diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 9455d58dee59c029ea8d37e3d82804f63b625021..66b14294022870a6dfe967ce407994388ef6679d 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -374,6 +374,22 @@ The following function detects steric clashes in atomic structures. Two atoms ar
:returns: :class:`~ost.mol.alg.ClashingDistances` and :class:`~ost.mol.alg.StereoChemicalParams` respectively
+.. function:: ResidueNamesMatch(probe,reference)
+
+ The function requires a reference structure and a probe structure. The function checks that all the
+ residues in the reference structure that appear in the probe structure (i.e., that have the
+ same ResNum) are of the same residue type. Chains are comapred by order, not by chain name
+ (i.e.: the first chain of the reference will be compared with the first chain of the probe
+ structure, etc.)
+
+ :param probe: the structure to test
+ :type probe: :class:`~ost.mol.EntityView`
+ :param reference: the reference structure
+ :type reference: :class:`~ost.mol.EntityView`
+
+ :returns: true if the residue names are the same, false otherwise
+
+
.. _traj-analysis:
Trajectory Analysis
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 1455b635bceb17e7ebfba141317a811e119351b0..08ad6631efe89ce483e9cc653c2baec321db6927 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -162,7 +162,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
def("PrintGlobalRDMap",&mol::alg::PrintGlobalRDMap);
def("PrintResidueRDMap",&mol::alg::PrintResidueRDMap);
- def("CheckResidueTypes",&mol::alg::CheckResidueTypes);
+ def("ResidueNamesMatch",&mol::alg::ResidueNamesMatch);
}
diff --git a/modules/mol/alg/src/consistency_checks.cc b/modules/mol/alg/src/consistency_checks.cc
index 3807e461e712ff7cd76b639b24f592208c860437..371f3c37b6b8fbc921ecd3a82fa647251992b216 100644
--- a/modules/mol/alg/src/consistency_checks.cc
+++ b/modules/mol/alg/src/consistency_checks.cc
@@ -28,22 +28,30 @@ namespace ost { namespace mol { namespace alg {
///
/// Requires a reference structure and a probe structure. The function checks that all the
/// residues in the reference structure that appear in the probe structure (i.e., that have the
-/// same ResNum) are of the same residue type.
+/// same ResNum) are of the same residue type. Chains are paired by index, not by chain name
+/// (i.e., the first chain of the reference will be compared with the first chain of the probe,
+/// the second with the second, etc.)
-bool CheckResidueTypes (const mol::EntityView& probe, const mol::EntityView& reference)
+
+
+
+
+bool ResidueNamesMatch (const mol::EntityView& probe, const mol::EntityView& reference)
{
bool return_value = true;
ChainViewList ref_chains = reference.GetChainList();
- for (ChainViewList::const_iterator rci = ref_chains.begin(), rce=ref_chains.end(); rci!=rce; ++rci) {
- ChainView probe_chain = probe.FindChain(rci->GetName());
- if (probe_chain.IsValid()) {
- ResidueViewList ref_residues = rci->GetResidueList();
+ ChainViewList probe_chains = probe.GetChainList();
+ for (unsigned int rci = 0; rci < ref_chains.size(); ++rci) {
+ ChainView ref_chain= ref_chains[rci];
+ if (rci<probe_chains.size()) {
+ ChainView probe_chain = probe_chains[rci];
+ ResidueViewList ref_residues = ref_chain.GetResidueList();
for (ResidueViewList::iterator rri=ref_residues.begin(), rre=ref_residues.end(); rri!=rre; ++rri) {
ResidueView probe_residue = probe_chain.FindResidue(rri->GetNumber());
if (probe_residue.IsValid()) {
if (probe_residue.GetName()!=rri->GetName()) {
- return_value =false;
- LOG_VERBOSE("Type mismatch for residue " << probe_residue.GetNumber());
+ return_value = false;
+ LOG_VERBOSE("Name mismatch for residue " << probe_residue.GetNumber() << " in chain " << rci);
LOG_VERBOSE("In reference: " << rri->GetName() << ", in compared structure: " << probe_residue.GetName());
}
}
diff --git a/modules/mol/alg/src/consistency_checks.hh b/modules/mol/alg/src/consistency_checks.hh
index 4833df2474c5d82d6056663f4ee4eca677053487..77cffda1ce3639c37111cc0b7d8fa120015e9958 100644
--- a/modules/mol/alg/src/consistency_checks.hh
+++ b/modules/mol/alg/src/consistency_checks.hh
@@ -28,9 +28,11 @@ namespace ost { namespace mol { namespace alg {
///
/// Requires a reference structure and a probe structure. The function checks that all the
/// residues in the reference structure that appear in the probe structure (i.e., that have the
-/// same ResNum) are of the same residue type.
+/// same ResNum) are of the same residue type. Chains are comapred by order, not by chain name
+/// (i.e.: the first chain of the reference will be compared with the first chain of the probe
+/// structure, etc.)
