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Cleanup warnings from clang-10 (#3238)

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* stop returning local memory in exceptions

* remove a couple unnecessary copies in loops

* fix a bug in the way the default MMFF aromatic parameters are constructed

* remove a bunch of loop-variable warnings

* remove a bunch of clang warnings

* disable clang warnings in python wrappers

* remove some warnings when building the python wrappers
This commit is contained in:
Greg Landrum
2020-06-19 23:16:22 +02:00
committed by GitHub
parent 69d89f10c0
commit edd922c99c
28 changed files with 184 additions and 149 deletions
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45
Code/GraphMol/ScaffoldNetwork/catch_tests.cpp
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@@ -153,7 +153,7 @@ TEST_CASE("getMolFragments", "[unittest][scaffolds]") {
std::vector<std::pair<std::string, std::string>> res;
res.reserve(frags.size());
for (const auto frag : frags) {
for (const auto &frag : frags) {
res.push_back(std::make_pair(frag.first, MolToSmiles(*frag.second)));
}
std::sort(res.begin(), res.end());
@@ -204,7 +204,7 @@ TEST_CASE("addMolToNetwork", "[unittest][scaffolds]") {
return e.type ==
ScaffoldNetwork::EdgeType::RemoveAttachment;
}) == 2);
CHECK(std::count(net.counts.begin(), net.counts.end(), 1) ==
CHECK(rdcast<size_t>(std::count(net.counts.begin(), net.counts.end(), 1)) ==
net.counts.size());
// make sure adding the same molecule again doesn't do anything except
@@ -213,7 +213,7 @@ TEST_CASE("addMolToNetwork", "[unittest][scaffolds]") {
CHECK(net.nodes.size() == 9);
CHECK(net.counts.size() == net.nodes.size());
CHECK(net.edges.size() == 8);
CHECK(std::count(net.counts.begin(), net.counts.end(), 2) ==
CHECK(rdcast<size_t>(std::count(net.counts.begin(), net.counts.end(), 2)) ==
net.counts.size());
}
SECTION("flucloxacillin") {
@@ -382,7 +382,7 @@ TEST_CASE("no attachment points", "[unittest][scaffolds]") {
[](ScaffoldNetwork::NetworkEdge e) {
return e.type == ScaffoldNetwork::EdgeType::Generic;
}) == 2);
CHECK(std::count(net.counts.begin(), net.counts.end(), 1) ==
CHECK(rdcast<size_t>(std::count(net.counts.begin(), net.counts.end(), 1)) ==
net.counts.size());
}
SECTION("no generic") {
@@ -398,7 +398,7 @@ TEST_CASE("no attachment points", "[unittest][scaffolds]") {
[](ScaffoldNetwork::NetworkEdge e) {
return e.type == ScaffoldNetwork::EdgeType::Fragment;
}) == 2);
CHECK(std::count(net.counts.begin(), net.counts.end(), 1) ==
CHECK(rdcast<size_t>(std::count(net.counts.begin(), net.counts.end(), 1)) ==
net.counts.size());
}
SECTION("generic bonds") {
@@ -751,19 +751,22 @@ TEST_CASE("Github #3177: seg fault with null molecules", "[bug]") {
mols.emplace_back(nullptr);
ScaffoldNetwork::ScaffoldNetworkParams ps =
ScaffoldNetwork::getBRICSNetworkParams();
REQUIRE_THROWS_AS(ScaffoldNetwork::createScaffoldNetwork(mols,ps),ValueErrorException);
REQUIRE_THROWS_AS(ScaffoldNetwork::createScaffoldNetwork(mols, ps),
ValueErrorException);
}
SECTION("including one valid molecule") {
std::vector<ROMOL_SPTR> mols;
mols.emplace_back(SmilesToMol("Cc1ccccc1"));
mols.emplace_back(nullptr);
ScaffoldNetwork::ScaffoldNetworkParams ps =
ScaffoldNetwork::getBRICSNetworkParams();
REQUIRE_THROWS_AS(ScaffoldNetwork::createScaffoldNetwork(mols,ps),ValueErrorException);
ScaffoldNetwork::getBRICSNetworkParams();
REQUIRE_THROWS_AS(ScaffoldNetwork::createScaffoldNetwork(mols, ps),
ValueErrorException);
}
}
TEST_CASE("GitHub #3153: Kekulization error in molecules with aromatic C+", "[bug]") {
TEST_CASE("GitHub #3153: Kekulization error in molecules with aromatic C+",
"[bug]") {
SECTION("Standard Representation") {
auto smis = {"O=C1C=CC(CC2=CC=CC2)=CC=C1"};
std::vector<ROMOL_SPTR> ms;
@@ -773,13 +776,11 @@ TEST_CASE("GitHub #3153: Kekulization error in molecules with aromatic C+", "[bu
ms.push_back(ROMOL_SPTR(m));
}
ScaffoldNetwork::ScaffoldNetworkParams ps;
ScaffoldNetwork::ScaffoldNetwork net =
ScaffoldNetwork::ScaffoldNetwork net =
ScaffoldNetwork::createScaffoldNetwork(ms, ps);
CHECK(net.nodes.size() == 9);
CHECK(
std::find(net.nodes.begin(), net.nodes.end(), "O=c1cccccc1") !=
net.nodes.end()
);
CHECK(std::find(net.nodes.begin(), net.nodes.end(), "O=c1cccccc1") !=
net.nodes.end());
CHECK(net.counts.size() == net.nodes.size());
CHECK(net.edges.size() == 8);
}
@@ -792,14 +793,12 @@ TEST_CASE("GitHub #3153: Kekulization error in molecules with aromatic C+", "[bu
ms.push_back(ROMOL_SPTR(m));
}
ScaffoldNetwork::ScaffoldNetworkParams ps;
ScaffoldNetwork::ScaffoldNetwork net =
ScaffoldNetwork::ScaffoldNetwork net =
ScaffoldNetwork::createScaffoldNetwork(ms, ps);
CHECK(net.nodes.size() == 3);
CHECK(
std::find(net.nodes.begin(), net.nodes.end(), "c1cc[nH]c1") !=
net.nodes.end()
);
CHECK(std::find(net.nodes.begin(), net.nodes.end(), "c1cc[nH]c1") !=
net.nodes.end());
CHECK(net.counts.size() == net.nodes.size());
CHECK(net.edges.size() == 2);
}
@@ -812,12 +811,10 @@ TEST_CASE("GitHub #3153: Kekulization error in molecules with aromatic C+", "[bu
ms.push_back(ROMOL_SPTR(m));
}
ScaffoldNetwork::ScaffoldNetworkParams ps;
ScaffoldNetwork::ScaffoldNetwork net =
ScaffoldNetwork::ScaffoldNetwork net =
ScaffoldNetwork::createScaffoldNetwork(ms, ps);
CHECK(
std::find(net.nodes.begin(), net.nodes.end(), "C1=CCC(Cc2ccc[cH+]cc2)=C1") !=
net.nodes.end()
);
CHECK(std::find(net.nodes.begin(), net.nodes.end(),
"C1=CCC(Cc2ccc[cH+]cc2)=C1") != net.nodes.end());
CHECK(net.nodes.size() == 11);
CHECK(net.counts.size() == net.nodes.size());
CHECK(net.edges.size() == 10);