Molecule.from_pdb_with_smiles() warns about the pdb having unspecified stereochemistry
#1000
Labels
Comments
|
Woo! Issue 1000! |
|
This seems to not happen when the PDB coordinates are not all zero; the following code provides no warning: from openff.toolkit.topology import Molecule
smiles = "C[C@H]([NH3+])C(=O)[O-]"
path = "mol.pdb"
from_smiles = Molecule.from_smiles(smiles)
from_smiles.generate_conformers()
from_smiles.to_file(path, "pdb")
mol = Molecule.from_pdb_and_smiles(
path,
smiles,
allow_undefined_stereo=False
)Perhaps because RdKit is inferring the stereochemistry from the coordinates? |
|
Oh, this problem isn't what I thought it was. This function is really well-written and is behaving safely (the resulting molecule DOES get its stereochemistry from the SMILES, and NOT from the PDB), the warning just needs to be squelched. |
5 tasks
# for free
to join this conversation on GitHub.
Already have an account?
# to comment
Describe the bug
Molecule.from_pdb_and_smilesgives a spurious warning about the PDB file having unspecified stereochemistry. This is spurious because the whole purpose of the method is to work around this limitation of the PDB format. I'm worried that the warning will be confusing to users.To Reproduce
This succeeds, but gives a spurious warning.
Output
I've added line breaks for clarity
This is a very confusing warning, as the
from_pdb_and_smilesmethod has theallow_undefined_stereoargument. I'm worried that users will see this error and think that they've done something wrong or that the toolkit has a bug and is unable to assign stereochemistry to the PDB from the SMILES, when in fact this is raised in the course of reading the PDB, before the SMILES is processed.Computing environment (please complete the following information):
conda listAdditional context
The offending call to
from_rdkitis made here:https://github.com/openforcefield/openff-toolkit/blob/cb46142b84690103b60dbf2de12cd65bcd3d74ea/openff/toolkit/utils/toolkits.py#L2910-2915
The text was updated successfully, but these errors were encountered: