{"id":19849516,"url":"https://github.com/filipspl/fingernat-pymol-plugin","last_synced_at":"2026-02-19T15:03:56.233Z","repository":{"id":45537171,"uuid":"429062363","full_name":"filipsPL/fingernat-pymol-plugin","owner":"filipsPL","description":"PyMOL plugin to visualize interactions detected by the fingeRNAt program","archived":false,"fork":false,"pushed_at":"2022-12-22T12:05:59.000Z","size":1902,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2026-02-11T10:45:42.151Z","etag":null,"topics":["molecular-interactions","molecular-modeling","pymol-plugin","visualization"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/filipsPL.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":".zenodo.json"}},"created_at":"2021-11-17T13:45:41.000Z","updated_at":"2024-02-27T14:33:58.000Z","dependencies_parsed_at":"2023-01-30T08:31:13.525Z","dependency_job_id":null,"html_url":"https://github.com/filipsPL/fingernat-pymol-plugin","commit_stats":null,"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"purl":"pkg:github/filipsPL/fingernat-pymol-plugin","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/filipsPL%2Ffingernat-pymol-plugin","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/filipsPL%2Ffingernat-pymol-plugin/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/filipsPL%2Ffingernat-pymol-plugin/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/filipsPL%2Ffingernat-pymol-plugin/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/filipsPL","download_url":"https://codeload.github.com/filipsPL/fingernat-pymol-plugin/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/filipsPL%2Ffingernat-pymol-plugin/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29619190,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-19T13:04:20.082Z","status":"ssl_error","status_checked_at":"2026-02-19T13:03:33.775Z","response_time":117,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["molecular-interactions","molecular-modeling","pymol-plugin","visualization"],"created_at":"2024-11-12T13:21:26.061Z","updated_at":"2026-02-19T15:03:56.215Z","avatar_url":"https://github.com/filipsPL.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"fingernat-pymol-plugin\n============\n\n\u003c!-- TOC START min:1 max:6 link:true asterisk:false update:true --\u003e\n- [fingernat-pymol-plugin](#fingernat-pymol-plugin)\n- [About](#about)\n- [Installation](#installation)\n  - [Prerequisities](#prerequisities)\n  - [Plugin installation in PyMOL](#plugin-installation-in-pymol)\n- [Compatibility and tests](#compatibility-and-tests)\n- [Usage](#usage)\n- [Screenshots](#screenshots)\n- [Contributors](#contributors)\n\u003c!-- TOC END --\u003e\n\n\n\n# About\n\n![logo_fingernat](logo_fingernat160.png)\n\nThis PyMOL plugin visualizes interactions detected by the [fingeRNAt progam](https://github.com/n-szulc/fingeRNAt/). This means that you need to run it first and generate data to be visualized in this plugin. But don't worry, it's quite simple :)\n\nThis plugin works best with PyMOL \u003e= 2.2.3 and Python 3.\n\n[![Check Markdown links](https://github.com/filipsPL/fingernat-pymol-plugin/actions/workflows/action-links.yml/badge.svg)](https://github.com/filipsPL/fingernat-pymol-plugin/actions/workflows/action-links.yml) [![DOI](https://zenodo.org/badge/429062363.svg)](https://zenodo.org/badge/latestdoi/429062363) [![cffconvert](https://github.com/filipsPL/fingernat-pymol-plugin/actions/workflows/cffconvert.yml/badge.svg)](https://github.com/filipsPL/fingernat-pymol-plugin/actions/workflows/cffconvert.yml)\n\n\n**To cite:** Szulc, N. A., Mackiewicz, Z., Bujnicki, J. M., \u0026 Stefaniak, F. (2022). fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PLOS Computational Biology, 18(6), e1009783. https://doi.org/10.1371/journal.pcbi.1009783\n\nThis repo DOI: [![DOI](https://zenodo.org/badge/429062363.svg)](https://zenodo.org/badge/latestdoi/429062363)\n\n# Installation\n\n## Prerequisities\n\nThe plugin works under the Python 3 and makes use of the pandas module. To install it:\n\n```bash\n# using pip\npython3 -m pip install pandas\n\n# or conda\nconda install pandas\n\n# or in debian/ubuntu using apt:\napt install python3-pandas\n\n# or install the full conda environment of pymol and pandas, ready to install this plugin\nconda create -y --name pymol-pandas -c conda-forge  python\"\u003e=3.5\" pandas pymol-open-source\n```\n\n## Plugin installation in PyMOL\n\n1. In PyMOL window go to top menu - Plugin -\u003e Plugin manager -\u003e Install new plugin\n1. In the URL field paste one of the following links:\n  - the latest release: \u003c!