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forlilab / Ringtail

Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina
GNU Lesser General Public License v2.1
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Error occurred while writing SDF from RDKit Mol #28

Closed LeThucMinhChau closed 9 months ago

LeThucMinhChau commented 11 months ago

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 commented 11 months ago

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 commented 11 months ago

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 commented 11 months ago

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

sribone commented 11 months ago

I have version='0.5.0'. Thank you!

althea-hansel commented 11 months ago

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 commented 10 months ago

Fixed in https://github.com/forlilab/Meeko/commit/9e8a7ad679fb0577a2107e2d5c6dd8192e4198db. We are releasing meeko v0.6.0 soon and it will include this fix.

diogomart commented 9 months ago

Fixed in Meeko v0.6.0-alpha.3