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Bad radical values are now ignored for MRV generation (rdkit#8130)
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* Bad radical values are now ignored for MRV generation

* Update Code/GraphMol/MarvinParse/MarvinWriter.cpp

Co-authored-by: Greg Landrum <[email protected]>

---------

Co-authored-by: Greg Landrum <[email protected]>
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@tadhurst-cdd @greglandrum
tadhurst-cdd and greglandrum authored Dec 21, 2024
1 parent b8effb8 commit 454fe1c
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7 changes: 6 additions & 1 deletion Code/GraphMol/MarvinParse/MarvinWriter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -429,8 +429,13 @@ class MarvinCMLWriter {
marvinAtom->formalCharge = atom->getFormalCharge();

unsigned int nRadEs = atom->getNumRadicalElectrons();
// value of radical electrons has to be one of the expected values or it
// is ignored
if (nRadEs != 0) {
marvinAtom->radical = radicalElectronsToMarvinRadical.at(nRadEs);
if (const auto iter = radicalElectronsToMarvinRadical.find(nRadEs);
iter != radicalElectronsToMarvinRadical.end()) {
marvinAtom->radical = iter->second;
}
}

if (marvinAtom->isElement()) {
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1 change: 1 addition & 0 deletions Code/GraphMol/MarvinParse/testMrvToMol.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -894,6 +894,7 @@ class MrvTests {
// the molecule tests - starting with molfiles/sdf
if (testToRun == "" || testToRun == "sdfTests") {
std::list<MolTest> sdfTests{
MolTest("145323811.mol", true, 172, 176, true, false),
MolTest("NewChiralTest.sdf", true, 13, 14, true,
false), // wedges NOT reapplied
MolTest("NewChiralTest.sdf", true, 13, 14, false,
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354 changes: 354 additions & 0 deletions Code/GraphMol/MarvinParse/test_data/145323811.mol
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@@ -0,0 +1,354 @@

Generated by WebMolKit

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M END
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