonded_table = FillClashingDistances(stereo_chemical_props,min_default_distance,min_distance_tolerance);
+ ClashingDistances nonbonded_table = FillClashingDistances(stereo_chemical_props);
if (nonbonded_table.IsEmpty()) {
std::cout << "Error reading the Clashing section of the stereo-chemical parameter file." << std::endl;
--
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