Add molecule encodings for contextual bandit

[YamLyubov]

Adds molecular encoders for contextual graphs. Implemented approaches:

• ECPF - Extended-Connectivity Fingerprints - https://www.semanticscholar.org/paper/Extended-Connectivity-Fingerprints-Rogers-Hahn/d1b796ff0c1895426de11a1eaafc5443be29645d
• RDKF - RDKit topological fingerprint - https://www.rdkit.org/docs/GettingStartedInPython.html#rdkit-topological-fingerprints
• atom_pair - atom pair fingerprint - https://pubs.acs.org/doi/10.1021/ci00046a002
• topoligical_torsion - topoligical torsion fingerprint - https://pubs.acs.org/doi/10.1021/ci00054a008
• mol_descriptors - molecular descriptors - https://www.semanticscholar.org/paper/Molecular-representation-learning-with-language-and-Fabian-Edlich/e4c5e81e6e337bb94af3eb719df5f029b40434fa
• Mol2Vec - vector representations (pretrained model) - https://pubs.acs.org/doi/10.1021/acs.jcim.7b00616
• MoleculeTransformer - vector representation (pretrained model) -
  https://pdfs.semanticscholar.org/2b80/1b911a5a33a4fe523b667c5f6b1b8bbadbbf.pdf

Collected materials: https://docs.google.com/spreadsheets/d/1qDx6hhRMeA185_fLxBRwwcHHmvUOxbG9ID_IkOYZV-g/edit?usp=sharing

Results for 10 trials: qed score

normalized sa score

176

[aim-pep8-bot]

Hello @YamLyubov! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file examples/molecule_search/mol_metrics.py:

Line 18:1: E402 module level import not at top of file

Comment last updated at 2023-09-05 12:37:59 UTC

[codecov-commenter]

Codecov Report

Merging #179 (909d251) into main (d5d1dfa) will increase coverage by 0.10%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #179      +/-   ##
==========================================
+ Coverage   74.02%   74.12%   +0.10%     
==========================================
  Files         129      129              
  Lines        7688     7688              
==========================================
+ Hits         5691     5699       +8     
+ Misses       1997     1989       -8     

Files Changed	Coverage Δ
golem/core/optimisers/genetic/gp_params.py	100.00% <100.00%> (ø)

... and 4 files with indirect coverage changes