diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index e0792e93ee64ec6038451cad5a283a5c5c12144c..c88d99db8690af8efafc44a896f1cd017d03ff19 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -20,6 +20,7 @@ star_parser.cc
mmcif_reader.cc
mmcif_info.cc
pdb_str.cc
+stereochemical_params_reader.cc
PARENT_SCOPE
)
@@ -47,5 +48,6 @@ surface_io_handler.hh
load_surface.hh
surface_io_msms_handler.hh
pdb_str.hh
+stereochemical_params_reader.hh
PARENT_SCOPE
)
diff --git a/modules/io/src/mol/stereochemical_params_reader.cc b/modules/io/src/mol/stereochemical_params_reader.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e934177436ea4ca49f977144f2b7b3dd4081d01a
--- /dev/null
+++ b/modules/io/src/mol/stereochemical_params_reader.cc
@@ -0,0 +1,64 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <boost/filesystem/fstream.hpp>
+#include <ost/platform.hh>
+#include <ost/mol/alg/filter_clashes.hh>
+#include <ost/io/stereochemical_params_reader.hh>
+
+
+namespace {
+ std::vector<String> ReadStereoChemicalFile(const String& filename){
+ boost::filesystem::path loc(filename);
+ boost::filesystem::ifstream infile(loc);
+ if (!infile) {
+ std::stringstream serr;
+ serr << "Could not find " << filename;
+ throw ost::Error(serr.str());
+ }
+ std::vector<String> stereo_chemical_props;
+ String line;
+ while (std::getline(infile, line))
+ {
+ std::stringstream line_stream(line);
+ stereo_chemical_props.push_back(line);
+ }
+
+ return stereo_chemical_props;
+ }
+}
+
+namespace ost { namespace io {
+
+StereoChemicalParamsReader::StereoChemicalParamsReader() {
+ filename = ost::GetSharedDataPath() + "/stereo_chemical_propsd.txt";
+}
+
+StereoChemicalParamsReader::StereoChemicalParamsReader(const String& init_filename): filename(init_filename) {}
+
+void StereoChemicalParamsReader::Read(bool check) {
+ std::vector<String> stereo_chemical_props = ReadStereoChemicalFile(filename);
+ // Bonds
+ bond_table = ost::mol::alg::FillStereoChemicalParams("Bond", stereo_chemical_props, check);
+ // Angles
+ angle_table = ost::mol::alg::FillStereoChemicalParams("Angle", stereo_chemical_props, check);
+ // Not bonded
+ nonbonded_table = ost::mol::alg::FillClashingDistances(stereo_chemical_props, check);
+}
+}} // ns
+
diff --git a/modules/io/src/mol/stereochemical_params_reader.hh b/modules/io/src/mol/stereochemical_params_reader.hh
new file mode 100644
index 0000000000000000000000000000000000000000..f8990f55268de150d6f17a28160f53e695781bfa
--- /dev/null
+++ b/modules/io/src/mol/stereochemical_params_reader.hh
@@ -0,0 +1,40 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_IO_STEREOCHEMICAL_PARAMS_READER_H
+#define OST_IO_STEREOCHEMICAL_PARAMS_READER_H
+
+#include <ost/io/module_config.hh>
+#include <ost/mol/alg/filter_clashes.hh>
+
+namespace ost { namespace io {
+
+struct StereoChemicalParamsReader {
+ String filename;
+ ost::mol::alg::StereoChemicalParams bond_table;
+ ost::mol::alg::StereoChemicalParams angle_table;
+ ost::mol::alg::ClashingDistances nonbonded_table;
+
+ StereoChemicalParamsReader();
+ StereoChemicalParamsReader(const String& filename);
+ void Read(bool check=false);
+};
+
+}} // ns
+
+#endif
\ No newline at end of file
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 690a10aff11a238a45663186ac6b98c3ace29db5..455d1e7dbd8114aeb7ef972cc50691de2e9a0e8c 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -201,7 +201,7 @@ bool StereoChemicalParams::IsEmpty() const
return false;
}
-StereoChemicalParams FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file)
+StereoChemicalParams FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file, bool check)
{
