diff --git a/modules/conop/src/compound.cc b/modules/conop/src/compound.cc
index dfa1a69f92677cb163fd1826313dfd09c8e255e5..b6ccaef833665409ec1bd6f0566168b37f279ae1 100644
--- a/modules/conop/src/compound.cc
+++ b/modules/conop/src/compound.cc
@@ -23,10 +23,17 @@ namespace ost { namespace conop {
int Compound::GetAtomSpecIndex(const String& name) const {
AtomSpecList::const_iterator i=atom_specs_.begin();
+ // BZDNG-261: first search all primary atom names before falling back to
+ // alternative names. There are some files where alternative atom names are
+ // used as primary names for other atoms
for (; i!=atom_specs_.end(); ++i) {
- if ((*i).name==name || (*i).alt_name==name)
+ if ((*i).name==name)
+ return std::distance(atom_specs_.begin(), i);
+ }
+ for (; i!=atom_specs_.end(); ++i) {
+ if ((*i).alt_name==name)
return std::distance(atom_specs_.begin(), i);
}
- return -1;
+ return -1;
}
}}
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index 33d33c667faebb47593eebe53f28285c448b1956..529fbcbc65f29be69c4b6391b346e45d9f382e3a 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -238,18 +238,20 @@ void RuleBasedBuilder::ConnectAtomsOfResidue(mol::ResidueHandle rh)
mol::AtomHandle a1=this->LocateAtom(atoms, bond.atom_one);
mol::AtomHandle a2=this->LocateAtom(atoms, bond.atom_two);
if (a1.IsValid() && a2.IsValid()) {
- if (this->GetBondFeasibilityCheck()==false) {
- if (this->GetStrictHydrogenMode() && (a1.GetElement()=="H" || a2.GetElement()=="D")) {
+ if (this->GetBondFeasibilityCheck()==false) {
+ if (this->GetStrictHydrogenMode() && (a1.GetElement()=="H" ||
+ a2.GetElement()=="D")) {
continue;
}
e.Connect(a1, a2, bond.order);
- } else {
- if (IsBondFeasible(a1, a2)) {
- if (this->GetStrictHydrogenMode() && (a1.GetElement()=="H" || a2.GetElement()=="D")) {
+ } else {
+ if (IsBondFeasible(a1, a2)) {
+ if (this->GetStrictHydrogenMode() && (a1.GetElement()=="H" ||
+ a2.GetElement()=="D")) {
continue;
- }
+ }
e.Connect(a1, a2, bond.order);
- }
+ }
}
}
}
diff --git a/modules/conop/tests/test_rule_based_builder.cc b/modules/conop/tests/test_rule_based_builder.cc
index 364ebf387be1b5bd6cd10bd4b721a56e85a1ceef..bc89d94a5a297f1e3c690d8ddcc05a0a643e5dda 100644
--- a/modules/conop/tests/test_rule_based_builder.cc
+++ b/modules/conop/tests/test_rule_based_builder.cc
@@ -20,7 +20,7 @@
#include <ost/mol/mol.hh>
#include <ost/platform.hh>
#include <ost/conop/rule_based_builder.hh>
-
+#include <ost/conop/conop.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
@@ -149,6 +149,139 @@ ResidueHandle make_defective_uracil2(ChainHandle chain)
return res;
}
+ResidueHandle make_1zk(ChainHandle chain)
+{
+ XCSEditor edi=chain.GetEntity().EditXCS();
+ ResidueHandle r=edi.AppendResidue(chain, "1ZK");
+ edi.InsertAtom(r, "C", geom::Vec3(3.946, 3.520, 10.861),"C");
+ edi.InsertAtom(r, "C1", geom::Vec3(6.308, 3.824, 8.036),"C");
+ edi.InsertAtom(r, "CA", geom::Vec3(4.856, 4.282, 9.931),"C");
+ edi.InsertAtom(r, "C2", geom::Vec3(6.770, 5.099, 8.019),"C");
+ edi.InsertAtom(r, "C3", geom::Vec3(7.805, 5.484, 7.142),"C");
+ edi.InsertAtom(r, "C4", geom::Vec3(8.363, 4.590, 6.284),"C");
+ edi.InsertAtom(r, "C5", geom::Vec3(8.469, 2.345, 5.318),"C");
+ edi.InsertAtom(r, "C6", geom::Vec3(7.986, 1.072, 5.322),"C");
+ edi.InsertAtom(r, "C4A", geom::Vec3(7.885, 3.277, 6.208),"C");
+ edi.InsertAtom(r, "C7", geom::Vec3(6.949, 0.682, 6.190),"C");
+ edi.InsertAtom(r, "C8", geom::Vec3(6.398, 1.548, 7.074),"C");
+ edi.InsertAtom(r, "C9", geom::Vec3(4.018, 0.269, 12.183),"C");
+ edi.InsertAtom(r, "C1A", geom::Vec3(6.824, 2.882, 7.117),"C");
+ edi.InsertAtom(r, "O", geom::Vec3(3.224, 4.213, 11.565),"O");
+ edi.InsertAtom(r, "O1", geom::Vec3(5.331, 3.476, 8.904),"O");
+ edi.InsertAtom(r, "O3", geom::Vec3(5.748, -4.044, 14.612),"O");
+ edi.InsertAtom(r, "N", geom::Vec3(3.855, 2.201, 10.790),"N");
+ edi.InsertAtom(r, "N1", geom::Vec3(4.814, 0.719, 13.173),"N");
+ edi.InsertAtom(r, "CA1", geom::Vec3(3.077, 1.346, 11.644),"C");
+ edi.InsertAtom(r, "O2", geom::Vec3(4.203, -0.810, 11.651),"O");
+ edi.InsertAtom(r, "O4", geom::Vec3(7.311, -5.667, 18.880),"O");
+ edi.InsertAtom(r, "CB", geom::Vec3(1.856, 0.712, 11.049),"C");
