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check molecule consists of a single fragment and has no queries #120

Merged
merged 3 commits into from
Aug 20, 2024
Merged

check molecule consists of a single fragment and has no queries #120

merged 3 commits into from
Aug 20, 2024

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diogomart
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Fixes #118

diogomart added 2 commits May 18, 2024 17:34
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check molecule consists of a single fragment
2a54735
@diogomart
raise error for RDKit mol with queries
3091839 
improves over ba15b7d
which was a fix for a specific type of query that addressed
#62
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Added commit to raise error for rdkit mols with queries.
Earlier, a fix for a specific type of query reported in #62 was implemented in 3091839
Other types of queries have been observed in SD files (aka SDF) from PDBBind.
This added commit (3091839) is a general "solution".

@diogomart diogomart changed the title check molecule consists of a single fragment check molecule consists of a single fragment and has no queries May 31, 2024
@diogomart diogomart requested a review from psharma-sr August 2, 2024 17:27
@diogomart diogomart requested a review from nbruciaferri August 14, 2024 05:50
This was referenced Aug 14, 2024
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nbruciaferri
nbruciaferri approved these changes Aug 20, 2024
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meeko/molsetup.py
@@ -1615,6 +1615,10 @@ def from_mol(
if mol.GetNumConformers() > 1 and conformer_id == -1:
msg = "RDKit molecule has multiple conformers. Considering only the first one."
print(msg, file=sys.stderr)
if len(Chem.GetMolFrags(mol)) != 1:
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Looks good to me!

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Thanks @nbruciaferri!

@diogomart diogomart merged commit 2b026f2 into develop Aug 20, 2024
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@diogomart diogomart deleted the check_fragments branch August 20, 2024 16:43
@diogomart diogomart mentioned this pull request Oct 1, 2024
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@nbruciaferri nbruciaferri nbruciaferri approved these changes

@psharma-sr psharma-sr Awaiting requested review from psharma-sr

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@diogomart @nbruciaferri