Closed dkoes closed 8 months ago
This problem is because the SMILES names have a period in them. The period is there because you wouldn't let me have an underscore. I recommend using a regular expression to extract the conformer id and let the name be whatever (including containing spaces, underscores, and periods).
Hi David, thanks for the comment and detailed feedback!
That's indeed something we need to improve.
For now, there is a utility function called replace_
to help to replace the underscores in SMILES names:
from Auto3D.utils import replace_
names = ['smi_1', 'smi-2', 'smi3']
new_names = [replace_(name) for name in names]
print(new_names) # output: ['smi-1', 'smi-2', 'smi3']
The replace_
function returns a new name with underscores replaced by dashes, leaving all other characters unchanged.
Hello @dkoes , just an update that I updated auto3d and it accepts any names now. Please let us know in case any additional issues. For now, I will close this issue. Thanks!
Describe the bug I have tried setting
--k 25
and--max_confs 25
and I still only get a single conformer per a smile.To Reproduce Steps to reproduce the behavior:
~/git/Auto3D_pkg/auto3D.py rdrefined.smi --k 25 --max_confs
rdrefined.smi contains all the smiles from PDBbind2020 refined set. rdrefined.smi.gz
Expected behavior More than one conformer per smile.
System information:
Additional context Add any other context about the problem here.