{"id":17255098,"url":"https://github.com/unixjunkie/mmo","last_synced_at":"2025-04-14T05:40:35.166Z","repository":{"id":223795390,"uuid":"761573854","full_name":"UnixJunkie/MMO","owner":"UnixJunkie","description":"Molecular Mechanics in OCaml","archived":false,"fork":false,"pushed_at":"2025-01-20T17:50:40.000Z","size":1628,"stargazers_count":7,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-27T19:23:11.400Z","etag":null,"topics":["ani-2x","docking","ligand","molecular-mechanics","monte-carlo","ocaml-library","ocaml-program","protein","universal-force-field"],"latest_commit_sha":null,"homepage":"","language":"OCaml","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/UnixJunkie.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-02-22T04:45:15.000Z","updated_at":"2025-01-16T10:56:44.000Z","dependencies_parsed_at":"2025-01-15T15:50:52.079Z","dependency_job_id":"3b0a01c6-d6b7-4f82-80f4-32e2a53c58d7","html_url":"https://github.com/UnixJunkie/MMO","commit_stats":null,"previous_names":["unixjunkie/mmo"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FMMO","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FMMO/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FMMO/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FMMO/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/MMO/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248830416,"owners_count":21168271,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ani-2x","docking","ligand","molecular-mechanics","monte-carlo","ocaml-library","ocaml-program","protein","universal-force-field"],"created_at":"2024-10-15T07:10:41.815Z","updated_at":"2025-04-14T05:40:35.143Z","avatar_url":"https://github.com/UnixJunkie.png","language":"OCaml","readme":"# MMO: Molecular Mechanics in OCaml\n\nSome code for flexible ligand / rigid protein calculations.\n\nWarning: this code is prototypical in nature.\nMaybe, part of it will be released as a proper standalone library in the long-term\n(the Mol and Mol2 modules plus their dependencies).\n\n# Dataset\n\nThe dataset that was produced using this software can be downloaded from:\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10682034.svg)](https://doi.org/10.5281/zenodo.10682034)\n\n## To compile the software\n\nTested on Ubuntu Linux 24.04 w/ ocaml-4.14.1.\n\nOn Linux or a UNIX-like:\n```bash\nmkdir -p ~/src\ncd src\ngit clone https://github.com/UnixJunkie/MMO.git\ncd MMO\nsudo apt install opam\nopam init\neval `opam env --shell=bash`\nopam pin add mmo .\nmake\n```\n## How to score a ligand conformer w/ psi4 (true QM calculation)\n\nThis requires mayachemtools and psi4 to be installed.\n\n```bash\n~/src/MMO/bin/psi4_ene.sh ligand.sdf\n```\n\n## How to score a ligand conformer w/ ANI-2 (approximated QM)\n\nThis requires the Python package torchani to be installed:\n\n```bash\n~/src/MMO/bin/QM_score_mol2.sh ligand.mol2\n```\n\n## How to run a MC simulation in dihedral space to minimize a docked ligand using ANI-2?\n\nIf you have compiled the software and you have torchani installed, you can run:\n```bash\n./lds -f --no-interp --ligand-only --intra-QM -lig docked_ligand.mol2 \\\n  -rec prot_rec.pqrs -roi prot_ROI.bild -steps 10k --ene 50 --no-compress --out-dir MC10kQM\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fmmo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Fmmo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Fmmo/lists"}