StereoChemicalParams table;
bool found=false;
@@ -276,11 +276,18 @@ StereoChemicalParams FillStereoChemicalParams(const String& header, std::vector<
if (found==false) {
std::cout << "Could not find the relevant section in the stereo-chemical parameter file" << std::endl;
return StereoChemicalParams();
- };
+ };
+ if (check) {
+ if (table.IsEmpty()) {
+ std::stringstream serr;
+ serr << "Error reading the " << header << " section of the stereo-chemical parameter file.";
+ throw ost::Error(serr.str());
+ }
+ }
return table;
};
-ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_props_file)
+ClashingDistances FillClashingDistances(std::vector<String>& stereo_chemical_props_file, bool check)
{
ClashingDistances table;
bool found=false;
@@ -340,7 +347,14 @@ 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();
- }
+ }
+ if (check) {
+ if (table.IsEmpty()) {
+ std::stringstream serr;
+ serr << "Error reading the Clashing section of the stereo-chemical parameter file.";
+ throw ost::Error(serr.str());
+ }
+ }
return table;
}
diff --git a/modules/mol/alg/src/filter_clashes.hh b/modules/mol/alg/src/filter_clashes.hh
index f53f123dc09922937382a5bb67502b0add7603c2..fe6d12c75a7303ec637e194d341831c1200ac4b0 100644
--- a/modules/mol/alg/src/filter_clashes.hh
+++ b/modules/mol/alg/src/filter_clashes.hh
@@ -244,13 +244,13 @@ private:
/// \brief Fills a list of reference clashing distances from the content of a parameter file
///
/// Requires a list of strings holding the contents of a parameter file, one line per string
-ClashingDistances DLLEXPORT_OST_MOL_ALG FillClashingDistances(std::vector<String>& stereo_chemical_props_file);
+ClashingDistances DLLEXPORT_OST_MOL_ALG FillClashingDistances(std::vector<String>& stereo_chemical_props_file, bool check=false);
/// \brief Fills a list of stereo-chemical statistics from the content of a parameter file
///
/// Requires a list of strings holding the contents of a parameter file, one line per string
/// The header can be 'Bonds' to read bond statistics or 'Angles' to read angle statistics
-StereoChemicalParams DLLEXPORT_OST_MOL_ALG FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file);
+StereoChemicalParams DLLEXPORT_OST_MOL_ALG FillStereoChemicalParams(const String& header, std::vector<String>& stereo_chemical_props_file, bool check=false);
/// \brief Filters a structure based on detected clashes between non bonded atoms. Entity version
///
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index dcde44f0f8111a01094e26da90ca84d0deb54731..406647f479ad8324d9f3486e300edd72235ad38a 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -32,6 +32,7 @@
#include <ost/mol/alg/filter_clashes.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/io_exception.hh>
+#include <ost/io/stereochemical_params_reader.hh>
#include <ost/conop/conop.hh>
#include <ost/conop/compound_lib.hh>
#include <ost/string_ref.hh>
@@ -390,74 +391,27 @@ int main (int argc, char **argv)
}
if (structural_checks) {
- // reads in parameter files
- boost::filesystem::path loc(parameter_filename);
- boost::filesystem::ifstream infile(loc);
- if (!infile) {
- std::cout << "Could not find " << parameter_filename << std::endl;
- exit(-1);
- }
- std::vector<String> stereo_chemical_props;
- String line;
- while (std::getline(infile, line))
- {
- std::stringstream line_stream(line);
- stereo_chemical_props.push_back(line);
- }
- StereoChemicalParams bond_table = FillStereoChemicalParams("Bond",stereo_chemical_props);
- if (bond_table.IsEmpty()) {
- std::cout << "Error reading the Bond section of the stereo-chemical parameter file." << std::endl;
- exit(-1);
- }
