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Add H and X specification to P tautomerization rules (#5077)

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Fixes #5008
This commit is contained in:
Greg Landrum
2022-03-14 04:41:09 +01:00
committed by GitHub
parent 2489b6cdfb
commit 54ff5ec5dd
3 changed files with 30 additions and 6 deletions
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6
Code/GraphMol/MolStandardize/TautomerCatalog/tautomerTransforms.in
View File

@@ -49,7 +49,7 @@ const std::vector<
std::make_tuple(
std::string("1,3 heteroatom H shift"),
std::string(
"[#7+0,S,O,Se,Te;!H0]-[#7X2,#6,#15]=[#7+0,#16,#8,Se,Te]"),
"[#7+0,S,O,Se,Te;!H0]-[#7X2,#6,#15X3H0]=[#7+0,#16,#8,Se,Te]"),
std::string(""), std::string("")),
std::make_tuple(
std::string("1,5 aromatic heteroatom H shift"),
@@ -135,9 +135,9 @@ const std::vector<
std::string("[N+!H0]#[C-]"), std::string("#"),
std::string("-+")),
std::make_tuple(std::string("phosphonic acid f"),
std::string("[OH]-[PH0]"), std::string("="),
std::string("[OH]-[PX3H0]"), std::string("="),
std::string("")),
std::make_tuple(std::string("phosphonic acid r"),
std::string("[PH]=[O]"), std::string("-"),
std::string("[PX4H]=[O]"), std::string("-"),
std::string(""))};
} // namespace defaults

24
Code/GraphMol/MolStandardize/catch_tests.cpp
View File

@@ -843,4 +843,28 @@ TEST_CASE(
CHECK(m2->getAtomWithIdx(0)->getFormalCharge() == 2);
CHECK(m2->getAtomWithIdx(1)->getFormalCharge() == -1);
}
}
TEST_CASE("Github #5008: bad tautomers for phosphorous compounds") {
SECTION("as reported") {
auto m = "NP(=O)(O)N(CCCl)CCCl"_smiles;
REQUIRE(m);
MolStandardize::TautomerEnumerator tenum;
auto tauts = tenum.enumerate(*m);
CHECK(tauts.size() == 1);
}
SECTION("P which should tautomerize") {
auto m = "CP(O)C"_smiles;
REQUIRE(m);
MolStandardize::TautomerEnumerator tenum;
auto tauts = tenum.enumerate(*m);
CHECK(tauts.size() == 2);
}
SECTION("Canonical version") {
auto m = "CP(O)C"_smiles;
REQUIRE(m);
std::unique_ptr<RWMol> ct(MolStandardize::canonicalTautomer(m.get()));
REQUIRE(ct);
CHECK(MolToSmiles(*ct) == "C[PH](C)=O");
}
}

6
Code/GraphMol/MolStandardize/test_data/tautomerTransforms.in
View File

@@ -9,7 +9,7 @@ special imine f [N!H0]-[C]=[CX3R0]
special imine r [CX4!H0]-[c]=[n]
1,3 aromatic heteroatom H shift f [#7+0!H0]-[#6R1]=[O,#7X2+0]
1,3 aromatic heteroatom H shift [O,#7+0;!H0]-[#6R1]=[#7+0X2]
1,3 heteroatom H shift [#7+0,S,O,Se,Te;!H0]-[#7X2,#6,#15]=[#7+0,#16,#8,Se,Te]
1,3 heteroatom H shift [#7+0,S,O,Se,Te;!H0]-[#7X2,#6,#15X3H0]=[#7+0,#16,#8,Se,Te]
1,5 aromatic heteroatom H shift [#7+0,#16,#8;!H0]-[#6,#7]=[#6]-[#6,#7]=[#7+0,#16,#8;H0]
1,5 aromatic heteroatom H shift [#7+0,#16,#8,Se,Te;!H0]-[#6,nX2]=[#6,nX2]-[#6,#7X2]=[#7X2+0,S,O,Se,Te]
1,5 aromatic heteroatom H shift r [#7+0,S,O,Se,Te;!H0]-[#6,#7X2]=[#6,nX2]-[#6,nX2]=[#7+0,#16,#8,Se,Te]
@@ -33,5 +33,5 @@ formamidinesulfinic acid f [O,N;!H0]-[C]=[S,Se,Te;v6]=[O] =--
formamidinesulfinic acid r [O!H0]-[S,Se,Te;v4]-[C]=[O,N] ==-
isocyanide f [C-0!H0]#[N+0] # -+
isocyanide r [N+!H0]#[C-] # -+
phosphonic acid f [OH]-[PH0] =
phosphonic acid r [PH]=[O] -
phosphonic acid f [OH]-[PX3H0] =
phosphonic acid r [PX4H]=[O] -