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Read SD property names till the last '>' (#9047)

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* add a test

* fix
This commit is contained in:
Ricardo Rodriguez
2026-01-09 05:23:26 +01:00
committed by greg landrum
parent 2f26e34c25
commit e536234a41
2 changed files with 21 additions and 9 deletions
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6
Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp
View File

@@ -85,9 +85,9 @@ void ForwardSDMolSupplier::readMolProps(ROMol &mol) {
// situation - so ignore such data items for now
hasProp = true;
warningIssued = false;
tempStr = tempStr.substr(1); // remove the first ">" sign
size_t sl = tempStr.find("<"); // begin datalabel
size_t se = tempStr.find(">"); // end datalabel
tempStr = tempStr.substr(1); // remove the first ">" sign
size_t sl = tempStr.find("<"); // begin datalabel
size_t se = tempStr.rfind(">"); // end datalabel
if ((sl == std::string::npos) || (se == std::string::npos) ||
(se == (sl + 1))) {
// we either do not have a data label or the label is empty

24
Code/GraphMol/FileParsers/testMolSupplier.cpp
View File

@@ -845,13 +845,11 @@ TEST_CASE("testSDWriter") {
// now read in the file we just finished writing
SDMolSupplier reader(ofile);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
CHECK(mol->hasProp(common_properties::_Name));
delete mol;
i++;
}
}
@@ -961,7 +959,6 @@ TEST_CASE("testStereoRound") {
rdbase +
"/Code/GraphMol/FileParsers/test_data/cdk2_stereo_molsupplier.sdf";
auto *writer = new SDWriter(ofile);
int count = 0;
while (!smiSup->atEnd()) {
ROMol *mol = smiSup->next();
@@ -977,7 +974,6 @@ TEST_CASE("testStereoRound") {
RDDepict::compute2DCoords(*mol);
writer->write(*mol);
count++;
delete mol;
delete nmol;
}
@@ -989,7 +985,6 @@ TEST_CASE("testStereoRound") {
SDMolSupplier *reader;
REQUIRE_NOTHROW(reader = new SDMolSupplier(ofile));
REQUIRE(reader);
count = 0;
while (!reader->atEnd()) {
ROMol *mol = reader->next();
@@ -999,7 +994,6 @@ TEST_CASE("testStereoRound") {
mol->getProp(common_properties::_Name, mname);
CHECK(nameSmi[mname] == smiles);
delete mol;
count++;
}
delete reader;
}
@@ -2692,4 +2686,22 @@ $$$$)CTAB";
CHECK(mol->getNumAtoms() == 5); // only heavy atoms are kept
CHECK(getSubstanceGroups(*mol).size() == 1);
}
}
TEST_CASE("Read SD properties till last '>'") {
auto m = v2::SmilesParse::MolFromSmiles("C");
REQUIRE(m);
constexpr const char *prop_name = "654 > 321";
m->setProp(prop_name, "this is not important");
auto molblock = SDWriter::getText(*m);
REQUIRE_THAT(molblock, Catch::Matchers::ContainsSubstring(prop_name));
SDMolSupplier supplier;
supplier.setData(molblock);
auto m2 = supplier.next();
REQUIRE(m2);
CHECK(m2->hasProp(prop_name));
}