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Fixes #5785 (#5871)

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* make the test for how to write valences more robust w.r.t. unsanitized molecules

* Fixes #5785
This commit is contained in:
Greg Landrum
2022-12-16 16:00:30 +01:00
committed by GitHub
parent ca1e705693
commit cba7ecf3a4
3 changed files with 135 additions and 16 deletions
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42
Code/GraphMol/ChemReactions/ReactionWriter.cpp
View File

@@ -119,18 +119,17 @@ std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn,
//! returns an RXN block for a reaction
std::string ChemicalReactionToV3KRxnBlock(const ChemicalReaction &rxn,
bool separateAgents) {
if (separateAgents) {
// V3000 doesn't seem to support agent blocks
BOOST_LOG(rdWarningLog)
<< "V3000 RXN blocks do not support separating agents. Agents will be "
"written to the reactants block"
<< std::endl;
}
std::ostringstream res;
res << "$RXN V3000\n\n RDKit\n\n";
res << "M V30 COUNTS "
<< rxn.getNumReactantTemplates() + rxn.getNumAgentTemplates() << " "
<< rxn.getNumProductTemplates();
if (separateAgents) {
res << "M V30 COUNTS " << rxn.getNumReactantTemplates() << " "
<< rxn.getNumProductTemplates() << " " << rxn.getNumAgentTemplates();
} else {
res << "M V30 COUNTS "
<< rxn.getNumReactantTemplates() + rxn.getNumAgentTemplates() << " "
<< rxn.getNumProductTemplates();
}
res << "\n";
res << "M V30 BEGIN REACTANT\n";
@@ -140,11 +139,13 @@ std::string ChemicalReactionToV3KRxnBlock(const ChemicalReaction &rxn,
MolOps::findSSSR(*rt);
res << FileParserUtils::getV3000CTAB(*rt, -1);
}
for (const auto &rt : boost::make_iterator_range(rxn.beginAgentTemplates(),
rxn.endAgentTemplates())) {
// to write the mol block, we need ring information:
MolOps::findSSSR(*rt);
res << FileParserUtils::getV3000CTAB(*rt, -1);
if (!separateAgents) {
for (const auto &rt : boost::make_iterator_range(rxn.beginAgentTemplates(),
rxn.endAgentTemplates())) {
// to write the mol block, we need ring information:
MolOps::findSSSR(*rt);
res << FileParserUtils::getV3000CTAB(*rt, -1);
}
}
res << "M V30 END REACTANT\n";
res << "M V30 BEGIN PRODUCT\n";
@@ -155,6 +156,17 @@ std::string ChemicalReactionToV3KRxnBlock(const ChemicalReaction &rxn,
res << FileParserUtils::getV3000CTAB(*rt, -1);
}
res << "M V30 END PRODUCT\n";
if (separateAgents) {
res << "M V30 BEGIN AGENT\n";
for (const auto &rt : boost::make_iterator_range(rxn.beginAgentTemplates(),
rxn.endAgentTemplates())) {
// to write the mol block, we need ring information:
MolOps::findSSSR(*rt);
res << FileParserUtils::getV3000CTAB(*rt, -1);
}
res << "M V30 END AGENT\n";
}
res << "M END\n";
return res.str();
}

104
Code/GraphMol/ChemReactions/catch_tests.cpp
View File

@@ -1269,3 +1269,107 @@ TEST_CASE("CDXML Parser") {
CHECK(smarts == "[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](:[#6&D2:5]:[#6&D2:6]:1)-[#17&D1].[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>[#6:1]1=[#6:5]-[#6:6](=[#6:2]-[#6:3]=[#6:4]-1)-[#6:7]1-[#6:8]=[#6:9]-[#6:10]=[#6:11]-[#6:12]=1");
}
}
TEST_CASE("Github #5785: separateAgents ignored for V3000 RXN files") {
SECTION("general separateAgents parse testing: V2000"){
std::string rxnb = R"RXN($RXN
RDKit
1 1 1
$MOL
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
1 2 1 0
M END
$MOL
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
1 2 2 0
M END
$MOL
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 Pt 0 0 0 0 0 0 0 0 0 0 0 0
M END
)RXN";
std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnb));
REQUIRE(rxn);
CHECK(rxn->getNumReactantTemplates()==1);
CHECK(rxn->getNumProductTemplates()==1);
CHECK(rxn->getNumAgentTemplates()==1);
auto orxn = ChemicalReactionToRxnBlock(*rxn,true);
CHECK(orxn.find(" 1 1 1") != std::string::npos);
}
SECTION("general separateAgents parse testing: V3000"){
std::string rxnb = R"RXN($RXN V3000
Mrv2211 121520220816
M V30 COUNTS 1 1 1
M V30 BEGIN REACTANT
M V30 BEGIN CTAB
M V30 COUNTS 2 1 0 0 0
M V30 BEGIN ATOM
M V30 1 C -4.8977 -0.385 0 1
M V30 2 O -3.564 0.385 0 2
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 END BOND
M V30 END CTAB
M V30 END REACTANT
M V30 BEGIN PRODUCT
M V30 BEGIN CTAB
M V30 COUNTS 2 1 0 0 0
M V30 BEGIN ATOM
M V30 1 C 4.444 -0.385 0 1
M V30 2 O 5.7777 0.385 0 2
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 1 2
M V30 END BOND
M V30 END CTAB
M V30 END PRODUCT
M V30 BEGIN AGENT
M V30 BEGIN CTAB
M V30 COUNTS 1 0 0 0 0
M V30 BEGIN ATOM
M V30 1 Pt 0 1.54 0 0
M V30 END ATOM
M V30 END CTAB
M V30 END AGENT
M END
)RXN";
std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnb));
REQUIRE(rxn);
CHECK(rxn->getNumReactantTemplates()==1);
CHECK(rxn->getNumProductTemplates()==1);
CHECK(rxn->getNumAgentTemplates()==1);
{ // with separate agents
auto orxn = ChemicalReactionToV3KRxnBlock(*rxn,true);
CHECK(orxn.find("COUNTS 1 1 1") != std::string::npos);
CHECK(orxn.find("BEGIN AGENT") != std::string::npos);
CHECK(orxn.find("END AGENT") != std::string::npos);
}
{ // without separate agents
auto orxn = ChemicalReactionToV3KRxnBlock(*rxn,false);
CHECK(orxn.find("COUNTS 2 1") != std::string::npos);
CHECK(orxn.find("BEGIN AGENT") == std::string::npos);
CHECK(orxn.find("END AGENT") == std::string::npos);
}
}
}

5
Code/GraphMol/FileParsers/MolFileWriter.cpp
View File

@@ -530,9 +530,12 @@ bool hasNonDefaultValence(const Atom *atom) {
if (atom->getNumRadicalElectrons() != 0) {
return true;
}
if (atom->hasQuery()) {
// for queries and atoms which don't have computed properties, the answer is
// always no:
if (atom->hasQuery() || atom->needsUpdatePropertyCache()) {
return false;
}
if (atom->getAtomicNum() == 1 ||
SmilesWrite ::inOrganicSubset(atom->getAtomicNum())) {
// for the ones we "know", we may have to specify the valence if it's