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chem-usecase

Chemical Similarity Usecase

Background

Chemical Similarity usecase uses Tanimoto algorithm to calculate % similarity between 1 molecule with others. We need to scan the whole data set to filter closest molecules, which inputs are molecule and threshold. For example, given a molecule with SMILE as "IC=C1/CCC(C(=O)O1)c2cccc3ccccc23" and threshold = 90%, returns set of molecules that have similarity >= 90%

Requirements

RDKit Python: http://www.rdkit.org/docs/Install.html
ChemBL Dataset: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/
Pilosa: https://github.com/pilosa/pilosa

Import dataset to pilosa

Export data from sdf or mysql to csv file, then import csv to pilosa. Since chembl_id in SD file always come with CHEMBL, e.g CHEMBL6329, which pilosa hasn’t support string id yet, we will remove CHEMBL and import chembl_id with integer after that. If you export data from mysql, it uses molregno in compound_structures as unique integer ID for molecule, so you just need to import molregno as chembl_id

Export to csv from sdf file: python import_from_sdf -p ~/Downloads/chembl_22.sdf -file id_fingerprint.csv
Export to csv from mysql: python import_from_mysql -d chembl_22 -u root -file id_fingerprint.csv

Import from csv file to pilosa (mol and inverse-mol are default database, mole.n is default frame)

Open Pilosa server:
```
 pilosa server
```

Create mole database

 curl localhost:10101/index/mole -X POST -d '{"options": {"columnLabel": "position_id"}}'

Create frame fingerprint

  curl localhost:10101/index/mole/frame/fingerprint -X POST -d '{"options": {"rowLabel": "chembl_id", "inverseEnabled": true, "cacheSize": 2000000}}'

Run import script

 pilosa import -d mole -f fingerprint id_fingerprint.csv

Queries

Retrieve molecule_ids that have similarity >= 90%. (Default db="mole", frame="fingerprint", hosts=127.0.0.1:10101)
```
python similar.py -s "I\C=C/1\CCC(C(=O)O1)c2cccc3ccccc23" -t 90
```

Retrive molecule_id from a smile

python get_mol_fr_smile.py -s "I\C=C/1\CCC(C(=O)O1)c2cccc3ccccc23"

Benchmark running for thresholds = [50, 70, 75, 80, 85, 90]
```
python benchmarks -id 24
```

License

chem-usecase by Linh Vo

To the extent possible under law, the person who associated CC0 with pilosa chem-usecase has waived all copyright and related or neighboring rights to chem-usecase.

You should have received a copy of the CC0 legalcode along with this work. If not, see http://creativecommons.org/publicdomain/zero/1.0/.

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chem-usecase's Issues

Review use case for compatibility with Pilosa changes

Missing license

Please add a license to this. Should be consistent with FeatureBaseDB/notebooks#2 which I think will be CC-BY. Check with Alan on this. Thanks!

Remove dependency on inverse frames

The inverse frames feature is being deprecated, so this use case should not depend on it. If the use case requires inverse frames, they could be implemented externally. In that case we may need to rethink the use case more broadly, as inverse frames won't scale well.

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