+ edi.InsertAtom(r, "CG", geom::Vec3(1.015, 1.845, 10.511),"C");
+ edi.InsertAtom(r, "ND1", geom::Vec3(1.467, 2.439, 9.321),"N");
+ edi.InsertAtom(r, "N2", geom::Vec3(6.478, -3.958, 16.751),"N");
+ edi.InsertAtom(r, "CD2", geom::Vec3(-0.105, 2.479, 10.887),"C");
+ edi.InsertAtom(r, "CE1", geom::Vec3(0.638, 3.428, 9.002),"C");
+ edi.InsertAtom(r, "NE2", geom::Vec3(-0.372, 3.461, 9.881),"N");
+ edi.InsertAtom(r, "N3", geom::Vec3(6.871, -7.136, 17.332),"N");
+ edi.InsertAtom(r, "CA2", geom::Vec3(5.881, -0.001, 13.808),"C");
+ edi.InsertAtom(r, "CB1", geom::Vec3(7.140, 0.860, 13.743),"C");
+ edi.InsertAtom(r, "CG1", geom::Vec3(7.503, 1.324, 12.299),"C");
+ edi.InsertAtom(r, "C21", geom::Vec3(5.126, -8.557, 18.179),"C");
+ edi.InsertAtom(r, "CD1", geom::Vec3(8.185, 0.142, 11.507),"C");
+ edi.InsertAtom(r, "CD21", geom::Vec3(8.420, 2.537, 12.325),"C");
+ edi.InsertAtom(r, "CE11", geom::Vec3(8.381, 0.689, 10.066),"C");
+ edi.InsertAtom(r, "CE2", geom::Vec3(8.907, 2.979, 10.922),"C");
+ edi.InsertAtom(r, "CZ", geom::Vec3(9.409, 1.807, 10.075),"C");
+ edi.InsertAtom(r, "CH", geom::Vec3(5.592, -0.511, 15.204),"C");
+ edi.InsertAtom(r, "OH", geom::Vec3(5.225, 0.377, 16.238),"O");
+ edi.InsertAtom(r, "CB11", geom::Vec3(4.426, -1.543, 15.170),"C");
+ edi.InsertAtom(r, "CA'", geom::Vec3(4.451, -2.730, 16.152),"C");
+ edi.InsertAtom(r, "CB'", geom::Vec3(3.124, -3.441, 16.281),"C");
+ edi.InsertAtom(r, "CG11", geom::Vec3(2.553, -3.986, 14.933),"C");
+ edi.InsertAtom(r, "C31", geom::Vec3(4.413, -7.811, 19.117),"C");
+ edi.InsertAtom(r, "CG2", geom::Vec3(3.204, -4.586, 17.345),"C");
+ edi.InsertAtom(r, "OB1", geom::Vec3(3.249, -0.875, 15.134),"O");
+ edi.InsertAtom(r, "CC", geom::Vec3(5.603, -3.655, 15.782),"C");
+ edi.InsertAtom(r, "CA3", geom::Vec3(7.592, -4.867, 16.603),"C");
+ edi.InsertAtom(r, "CD", geom::Vec3(7.274, -5.947, 17.691),"C");
+ edi.InsertAtom(r, "CB2", geom::Vec3(8.986, -4.351, 16.803),"C");
+ edi.InsertAtom(r, "CG12", geom::Vec3(9.488, -3.108, 16.016),"C");
+ edi.InsertAtom(r, "CG21", geom::Vec3(10.000, -5.461, 16.472),"C");
+ edi.InsertAtom(r, "CD11", geom::Vec3(9.099, -3.257, 14.571),"C");
+ edi.InsertAtom(r, "CM", geom::Vec3(6.587, -8.286, 18.106),"C");
+ edi.InsertAtom(r, "C41", geom::Vec3(3.045, -7.980, 19.287),"C");
+ edi.InsertAtom(r, "C51", geom::Vec3(2.423, -8.911, 18.456),"C");
+ edi.InsertAtom(r, "C61", geom::Vec3(3.164, -9.631, 17.518),"C");
+ edi.InsertAtom(r, "N11", geom::Vec3(4.497, -9.459, 17.386),"N");
+ return r;
+}
+
+void verify_1zk_connectivity(const ResidueHandle& r1)
+{
+ BOOST_CHECK(BondExists(r1.FindAtom("C"), r1.FindAtom("CA")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C"), r1.FindAtom("O")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA"), r1.FindAtom("O1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C1"), r1.FindAtom("C2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C1"), r1.FindAtom("C1A")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C1"), r1.FindAtom("O1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C2"), r1.FindAtom("C3")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C3"), r1.FindAtom("C4")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C4"), r1.FindAtom("C4A")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C4A"), r1.FindAtom("C5")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C4A"), r1.FindAtom("C1A")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C5"), r1.FindAtom("C6")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C6"), r1.FindAtom("C7")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C7"), r1.FindAtom("C8")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C8"), r1.FindAtom("C1A")));