- StereoChemicalParams angle_table = FillStereoChemicalParams("Angle",stereo_chemical_props);
- if (angle_table.IsEmpty()) {
- std::cout << "Error reading the Angles section of the stereo-chemical parameter file." << std::endl;
- exit(-1);
- }
-
- 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;
- exit(-1);
- }
- // performs structural checks and filters the structure
- StereoChemistryInfo stereo_chemistry_info;
- try {
- std::pair<EntityView,StereoChemistryInfo> csc_result = alg::CheckStereoChemistry(v,bond_table,angle_table,bond_tolerance,angle_tolerance);
- v = csc_result.first;
- stereo_chemistry_info = csc_result.second;
- } catch (std::exception& e) {
- std::cout << "An error occurred during the structure quality checks, stage 1:" << std::endl;
+ StereoChemicalParamsReader stereochemical_params(parameter_filename);
+ try {
+ stereochemical_params.Read(true);
+ } catch (std::exception& e) {
std::cout << e.what() << std::endl;
exit(-1);
}
- std::cout << "Average Z-Score for bond lengths: " << std::fixed << std::setprecision(5) << stereo_chemistry_info.GetAvgZscoreBonds() << std::endl;
- std::cout << "Bonds outside of tolerance range: " << stereo_chemistry_info.GetBadBondCount() << " out of " << stereo_chemistry_info.GetBondCount() << std::endl;
- std::cout << "Bond\tAvg Length\tAvg zscore\tNum Bonds" << std::endl;
- std::map<String,BondLengthInfo> avg_bond_length_info = stereo_chemistry_info.GetAvgBondLengthInfo();
- for (std::map<String,BondLengthInfo>::const_iterator abli_it=avg_bond_length_info.begin();abli_it!=avg_bond_length_info.end();++abli_it) {
- String key = (*abli_it).first;
- BondLengthInfo bond_length_info = (*abli_it).second;
- std::cout << key << "\t" << std::fixed << std::setprecision(5) << std::left << std::setw(10) <<
- bond_length_info.GetAvgLength() << "\t" << std::left << std::setw(10) << bond_length_info.GetAvgZscore() << "\t" << bond_length_info.GetCount() << std::endl;
- }
- std::cout << "Average Z-Score angle widths: " << std::fixed << std::setprecision(5) << stereo_chemistry_info.GetAvgZscoreAngles() << std::endl;
- std::cout << "Angles outside of tolerance range: " << stereo_chemistry_info.GetBadAngleCount() << " out of " << stereo_chemistry_info.GetAngleCount() << std::endl;
- ClashingInfo clash_info;
+
try {
- std::pair<EntityView,ClashingInfo> fc_result = alg::FilterClashes(v,nonbonded_table);
- v = fc_result.first;
- clash_info = fc_result.second;
- } catch (std::exception& e) {
- std::cout << "An error occurred during the structure quality checks, stage 2:" << std::endl;
+ CheckStructure(v,
+ stereochemical_params.bond_table,
+ stereochemical_params.angle_table,
+ stereochemical_params.nonbonded_table,
+ bond_tolerance,
+ angle_tolerance);
+ } catch (std::exception& e) {
std::cout << e.what() << std::endl;
exit(-1);
}
- std::cout << clash_info.GetClashCount() << " non-bonded short-range distances shorter than tolerance distance" << std::endl;
- std::cout << "Distances shorter than tolerance are on average shorter by: " << std::fixed << std::setprecision(5) << clash_info.GetAverageOffset() << std::endl;
-
}
+
if (cov.first==0) {
std::cout << "Global LDDT score: 0.0" << std::endl;
return 0;
diff --git a/modules/mol/alg/src/local_dist_diff_test.cc b/modules/mol/alg/src/local_dist_diff_test.cc
index b6e0ecc046cca187cedc3473657a7de62e7c0a31..3ad22db00bcea5b2d078e004e10fe909912d62b6 100644
--- a/modules/mol/alg/src/local_dist_diff_test.cc
+++ b/modules/mol/alg/src/local_dist_diff_test.cc
@@ -1,3 +1,4 @@
+#include <iomanip>
#include <ost/log.hh>
#include <ost/mol/mol.hh>
#include "local_dist_diff_test.hh"
