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https://github.com/unixjunkie/molenc

MolEnc: a molecular encoder using rdkit and OCaml.
https://github.com/unixjunkie/molenc

atom-pairs chemical-fingerprint chemoinformatics counted-unfolded-fingerprint lbvs molecular-encoding ocaml-program pharmacophore-points python-script qsar rdkit signature-molecular-descriptor

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MolEnc: a molecular encoder using rdkit and OCaml.

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README 

        
# Introduction



MolEnc: a molecular encoder using rdkit and OCaml.



[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3546675.svg)](https://doi.org/10.5281/zenodo.3546675)



The implemented fingerprint is J-L Faulon's "Signature Molecular Descriptor"

(SMD [1]).

This is an unfolded-counted chemical fingerprint.

Such fingerprints are less lossy than famous chemical fingerprints like ECFP4.

SMD encoding doesn't introduce feature collisions upon encoding.

Also, a feature dictionary is created at encoding time.

This dictionary can be used later on to map a given feature index to an

atom environment.

Molenc also implements unfolded-counted atom pairs [2].



For SMD, we recommend using a radius of zero to one (molenc.sh -r 0:1 ...) or

zero to two.



Currently, the atom typing scheme being used is:

(#pi-electrons, element symbol, #HA neighbors, formal charge).



In the future, we might add pharmacophore feature points[3]

(Donor, Acceptor, PosIonizable, NegIonizable, Aromatic, Hydrophobe),

to allow a fuzzier description of molecules.



# How to install the software



For beginners/non opam users:

download and execute the latest self-installer

shell script from (https://github.com/UnixJunkie/molenc/releases).



Then execute:

```

./molenc-5.0.1.sh ~/usr/molenc-5.0.1

```



This will create ~/usr/molenc-5.0.1/bin/molenc.sh, among other things

inside the same directory.



For opam users:

```

opam install molenc

```



Do not hesitate to contact the author in case you have problems installing

or using the software or if you have any question.



# Usage



```

molenc.sh -i input.smi -o output.txt

         [-d encoding.dix]: reuse existing feature dictionary

         [-r i:j]: fingerprint radius (default=0:1)

         [--pairs]: use atom pairs instead of Faulon's FP

         [-m ]: maximum allowed atom-pair distance

                     (default: no limit)

         [--seq]: sequential mode (disable parallelization)

         [-v]: debug mode; keep temp files

         [-n ]: max jobs in parallel

         [-c ]: chunk size

         [--no-std]: don't standardize input file molecules

                     ONLY USE IF THEY HAVE ALREADY BEEN STANDARDIZED

```



How to encode a database of molecules:



```

molenc.sh -i molecules.smi -o molecules.txt



```



How to encode another database of molecules, but reusing the feature

dictionary from another database:



```

molenc.sh -i other_molecules.smi -o other_molecules.txt -d molecules.txt.dix

```



# Bibliography



[1] Faulon, J. L., Visco, D. P., & Pophale, R. S. (2003). The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies. Journal of chemical information and computer sciences, 43(3), 707-720.



[2] Carhart, R. E., Smith, D. H., & Venkataraghavan, R. (1985). Atom pairs as molecular features in structure-activity studies: definition and applications. Journal of Chemical Information and Computer Sciences, 25(2), 64-73.



[3] Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., & Sheridan, R. P. (1996). Chemical similarity using physiochemical property descriptors. Journal of Chemical Information and Computer Sciences, 36(1), 118-127.