Matt Swain

Yes, PubChem now manually override the search results for some common chemical chemical names. There is a section about this in the docs: [Getting a full results list for common...

Sorry I've taken so long to review this - there's some great stuff here. But could you create separate branches for each individual change so they can have separate, more...

I think this is an error in the docs. The default identifier 'namespace' is CID, so if you want to query with SMILES you need to specify it with the...

Unfortunately it looks like the RSC "articlelanding" page is assembled dynamically using JavaScript, as you scroll down the page. So the HTML that you save may not include the full...

```python >>> compounds = pcp.get_compounds('methane', 'name', record_type='3d') >>> m = compounds[0] >>> m Compound(297) >>> m.atoms [Atom(1, C), Atom(2, H), Atom(3, H), Atom(4, H), Atom(5, H)] >>> m.atoms[2].x 0.6833 >>>...

I think this is caused by the phosphonic acid rules: https://github.com/mcs07/MolVS/blob/master/molvs/tautomer.py#L130 It can probably be fixed by making the SMARTS pattern more strict to match only the intended target: https://en.wikipedia.org/wiki/Phosphorous_acid

I'm afraid that won't work. Specifying `max_tautomers` will actually just stop the enumeration once that many have been enumerated, so there's no guarantee that the best scoring tautomer has been...

Yes that seems to be the case. Also it looks like SDF files will only process the first molecule.

This should be possible with the [FragmentRemover](https://github.com/mcs07/MolVS/blob/master/molvs/fragment.py#L136) class, possibly combined with the [Uncharger](https://github.com/mcs07/MolVS/blob/master/molvs/charge.py#L258). There is a [configurable list of SMARTS patterns](https://github.com/mcs07/MolVS/blob/master/molvs/fragment.py#L53) for what is removed.

Could you share an example with the string before and after the conversion?