From 454fe1c6f9c6b9db5e475ab6125b9e0f4dd1ec01 Mon Sep 17 00:00:00 2001 From: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com> Date: Sat, 21 Dec 2024 06:55:26 -0600 Subject: [PATCH] Bad radical values are now ignored for MRV generation (#8130) * Bad radical values are now ignored for MRV generation * Update Code/GraphMol/MarvinParse/MarvinWriter.cpp Co-authored-by: Greg Landrum --------- Co-authored-by: Greg Landrum --- Code/GraphMol/MarvinParse/MarvinWriter.cpp | 7 +- Code/GraphMol/MarvinParse/testMrvToMol.cpp | 1 + .../MarvinParse/test_data/145323811.mol | 354 +++++++++++++++++ .../test_data/145323811.mol.expected.cxsmi | 1 + .../test_data/145323811.mol.expected.mrv | 2 + .../test_data/145323811.mol.expected.sdf | 360 ++++++++++++++++++ 6 files changed, 724 insertions(+), 1 deletion(-) create mode 100644 Code/GraphMol/MarvinParse/test_data/145323811.mol create mode 100644 Code/GraphMol/MarvinParse/test_data/145323811.mol.expected.cxsmi create mode 100644 Code/GraphMol/MarvinParse/test_data/145323811.mol.expected.mrv create mode 100644 Code/GraphMol/MarvinParse/test_data/145323811.mol.expected.sdf diff --git a/Code/GraphMol/MarvinParse/MarvinWriter.cpp b/Code/GraphMol/MarvinParse/MarvinWriter.cpp index 06a73e901b8..45615ea254e 100644 --- a/Code/GraphMol/MarvinParse/MarvinWriter.cpp +++ b/Code/GraphMol/MarvinParse/MarvinWriter.cpp @@ -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()) { diff --git a/Code/GraphMol/MarvinParse/testMrvToMol.cpp b/Code/GraphMol/MarvinParse/testMrvToMol.cpp index f93c407da94..8c50c92b0aa 100644 --- a/Code/GraphMol/MarvinParse/testMrvToMol.cpp +++ b/Code/GraphMol/MarvinParse/testMrvToMol.cpp @@ -894,6 +894,7 @@ class MrvTests { // the molecule tests - starting with molfiles/sdf if (testToRun == "" || testToRun == "sdfTests") { std::list 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, diff --git a/Code/GraphMol/MarvinParse/test_data/145323811.mol b/Code/GraphMol/MarvinParse/test_data/145323811.mol new file mode 100644 index 00000000000..e12e1db152f --- /dev/null +++ b/Code/GraphMol/MarvinParse/test_data/145323811.mol @@ -0,0 +1,354 @@ + +Generated by WebMolKit + +172176 0 0 1 0 0 0 0 0999 V2000 + 4.9794 -14.9668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1217 -14.4029 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 5.9476 -12.7045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 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00000000000..9cc0719865e --- /dev/null +++ b/Code/GraphMol/MarvinParse/test_data/145323811.mol.expected.cxsmi @@ -0,0 +1 @@ +CN1CC(=O)N[C@@H](CO)C(=O)N[C@@H](Cc2ccc(-c3ccccc3)cc2)C(=O)NCC(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)NCC(=O)N[C@H](C(=O)NCC(=O)NCC(=O)NCC(=O)NC(CCCCNC(=O)CN2CCN3CC(=O)[O-][Ga+3]4[O-]C(=O)CN(CC2)CCN(CC(=O)[O-]4)CC3)C(N)=O)CSCC(=O)N[C@@H](Cc2ccccc2)C(=O)N[C@@H](Cc2ccc(O)cc2)C1=O.O=C(O)C(F)(F)F.O=C(O)C(F)(F)F.O=C(O)C(F)(F)F 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