{"id":17255126,"url":"https://github.com/unixjunkie/acpc","last_synced_at":"2025-04-14T05:40:54.545Z","repository":{"id":144782226,"uuid":"15753907","full_name":"UnixJunkie/ACPC","owner":"UnixJunkie","description":"Chemoinformatics tool for ligand-based virtual screening","archived":false,"fork":false,"pushed_at":"2023-01-11T03:43:14.000Z","size":689,"stargazers_count":19,"open_issues_count":8,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-27T19:23:30.956Z","etag":null,"topics":["chemoinformatics","lbvs","ligand","ocaml","partial-charges"],"latest_commit_sha":null,"homepage":null,"language":"OCaml","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","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}},"created_at":"2014-01-09T01:52:28.000Z","updated_at":"2024-05-21T09:11:26.000Z","dependencies_parsed_at":null,"dependency_job_id":"97431071-c67c-4a8b-8c37-98d2bc2a6939","html_url":"https://github.com/UnixJunkie/ACPC","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACPC","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACPC/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACPC/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACPC/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/ACPC/tar.gz/refs/heads/master","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":["chemoinformatics","lbvs","ligand","ocaml","partial-charges"],"created_at":"2024-10-15T07:10:45.555Z","updated_at":"2025-04-14T05:40:54.499Z","avatar_url":"https://github.com/UnixJunkie.png","language":"OCaml","funding_links":[],"categories":[],"sub_categories":[],"readme":"ACPC v1.0\n=========\n\n![Logo](ACPC_logo.png?raw=true)\n\nDon't hesitate to contact the author in case you have problems running\nthe software or discover a bug.\n\nInstallation\n------------\n\nTo install ACPC, you first need to install and configure\nthe OCaml package manager (OPAM). Cf. http://opam.ocaml.org/\n\nOnce this is done, you can automatically install ACPC\nwith the following command:\n\n    $ opam install acpc\n\nRecommended usage (protocol)\n----------------------------\n\nACPC was designed to be rotation and translation invariant.\nACPC is not invariant to the conformer of a molecule,\nneither to the charge model that was used to assign partial charges to it.\n\nThe following protocol has been validated:\nthe query molecule(s) _AND_ the database to screen must be prepared in\nthe same way. The same software with same parameters must be used\nto assign partial charges and generate conformers for _ALL_ molecules.\n\nThe recommended charge models are:\nMOE's MMFF94x or as a fallback Open Babel's Gasteiger.\n\nReading the related research article is highly recommended:\n\"A rotation-translation invariant molecular descriptor of\npartial charges and its use in ligand-based virtual screening\".\nCiting the article is kindly asked from users of the software.\n\nExamples\n--------\n\n1) one query on a small database\n\n    $ acpc -q query.mol2 -db database.mol2\n\n2) same but storing the top 10 molecules\n\n    $ acpc -q query.mol2 -db database.mol2 -top 10 -o ten_best.mol2\n\n3) one query on a large database\n\n    $ acpc_big -q query.mol2 -db database.mol2\n\n4) separate each molecule from a mol2 file into separate files\n\n    $ acpc_mol2tool some_molecules.mol2\n\nGet some help\n-------------\n\n    $ acpc -h\n      -cmp {CC|Tani|Tref|Tdb} LBAC+/- comparison method (default: CC)\n      -htq                    list molecules scoring Higher Than the Query with itself\n      -q query.mol2           query (incompatible with -qf)\n      -qf f                   file containing a list of mol2 files (incompatible with -q)\n      -db db.mol2             database\n      -dx float               X axis discretization (default: 0.005000)\n      -v                      output intermediate results\n      -nopp                   don't rm duplicate molecules\n      -np nprocs              max CPUs to use (default: 1)\n      -ng                     no gnuplot\n      -nr                     no ROC curve (also sets -ng)\n      -o output.mol2          output file (also requires -top, incompatible with -qf)\n      -top N                  nb. best scoring molecules to output (also requires -o)\n      -help                   Display this list of options\n      --help                  Display this list of options\n\n    # acpc_big -h\n      -q query.mol2 query\n      -db db.mol2   database\n      -dx float     X axis discretization (default: 0.005000)\n      -help         Display this list of options\n      --help        Display this list of options\n\nWARNING\n-------\n\nDon't do two queries at the same time on the same computer or on top of NFS\nwith a same query molecule file (-q SOME_QUERY.mol2), this may overwrite\nresult files in a strange way (SOME_QUERY.ranks, SOME_QUERY.scores and\nSOME_QUERY.scored-label).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Facpc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Facpc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Facpc/lists"}