+ BOOST_CHECK(BondExists(r1.FindAtom("N"), r1.FindAtom("CA1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA1"), r1.FindAtom("C9")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA1"), r1.FindAtom("CB")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C9"), r1.FindAtom("O2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CB"), r1.FindAtom("CG")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CG"), r1.FindAtom("ND1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CG"), r1.FindAtom("CD2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("ND1"), r1.FindAtom("CE1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CD2"), r1.FindAtom("NE2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CE1"), r1.FindAtom("NE2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("N1"), r1.FindAtom("CA2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA2"), r1.FindAtom("CB1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA2"), r1.FindAtom("CH")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CB1"), r1.FindAtom("CG1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CG1"), r1.FindAtom("CD1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CG1"), r1.FindAtom("CD21")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CD1"), r1.FindAtom("CE11")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CD21"), r1.FindAtom("CE2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CE11"), r1.FindAtom("CZ")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CE2"), r1.FindAtom("CZ")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CH"), r1.FindAtom("OH")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CH"), r1.FindAtom("CB11")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CB11"), r1.FindAtom("CA'")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CB11"), r1.FindAtom("OB1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA'"), r1.FindAtom("CB'")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA'"), r1.FindAtom("CC")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CB'"), r1.FindAtom("CG11")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CB'"), r1.FindAtom("CG2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CC"), r1.FindAtom("O3")));
+ BOOST_CHECK(BondExists(r1.FindAtom("N2"), r1.FindAtom("CA3")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA3"), r1.FindAtom("CD")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CA3"), r1.FindAtom("CB2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CD"), r1.FindAtom("O4")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CB2"), r1.FindAtom("CG12")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CB2"), r1.FindAtom("CG21")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CG12"), r1.FindAtom("CD11")));
+ BOOST_CHECK(BondExists(r1.FindAtom("N3"), r1.FindAtom("CM")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CM"), r1.FindAtom("C21")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C21"), r1.FindAtom("C31")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C21"), r1.FindAtom("N11")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C31"), r1.FindAtom("C41")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C41"), r1.FindAtom("C51")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C51"), r1.FindAtom("C61")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C61"), r1.FindAtom("N11")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C"), r1.FindAtom("N")));
+ BOOST_CHECK(BondExists(r1.FindAtom("C9"), r1.FindAtom("N1")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CC"), r1.FindAtom("N2")));
+ BOOST_CHECK(BondExists(r1.FindAtom("CD"), r1.FindAtom("N3")));
+}
+
void verify_nucleotide_connectivity(const ResidueHandle& res)
{
BOOST_CHECK(BondExists(res.FindAtom("P"),
@@ -297,4 +430,27 @@ BOOST_AUTO_TEST_CASE(nucleotide_based_connect)
}
+BOOST_AUTO_TEST_CASE(rule_based_connect_1zk)
+{
+ SetPrefixPath(getenv("OST_ROOT"));
+ String lib_path=GetSharedDataPath()+"/compounds.chemlib";
+ CompoundLibPtr compound_lib=CompoundLib::Load(lib_path);
+ if (!compound_lib) {
+ std::cout << "WARNING: skipping NUCLEOTIDE_BASED connect unit test. "
+ << "Rule-based builder is required" << std::endl;
+ return;
+ }
+
+ boost::shared_ptr<RuleBasedBuilder> drb_builder(new RuleBasedBuilder(compound_lib));
+ Conopology::Instance().RegisterBuilder(drb_builder, "RBB");
+ Conopology::Instance().SetDefaultBuilder("RBB");
+ drb_builder->SetBondFeasibilityCheck(false);
+ EntityHandle e=CreateEntity();
+ ChainHandle c=e.EditXCS().InsertChain("A");
+ ResidueHandle r1=make_1zk(c);
+ Conopology::Instance().ConnectAll(drb_builder, e);
+ Conopology::Instance().SetDefaultBuilder("HEURISTIC");
+ verify_1zk_connectivity(r1);
+}
+
BOOST_AUTO_TEST_SUITE_END( );