-bool DLLEXPORT_OST_MOL_ALG CheckResidueTypes (const mol::EntityView& probe, const mol::EntityView& reference);
+bool DLLEXPORT_OST_MOL_ALG ResidueNamesMatch (const mol::EntityView& probe, const mol::EntityView& reference);
}}}
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 8e8277dc098a239e3ffe734f7c39d2da52163b30..3f7813b98c584c8b5e0bd3fd623ebce0973b6878 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -35,6 +35,7 @@
#include <ost/mol/iterator.hh>
#include <ost/platform.hh>
#include <ost/log.hh>
+#include <ost/mol/alg/consistency_checks.hh>
#include <ost/conop/rule_based_builder.hh>
#include <ost/dyn_cast.hh>
@@ -85,6 +86,8 @@ void usage()
std::cerr << " -r <value> distance inclusion radius" << std::endl;
std::cerr << " -i <value> sequence separation" << std::endl;
std::cerr << " -e print version" << std::endl;
+ std::cerr << " -x ignore residue name consistency checks" << std::endl;
+
}
// computes coverage
@@ -123,12 +126,14 @@ int main (int argc, char **argv)
// parses options
String sel;
bool structural_checks=false;
+ bool consistency_checks=true;
po::options_description desc("Options");
desc.add_options()
("calpha,c", "consider only calpha atoms")
("sel,s", po::value<String>(&sel)->default_value(""), "selection performed on reference structure")
("tolerant,t", "fault tolerant mode")
("structural-checks,f", "perform stereo-chemical and clash checks")
+ ("ignore-consistency-checks,x", "ignore residue name consistency checks")
("version,e", "version")
("parameter-file,p", po::value<String>(), "stereo-chemical parameter file")
("verbosity,v", po::value<int>(), "verbosity level")
@@ -169,6 +174,9 @@ int main (int argc, char **argv)
if (vm.count("structural-checks")) {
structural_checks=true;
}
+ if (vm.count("ignore-consistency-checks")) {
+ consistency_checks=false;
+ }
if (vm.count("tolerant")) {
profile.fault_tolerant=true;
}
@@ -215,6 +223,8 @@ int main (int argc, char **argv)
cutoffs.push_back(1.0);
cutoffs.push_back(2.0);
cutoffs.push_back(4.0);
+
+ std::vector<EntityView> ref_list;
// loads the reference file and creates the list of distances to check in lddt
// if the reference file is a comma-separated list of files, switches to multi-
@@ -230,10 +240,10 @@ int main (int argc, char **argv)
if (!ref) {
exit(-1);
}
+ ref_list.push_back(ref.CreateFullView());
glob_dist_list = CreateDistanceList(ref.CreateFullView(),radius);
} else {
std::cout << "Multi-reference mode: On" << std::endl;
- std::vector<EntityView> ref_list;
for (std::vector<StringRef>::const_iterator ref_file_split_sr_it = ref_file_split_sr.begin();
ref_file_split_sr_it != ref_file_split_sr.end();++ref_file_split_sr_it) {
String ref_filename = ref_file_split_sr_it->str();
@@ -284,6 +294,19 @@ int main (int argc, char **argv)
}
EntityView v=model.CreateFullView();
+ for (std::vector<EntityView>::const_iterator ref_list_it = ref_list.begin();
+ ref_list_it != ref_list.end(); ++ref_list_it) {
+ bool cons_check = ResidueNamesMatch(v,*ref_list_it);
+ if (cons_check==false) {
+ if (consistency_checks==true) {
+ LOG_ERROR("Residue names in model: " << files[i] << " are inconsistent with one or more references");
+ exit(-1);
+ } else {
+ LOG_WARNING("Residue names in model: " << files[i] << " are inconsistent with one or more references");
+ }
+ }
+ }
+
boost::filesystem::path pathstring(files[i]);
String filestring=BFPathToString(pathstring);
diff --git a/modules/mol/alg/tests/test_consistency_checks.cc b/modules/mol/alg/tests/test_consistency_checks.cc
index 10696a5b6cf831194c3df4fff2bed28db90d3cb8..aad198febf3decc69d591cb16058cfe9d6e07a24 100644
--- a/modules/mol/alg/tests/test_consistency_checks.cc
+++ b/modules/mol/alg/tests/test_consistency_checks.cc
@@ -55,8 +55,6 @@ BOOST_AUTO_TEST_CASE(consistency_check)
ResidueHandle r3b = edb.AppendResidue(cb, "LEU",3);
ResidueHandle r4b = edb.AppendResidue(cb, "GLY",4);
ResidueHandle r5b = edb.AppendResidue(cb, "PRO",5);
- ChainHandle cb2=edb.InsertChain("B");
- ResidueHandle r1b2 = edb.AppendResidue(cb2, "ALA",1);
EntityHandle c=CreateEntity();
@@ -66,10 +64,9 @@ BOOST_AUTO_TEST_CASE(consistency_check)
ResidueHandle r2c = edc.AppendResidue(cc, "PRO",2);
ResidueHandle r3c = edc.AppendResidue(cc, "LEU",3);
ResidueHandle r4c = edc.AppendResidue(cc, "GLY",4);
-
-
- BOOST_CHECK(ost::mol::alg::CheckResidueTypes(a.CreateFullView(),b.CreateFullView())==true);
- BOOST_CHECK(ost::mol::alg::CheckResidueTypes(c.CreateFullView(),b.CreateFullView())==false);
+
+ BOOST_CHECK(ost::mol::alg::ResidueNamesMatch(a.CreateFullView(),b.CreateFullView())==true);
+ BOOST_CHECK(ost::mol::alg::ResidueNamesMatch(c.CreateFullView(),b.CreateFullView())==false);
}
BOOST_AUTO_TEST_SUITE_END();