@@ -566,6 +567,49 @@ GlobalRDMap PreparelDDTGlobalRDMap(const std::vector<EntityView>& ref_list,
return glob_dist_list;
}
+void CheckStructure(EntityView& ent,
+ StereoChemicalParams& bond_table,
+ StereoChemicalParams& angle_table,
+ ClashingDistances& nonbonded_table,
+ Real bond_tolerance,
+ Real angle_tolerance){
+ // performs structural checks and filters the structure
+ StereoChemistryInfo stereo_chemistry_info;
+ try {
+ std::pair<EntityView,StereoChemistryInfo> csc_result = alg::CheckStereoChemistry(ent,bond_table,angle_table,bond_tolerance,angle_tolerance);
+ ent = csc_result.first;
+ stereo_chemistry_info = csc_result.second;
+ } catch (std::exception& e) {
+ std::cout << "An error occurred during the structure quality checks, stage 1:" << std::endl;
+ std::cout << e.what() << std::endl;
+ exit(-1);
+ }
+ std::cout << "Average Z-Score for bond lengths: " << std::fixed << std::setprecision(5) << stereo_chemistry_info.GetAvgZscoreBonds() << std::endl;
+ std::cout << "Bonds outside of tolerance range: " << stereo_chemistry_info.GetBadBondCount() << " out of " << stereo_chemistry_info.GetBondCount() << std::endl;
+ std::cout << "Bond\tAvg Length\tAvg zscore\tNum Bonds" << std::endl;
+ std::map<String,BondLengthInfo> avg_bond_length_info = stereo_chemistry_info.GetAvgBondLengthInfo();
+ for (std::map<String,BondLengthInfo>::const_iterator abli_it=avg_bond_length_info.begin();abli_it!=avg_bond_length_info.end();++abli_it) {
+ String key = (*abli_it).first;
+ BondLengthInfo bond_length_info = (*abli_it).second;
+ std::cout << key << "\t" << std::fixed << std::setprecision(5) << std::left << std::setw(10) <<
+ bond_length_info.GetAvgLength() << "\t" << std::left << std::setw(10) << bond_length_info.GetAvgZscore() << "\t" << bond_length_info.GetCount() << std::endl;
+ }
+ std::cout << "Average Z-Score angle widths: " << std::fixed << std::setprecision(5) << stereo_chemistry_info.GetAvgZscoreAngles() << std::endl;
+ std::cout << "Angles outside of tolerance range: " << stereo_chemistry_info.GetBadAngleCount() << " out of " << stereo_chemistry_info.GetAngleCount() << std::endl;
+ ClashingInfo clash_info;
+ try {
+ std::pair<EntityView,ClashingInfo> fc_result = alg::FilterClashes(ent,nonbonded_table);
+ ent = fc_result.first;
+ clash_info = fc_result.second;
+ } catch (std::exception& e) {
+ std::stringstream serr;
+ serr << "An error occurred during the structure quality checks, stage 2: " << e.what();
+ throw ost::Error(serr.str());
+ }
+ std::cout << clash_info.GetClashCount() << " non-bonded short-range distances shorter than tolerance distance" << std::endl;
+ std::cout << "Distances shorter than tolerance are on average shorter by: " << std::fixed << std::setprecision(5) << clash_info.GetAverageOffset() << std::endl;
+}
+
// debugging code
/*
Real OldStyleLDDTHA(EntityView& v, const GlobalRDMap& global_dist_list)
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index 9eb5829fe6d9790b0030beab56067666469fbca7..05b9fd887c1631ef9e3c70123f6fb8667ead6757 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -22,6 +22,7 @@
#include <ost/mol/alg/module_config.hh>
#include <ost/seq/alignment_handle.hh>
#include <ost/mol/alg/distance_test_common.hh>
+#include <ost/mol/alg/filter_clashes.hh>
namespace ost { namespace mol { namespace alg {
@@ -144,6 +145,13 @@ GlobalRDMap DLLEXPORT_OST_MOL_ALG PreparelDDTGlobalRDMap(
int sequence_separation,
Real max_dist);
+void DLLEXPORT_OST_MOL_ALG CheckStructure(EntityView& ent,
+ StereoChemicalParams& bond_table,
+ StereoChemicalParams& angle_table,
+ ClashingDistances& nonbonded_table,
+ Real bond_tolerance,
+ Real angle_tolerance);
+
}}}
#endif