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arneschneuing / DiffSBDD

A Euclidean diffusion model for structure-based drug design.
MIT License
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Openbabel error #29

Open githubrudramani opened 1 year ago

githubrudramani commented 1 year ago

Hi Arne, Every time I run generate_ligands.py script, I get babel error:

*** Open Babel Error in TetStereoToWedgeHash Failed to set stereochemistry as unable to find an available bond. Though it writes the SDF file.

Below is my command. _python generate_ligands.py checkpoints/full_atom.ckpt --pdbfile ../test/protein.pdb --outdir ../test/results/ --resilist A:110 A:111 A:112 A:130 A:131 A:133 A:134 A:142 A:143 A:145 A:146 A:179 A:180 A:182 A:196 A:250 A:251 A:253 A:254 A:256 A:382 A:383 A:385 A:386 A:387 A:72 A:73 A:76 A:78 A:82 A:86 A:90

arneschneuing commented 1 year ago

Hi Rudramani, does the SDF file look reasonable? This error seems to occur in cases where Open Babel has trouble inferring the correct connectivity (see here)

xuhuangchao commented 3 months ago

Hi Arne, Every time I run generate_ligands.py script, I get babel error:

*** Open Babel Error in TetStereoToWedgeHash Failed to set stereochemistry as unable to find an available bond. Though it writes the SDF file.

Below is my command. _python generate_ligands.py checkpoints/full_atom.ckpt --pdbfile ../test/protein.pdb --outdir ../test/results/ --resilist A:110 A:111 A:112 A:130 A:131 A:133 A:134 A:142 A:143 A:145 A:146 A:179 A:180 A:182 A:196 A:250 A:251 A:253 A:254 A:256 A:382 A:383 A:385 A:386 A:387 A:72 A:73 A:76 A:78 A:82 A:86 A:90

have you already solved it? i also met this problem in generate_ligands.