-- RELEASE_START --\u003e`https://github.com/filipsPL/fingernat-pymol-plugin/archive/refs/tags/0-4-2-8.zip`\u003c!-- RELEASE_END --\u003e,\n  - or the latest code archive: `https://github.com/filipsPL/fingernat-pymol-plugin/archive/refs/heads/main.zip`\n\n\n\n![](obrazki/README-ff4621f4.png)\n\nclick `Fetch`, confirm the installation and the path.\n\n3. The fingeRNAt plugin is available from the Plugin menu:\n\n![](obrazki/README-ded6536c.png)\n\n\n# Compatibility and tests\n\nThis PyMOL plugin was tested in the following setups:\n\n| PyMOL version | Linux | MacOS | Windows |\n| ------------- |:-----:|:-----:|:-------:|\n| 2.2.3         |  ✅   |       |         |\n| 2.3.2         |  ✅   |       |         |\n| 2.4.0         |  ✅   |   ✅  |         |\n| 2.5.0         |  ✅   |       |         |\n| 2.6.0a        |  ✅   |       |         |\n\n\n\n# Usage\n\n1. Load into PyMOL nucleic acid and ligand structures you had used to detect interactions with the fingeRNAt.\n\n2. Open the fingeRNAt plugin, click Browse and point to the DETAIL_... tsv file which was generated by fingeRNAt.\n\n3. Click `Proceed!`\n\n![](obrazki/README-5b762be2.png)\n\n4. A bunch of new groups and objects are created:\n\n![](obrazki/README-851e9a88.png)\n\n- Interactions: objects holding detected interactions. The exact number depends of the detected inteactions types.\n- Receptor preferences: objects showing preferences of the receptor for forming/accomodating the given type of interaction.\n- Ligand preferences: objects showing preferences of the ligand binding pocket for forming/accomodating the given type of interaction.\n- Neighbours: fragment of the receptor containing residues which form interactions with ligand\n\nEach group and object can be hidden/shown separately.\n\n5. Each ligand's model (state) contains interactions detected for this particular model. The last model (state) contains the visual legend of the detected interactions:\n\n![](obrazki/README-777f64f7.png)\n\n\nAdditionally, the color codes are printed in the console.\n\n```\n---------- Colors legend: -----------\n  Hydrogen bond (HB) is presented in marine\n  Cation-anion (CA) is presented in red\n  Halogen bond (HAL) is presented in purple\n  Lipophilic (Lipophilic) is presented in silver\n  Pi-stacking (Pi_Stacking) is presented in orange\n  Pi-cation (Pi_Cation) is presented in green\n  Pi-anion (Pi_Anion) is presented in hotpink\n  Water-mediated (Water-mediated) is presented in blue\n  Ion-mediated (Ion-mediated) is presented in salmon\n  any_contact (any_contact) is presented in teal\n```\n\nThe exact number of interactions depends on the input data.\n\n# Screenshots\n\n\n| pymol                            | description                                                                    |\n| -------------------------------- | ------------------------------------------------------------------------------ |\n| ![](obrazki/README-65a8be8a.png) | Overview of the formed interactions                                            |\n| ![](obrazki/README-8890c249.png) | Receptor preferences                                                           |\n| ![](obrazki/README-e95e087b.png) | Ligand preferences in the ligand binding site                                 |\n| ![](obrazki/README-2765c99c.png) | Preferred positions of Pi-involving interactions and cation anion-interactions |\n| ![](obrazki/README-1945eb54.png) | As above, but for the receptor                                                 |\n| ![](obrazki/README-e481bf7b.png) | User defined interactions; some bonds are heading to implicit hydrogens        |\n\n\n# Contributors\n\n| :octocat:       | github                                   | contact                                                                  |\n| --------------- | ---------------------------------------- | ------------------------------------------------------------------------ |\n| Filip Stefaniak | [@filipsPL](https://github.com/filipsPL) | ![](https://img.shields.io/badge/fstefaniak-%40iimcb.gov.pl-brightgreen) |\n| Natalia Szulc   | [@n-szulc](https://github.com/n-szulc)   | ![](https://img.shields.io/badge/nszulc-%40iimcb.gov.pl-brightgreen)     |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffilipspl%2Ffingernat-pymol-plugin","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffilipspl%2Ffingernat-pymol-plugin","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffilipspl%2Ffingernat-pymol-plugin/lists"}