smiles attribute is empty

[fjaskolski-dot]

Using pubchempy 1.0.4 (updated) with Spyder 6 (also updated), I can't get 'smiles' form a get_compound request...
See exemple below :

import pubchempy as pcp

for compound in pcp.get_compounds("glucose", 'name'):
print(compound.cid)
print(compound.smiles)

5793

AttributeError Traceback (most recent call last)
Cell In[53], line 3
1 for compound in pcp.get_compounds("glucose", 'name'):
2 print(compound.cid)
----> 3 print(compound.smiles)

AttributeError: 'Compound' object has no attribute 'smiles'

Any other with such an issue ?
Many thanks.

[nbehrnd]

@fjaskolski-dot I'm able to replicate your observation (spyder 6.0.7 with Python 3.13.6 in Windows) with the last commit (4a58fc3) of the default branch of this blessed repository here run after a pip install .). Complementary observations:

• both print(compound.connectivity_smiles) (without information about stereochemistry, nor about isotopes) and print(compound.absolute_smiles) (includes the @ about R/S) are resolved within spyder while reporting 5793 about the cid. This is unexpected because the query for smiles should provide the former (default), or the later (if the database assigned a stereogenic centre).
• your code (i.e. print(compound.smiles)) however yields the absolute SMILES (with @) while running directly within a virtual environment from cmd.exe. (It equally reports cid if requested).

[umair313]

I am also not able to get the smiles, this code is from docs example

import pubchempy as pcp
c = pcp.Compound.from_cid(5090)
c.smiles

error

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[5], line 1
----> 1 c.smiles

AttributeError: 'Compound' object has no attribute 'smiles'

python and pubchemPy versions

python = ">=3.11,<4.0"
pubchempy = "^1.0.4"

[julianpollmann]

@umair313 the pypi release is outdated and installing it will result in that error. Try to install the current main from github:

[tool.poetry.dependencies]
pubchempy= { git = "https://github.com/mcs07/PubChemPy.git", rev = "a5d8646" }

or
pip install git+https://github.com/mcs07/PubChemPy.git@a5d8646