PubChemPy

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Hello, I'm trying to automate the generation of SMILES from GC/MS results. The version of PubChemPy that I just installed seems to block all CAS numbers with hyphens. Removing hyphens...

ecojimb

Can not generate SMILES of compounds from known CAS numbers

4

Hello, I recently began using PubChemPy, and thank you for creating this incredible platform! I am attempting to find the SMILES of over 500 compounds via the `get_compound()` function however...

MathewGolding

At some point, certain compounds have become irretrievable by their names. For example, this compound: https://pubchem.ncbi.nlm.nih.gov/substance/318704449 When I attempt to retrieve it by name, I get an empty list: ```...

gmboyer

Is it possible to get 3D coordinates of ligand using CID or SID?

1

Is it possible to get 3D coordinates of ligand using CID or SID? **Approach-1** ``` import pubchempy as pcp pcp.download('SDF', '4369521.sdf', 4369521, 'cid',overwrite=True) ``` **Approach-2** ``` c = pcp.Compound.from_cid(4369521) coords...

drorhunvural

Hi, Does anyone know if/how "Hazard classes and categories" can be obtained with PubChemPy? This would be an example on Pubchem itself. https://pubchem.ncbi.nlm.nih.gov/compound/15724678#section=Hazard-Classes-and-Categories&fullscreen=true Cheers, Adam

azalewski1

> /usr/local/miniconda/envs/QtMolpro-github/lib/python3.11/site-packages/pubchempy.py:563: SyntaxWarning: "is not" with a literal. Did you mean "!="? > if self.charge is not 0:

pjknowles

Fixing failed search example pcp.get_compounds('CC', searchtype='superstructure', listkey_count=3)

1

Example as given returns error: 'PUGREST.BadRequest' urllib.error.HTTPError: HTTP Error 400: PUGREST.BadRequest Adding 'smiles' as namespace solves the problem. Or perhaps there's a way to get the search to work without...

bertiewooster

Assay.from_aid(2016).to_dict() fails. The reason is that a lot of 'comment' entries are absent altogether. The result is access to other records (e.g. 'target') is denied even if they do exist....

watplatt

Hi, is there a way of obtaining the CCS values as listed on pubchem via pubchempy?

pbjarterot

It looks like there is no way to pass a `timeout` argument to the `urlopen` function within the `get_compouds` function. Could you please add such an option?

Academich