molenc

Molecular encoder/featurizer using rdkit and OCaml
README

MolEnc: a molecular encoder using rdkit and OCaml.

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.

We recommend using a radius of zero to one (molenc.sh -r 0:1 ...) or
zero to two.

Currently, the fingerprint can be run using atom types
(#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.
It is also planned to support atom pairs[2] in addition
to or in combination with SMD.

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 dictionary
         [-r i:j]; fingerprint radius (default=0:1)
         [--seq]; sequential mode (disable parallelization)
         [--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.

Install
Sources
v11.4.0.tar.gz
md5=71c69b02a616685dc37d6fed4d1e9707
Dependencies
Reverse Dependencies