Fix decoding fragments containing square brackets

[FNTwin]

Changelogs

• Fix issue Decoding fragments containing square brackets fail #24 by updating the regex used to find the branch attachment point
• Add support to encode smiles string with atom mapping (regex changes)

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Checklist:

• Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate).
• Update the API documentation if a new function is added, or an existing one is deleted. Eventually consider making a new tutorial for new features.
• Write concise and explanatory changelogs below.
• If possible, assign one of the following labels to the PR: feature, fix or test (or ask a maintainer to do it for you).

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Original discussion with explanation in: #24

Unrelated but it seems that we are not using isort for the formatting of the package import.

[maclandrol]

Thanks @FNTwin, see comments

[maclandrol]

@FNTwin, Could you revisit this regexp. I think it does not capture atom mapping properly:

import re
inp = "c1cc2c(cc1[C@@H]1CC[C:3][NH2+]1)O[13C]CO2"
re.sub("\[[^:\]]*?\]", "", inp) #c1cc2c(cc11CC[C:3]1)OCCO2

I think just removing anything anything between bracket would cover our cases: r"\[[^\]]*\d[^\]]*\]"

[FNTwin]

Just removing the brackets indeed cover our cases (first version in the issue is exactly like that), but I added the atom mapping case just in case to be "more precise" on the substitution.
After testing I think is safe to avoid this case and just remove the brackets.

[maclandrol]

Can you double check this ?

[FNTwin]

The problem here is that if we don't handle the atom mapping, the attach_pos set will contain the atom mapping pieces and will give us wrong molecules in some cases.

As an example:

smiles="c1cc2c(cc1[C@@H]1CC[C:3][NH2+]1)O[13C]CO2"
scaffold_str = ".".join(frags_str) # c1cc2c(cc1[1*])O[13C]CO2.[C@@H]1([1*])CC[C:3][NH2+]1
attach_pos = set(re.findall(r"(\[\d+\*\]|\[[^:]*:\d+\])", scaffold_str)) #  #{'[13C]CO2.[C@@H]1([1*])CC[C:3]', '[1*]'}

this will give us the safe string 'c1cc2c(cc13)O[13C]CO2.[C@@H]13CC[C:3][NH2+]1'

With my regex:

smiles="c1cc2c(cc1[C@@H]1CC[C:3][NH2+]1)O[13C]CO2"
scaffold_str = ".".join(frags_str) # c1cc2c(cc1[1*])O[13C]CO2.[C@@H]1([1*])CC[C:3][NH2+]1
attach_pos = set(re.findall(r"(\[\d+\*\]|\[[^:]*:\d+\])", scaffold_str)) #  {'[1*]'}

that will give us in this case the exact safe string 'c1cc2c(cc13)O[13C]CO2.[C@@H]13CC[C:3][NH2+]1'

For more difficult cases of atom mapping like [C+:1]#[C:2]CC(C[C:20][O:21]CN)C[C:3]1=[C:7]([H:10])[N-:6][O:5][C:4]1([H:8])[H:9]"

We will have the following attach_pos and final safe string:

modified_regex = {'[1*]'}
old_regex = {'[C:3]', '[N-:6]', '[C:4]', '[O:21]', '[H:9]', '[H:8]', '[C:7]', '[C+:1]', '[C:2]', '[1*]', '[O:5]', '[H:10]', '[C:20]'}
# modified regex
'[C+:1]#[C:2]CC(C[C:3]1=[C:7]([H:10])[N-:6][O:5][C:4]1([H:8])[H:9])C[C:20]2.[O:21]2CN'
# old regex
"[C+:1]#[C:2]CC(C[C:3]1=[C:7]([H:10])[N-:6][O:5][C:4]1([H:8])[H:9])C[C:20][1*].[O:21]([1*])CN"

That will lead at the following mols:
old regex

new regex

[FNTwin]

@maclandrol Addressed the issues, hopefully the second issue is fine!

[maclandrol]

This PR closes #24