Add SMILES standardizer code

[shntnu]

• Moves over https://github.com/jump-cellpainting/compound-annotator/blob/main/StandardizeMolecule.py to here, after factoring in @srijitseal's code from https://github.com/jump-cellpainting/jump-cellpainting/pull/156
• I had to use conda because rdkit is not on pypi
• Added a .gitignore because I wasn't sure how you want to handle some ignores globally @afermg
• Tests pass locally
• Did not check coverage
• The jump_canonical corresponds to the SMILES made public via Add SMILES to compounds.csv.gz jump-cellpainting/datasets#103 (comment) (except for 1 compound; see below)

---

import pandas as pd

df = pd.read_csv("/home/ec2-user/jump-cellpainting/3.standardize/standardize_ksiling_jumpmoa_jumptarget2/data/05_release/2022_10_18_JUMP-CP_compound_library_restandardized.csv", low_memory=False)
df = df.drop(columns=["jcp2020_id"])

df2 = df.loc[df.InChI_standardized != df.InChI_standardized_orig].drop_duplicates()

df2 = df2.transpose()
df2.columns = ['X1', 'X2']
df2

<style scoped> .dataframe tbody tr th:only-of-type { vertical-align: middle; }

.dataframe tbody tr th {
    vertical-align: top;
}

.dataframe thead th {
    text-align: right;
}

</style>

	X1	X2
SMILES_original	C=C(NC(=O)C(=C)NC(=O)c1csc(C2=NC3c4csc(n4)C4NC...	C=C(NC(=O)C(=C)NC(=O)c1csc(C2=NC3c4csc(n4)C4NC...
SMILES_standardized	CCC1NC(=O)C(C(C)O)NC(=O)c2csc(n2)C23CCC(c4nc(C...	CCC1NC(=O)C(C(C)O)NC(=O)c2csc(n2)C23CCC(c4nc(C...
InChI_standardized	InChI=1S/C72H85N19O18S5/c1-14-26(3)47-63(105)7...	InChI=1S/C72H85N19O18S5/c1-14-26(3)47-63(105)7...
InChIKey_standardized	AXHZBYJITSPJMH-UHFFFAOYSA-N	AXHZBYJITSPJMH-UHFFFAOYSA-N
jcp2022_id	JCP2022_091373	JCP2022_091373
pert_iname	thiostrepton	thiostrepton
InChIKey_orig	NSFFHOGKXHRQEW-DVRIZHICSA-N	NSFFHOGKXHRQEW-AIHSUZKVSA-N
InChIKey_standardized_orig	UTBOEBCWXGDOGI-UHFFFAOYSA-N	UTBOEBCWXGDOGI-UHFFFAOYSA-N
InChI_standardized_orig	InChI=1S/C72H85N19O18S5/c1-14-26(3)47-63(105)7...	InChI=1S/C72H85N19O18S5/c1-14-26(3)47-63(105)7...
jump_cp_control_type	NaN	NaN
pert_control_iname	NaN	NaN
Source[1]	Broad	Broad
Source[2]	NaN	NaN
Source[3]	NaN	NaN
Source[4]	NaN	NaN
Selection[1]	T	T
Selection[2]	NaN	NaN
Selection[3]	NaN	NaN

df2.loc[df2.X1 != df2.X2]

<style scoped> .dataframe tbody tr th:only-of-type { vertical-align: middle; }

.dataframe tbody tr th {
    vertical-align: top;
}

.dataframe thead th {
    text-align: right;
}

</style>

	X1	X2
InChIKey_orig	NSFFHOGKXHRQEW-DVRIZHICSA-N	NSFFHOGKXHRQEW-AIHSUZKVSA-N
jump_cp_control_type	NaN	NaN
pert_control_iname	NaN	NaN
Source[2]	NaN	NaN
Source[3]	NaN	NaN
Source[4]	NaN	NaN
Selection[2]	NaN	NaN
Selection[3]	NaN	NaN

[afermg]

I think there is some html leaking on the PR , such as " <style scoped> .dataframe tbody tr th:only-of-type { vertical-align: middle; } ". I am going to presume that is not relevant to the PR itself.

[shntnu]

Yes you can ignore the leak

[afermg]

It requires some minor adjustments, but looks okay to me. Let me know if you think some of my comments are too cumbersome to implement. Also, I was able to install all dependencies using pip and lock them (See 0e53775, it uses poetry though). Would you consider adding that as an alternative dependency management solution? Space is already very limited on DGX and conda is well known for its massive venv sizes.

[shntnu]

@afermg Thank you for your thorough review! I'll go ahead and merge now.