{"id":17255228,"url":"https://github.com/unixjunkie/acp4","last_synced_at":"2026-02-05T18:31:53.053Z","repository":{"id":144782227,"uuid":"563224774","full_name":"UnixJunkie/ACP4","owner":"UnixJunkie","description":"AutoCorrelation of Pharmacophore Features ","archived":false,"fork":false,"pushed_at":"2025-02-25T16:01:28.000Z","size":638,"stargazers_count":3,"open_issues_count":1,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-11-23T20:03:02.840Z","etag":null,"topics":["autocorrelation","binding-site","ligand","ocaml-program","pharmacophore","virtual-screening"],"latest_commit_sha":null,"homepage":"","language":"OCaml","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","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":null,"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}},"created_at":"2022-11-08T06:56:42.000Z","updated_at":"2025-09-14T21:45:50.000Z","dependencies_parsed_at":null,"dependency_job_id":"805f9279-ad7c-4fb7-ac71-e2f66406ae40","html_url":"https://github.com/UnixJunkie/ACP4","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/UnixJunkie/ACP4","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACP4","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACP4/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACP4/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACP4/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/ACP4/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2FACP4/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29128704,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-05T18:31:02.507Z","status":"ssl_error","status_checked_at":"2026-02-05T18:29:43.962Z","response_time":65,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["autocorrelation","binding-site","ligand","ocaml-program","pharmacophore","virtual-screening"],"created_at":"2024-10-15T07:10:59.929Z","updated_at":"2026-02-05T18:31:53.034Z","avatar_url":"https://github.com/UnixJunkie.png","language":"OCaml","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ACP4: AutoCorrelation of Pharmacophore Features\n\n```\nacp4 program usage:\n  ./acp4\n  [-i \u003cfilename.ph4\u003e]: input file to encode\n  [-q \u003cfilename.ph4\u003e]: query molecule\n  [--queries \u003cfilename.ph4\u003e]: query molecules\n  [-db \u003cfilename.ph4\u003e]: database to screen\n  -o \u003cfilename.{csv|scores}\u003e: output file (encoded db or query scores)\n  [-np \u003cint\u003e]: nprocs (default=1)\n  [-s \u003cint\u003e]: BST chunk size (default=100000)\n  [-c \u003cfloat\u003e]: cutoff distance (default=5.00)\n  [-f]: force overwriting binary cache files, if any\n  use -f if you are changing -dx or -c compared to previous queries\n  [-dx \u003cfloat\u003e]: radial discretization step (default=0.5)\n  [--no-plot]: turn OFF gnuplot\n  [--no-tap]: neither read nor write from/to binary cache files\n  [--confs]: if the DB has several _consecutive_ conformers\n  [--quick]: quick; exit right after scoring; no perf. metrics\n  [--index]: create a BST index for the DB being screened\n  [--BSTs \u003cfilename.txt\u003e]: file containing a list of serialized BST filenames\n  [-td \u003cfloat\u003e]: maximum Tanimoto _distance_ to (single) query\n  [--BS]: load optimal defaults for binding-sites (ignores -c and -dx)\n  [-v]: verbose/debug mode\n```\n\n```\nacp4_scissors program usage:\n  ./scissors\n  -l \u003cligand.sdf\u003e: binding-site ligand input file\n  -p \u003cprotein.ph4\u003e: receptor protein input file\n  [-d \u003cfloat\u003e]: distance cutoff (default=5.00)\n  -o \u003coutput.ph4\u003e: ligand-defined binding site output file\n  [-v]: verbose/debug mode\n```\n\nTo extract pharmacophore points from a molecule in SDF format,\nuse molenc_ph4.py:\n```\nusage: molenc_ph4.py [-h] [-i input.sdf] [-o output.ph4] [--bild] [--no-group]\n                   [--permissive]\n\ncompute pharmacophore features for 3D molecules\n\noptions:\n  -h, --help     show this help message and exit\n  -i input.sdf   conformers input file\n  -o output.ph4  ph4 features output file\n  --bild         output BILD files for visu in chimera\n  --no-group     turn OFF grouping of HYD features\n  --permissive   turn OFF rdkit valence check\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Facp4","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Facp4","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Facp4/lists"}