Error occurred while writing SDF from RDKit Mol

[LeThucMinhChau]

I try to write SDF file from my bookmark, however, I tried to export SDF files but it returns: 'Error occurred while writing SDF from RDKit Mol'. I am using the new version of Ringtail, is there any updates in the dependencies or is it a bug in the code?

rt_process_vs.py read -i input.db -s bookmark --export_sdf_path sdf

[althea-hansel]

Hi, thank you for reaching out! There is an additional dependency on chemicalite which is frequently the issue, in case you have not installed that yet.

If that does not resolve the issue, can you please run rt_process_vs.py read -i input.db -s bookmark --export_sdf_path sdf -d and share the output?

[sribone]

I have the same problem! I already update chemicalite, but the error persist. The -d option is returning the following message:

Logging level set to debug
Writing SR13.sdf
Closing database
Traceback (most recent call last):
File "/home/sribone/anaconda3/envs/ringtail/lib/python3.10/site-packages/ringtail/outputmanager.py", line 210, in write_out_mol
mol = RDKitMolCreate.combine_rdkit_mols(mol_flexres_list)
File "/home/sribone/anaconda3/envs/ringtail/lib/python3.10/site-packages/meeko/rdkit_mol_create.py", line 370, in combine_rdkit_mols
data = json.loads(mol.GetProp("meeko"))
KeyError: 'meeko'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/sribone/anaconda3/envs/ringtail/bin/rt_process_vs.py", line 86, in
rt_core.write_molecule_sdfs()
File "/home/sribone/anaconda3/envs/ringtail/lib/python3.10/site-packages/ringtail/ringtailcore.py", line 465, in write_molecule_sdfs
self.output_manager.write_out_mol(
File "/home/sribone/anaconda3/envs/ringtail/lib/python3.10/site-packages/ringtail/outputmanager.py", line 224, in write_out_mol
raise OutputError("Error occurred while writing SDF from RDKit Mol") from e
ringtail.exceptions.OutputError: Error occurred while writing SDF from RDKit Mol

ERROR: Error occurred while writing SDF from RDKit Mol

[althea-hansel]

Thank you for including the error traceback. Can you please check what version of Meeko you have installed?

[sribone]

I have version='0.5.0'. Thank you!

[althea-hansel]

Thank you very much. I was able to reproduce your error with the latest version of Meeko but not an older one. I have escalated this issue to the senior Meeko developer and we will keep you updated on the progress.

[diogomart]

Fixed in forlilab/Meeko@9e8a7ad. We are releasing meeko v0.6.0 soon and it will include this fix.

[diogomart]

Fixed in Meeko v0.6.0-alpha.3