Molecular Mechanics in OCaml
- OCaml 82.9%
- Python 14.6%
- Standard ML 1.4%
- Shell 1%
- Makefile 0.1%
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| data | ||
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| dune-project | ||
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| README.md | ||
MMO: Molecular Mechanics in OCaml
Some code for flexible ligand / rigid protein calculations.
Warning: this code is prototypical in nature. Maybe, part of it will be released as a proper standalone library in the long-term (the Mol and Mol2 modules plus their dependencies).
Dataset
The dataset that was produced using this software can be downloaded from:
To compile the software
Tested on Ubuntu Linux 24.04 w/ ocaml-4.14.1.
On Linux or a UNIX-like:
mkdir -p ~/src
cd src
git clone https://github.com/UnixJunkie/MMO.git
cd MMO
sudo apt install opam
opam init
eval `opam env --shell=bash`
opam pin add mmo .
make
How to score a ligand conformer w/ psi4 (true QM calculation)
This requires mayachemtools and psi4 to be installed.
~/src/MMO/bin/psi4_ene.sh ligand.sdf
How to score a ligand conformer w/ ANI-2 (approximated QM)
This requires the Python package torchani to be installed:
~/src/MMO/bin/QM_score_mol2.sh ligand.mol2
How to run a MC simulation in dihedral space to minimize a docked ligand using ANI-2?
If you have compiled the software and you have torchani installed, you can run:
./lds -f --no-interp --ligand-only --intra-QM -lig docked_ligand.mol2 \
-rec prot_rec.pqrs -roi prot_ROI.bild -steps 10k --ene 50 --no-compress --out-dir MC10kQM