{"id":19449378,"url":"https://github.com/insilichem/gaudiview","last_synced_at":"2025-04-25T03:31:53.488Z","repository":{"id":112797227,"uuid":"88639489","full_name":"insilichem/gaudiview","owner":"insilichem","description":"UCSF Chimera extension to explore and analyze GaudiMM \u0026 GOLD solutions","archived":false,"fork":false,"pushed_at":"2021-10-26T08:31:38.000Z","size":295,"stargazers_count":4,"open_issues_count":1,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2023-10-20T20:24:08.297Z","etag":null,"topics":["docking","molecular-structures","ucsf-chimera","visualization"],"latest_commit_sha":null,"homepage":"http://tangram-suite.readthedocs.io/en/latest/tangram_gaudiview.html","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/insilichem.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}},"created_at":"2017-04-18T15:15:01.000Z","updated_at":"2023-06-24T10:47:05.000Z","dependencies_parsed_at":"2023-04-07T01:07:04.596Z","dependency_job_id":null,"html_url":"https://github.com/insilichem/gaudiview","commit_stats":null,"previous_names":[],"tags_count":4,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insilichem%2Fgaudiview","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insilichem%2Fgaudiview/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insilichem%2Fgaudiview/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insilichem%2Fgaudiview/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/insilichem","download_url":"https://codeload.github.com/insilichem/gaudiview/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223979769,"owners_count":17235462,"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":["docking","molecular-structures","ucsf-chimera","visualization"],"created_at":"2024-11-10T16:32:12.154Z","updated_at":"2024-11-10T16:32:50.715Z","avatar_url":"https://github.com/insilichem.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GaudiView #\n\nLight interface to explore, view and analyze solutions from [GaudiMM](https://github.com/insilichem/gaudi) and [GOLD](https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/), inside [UCSF Chimera](http://www.cgl.ucsf.edu/chimera).\n\n## Usage\n\n1. Open up Chimera and launch `Tools\u003e InsiliChem\u003e GaudiView`. Select a YAML-formatted `*.gaudi.output` file, as generated by GaudiMM. It will also display GOLD results if you choose the corresponding `gold.conf` file.\n2. Click on the solutions you want to view. `Ctrl` and `shift` click will handle multiple selections. You can also navigate with up and down arrows.\n3. The list can be multisorted and filtered. Feel free to experiment.\n4. Double-click updates rotamers and mutamers in the protein, if available.\n5. If you want to perform some actions on every pose, write a Chimera command and it will be executed every time the selection changes.\n6. There's also a simple clustering algorithm!\n\nThere's a short tutorial written in the [GaudiMM docs](http://gaudi.readthedocs.io/en/latest/tutorial-visualization.html). Feel free to check it!\n\n## Requirements\n\n* **[UCSF Chimera](http://www.cgl.ucsf.edu/chimera/download.html)**. Main framework.\n\n* **[PyYaml](https://pypi.python.org/pypi/PyYAML) package**. GaudiMM file parsing.\n\n* **[tkintertable](https://pypi.python.org/pypi/tkintertable) package**. Sortable and filterable table.\n\n## Installation\n\n1 - If you don't have Chimera installed, download the [latest stable copy](http://www.cgl.ucsf.edu/chimera/download.html) and install it with:\n\n    chmod +x chimera-*.bin \u0026\u0026 ./chimera-*.bin\n\n2 - Create a new directory anywhere to host the GaudiView installation files. For example:\n\n    mkdir -p ~/insilichem  # any name is OK\n\n3 - Open a new Chimera instance and click on `Favorites\u003e Add to Favorites/Toolbar`. In this dialog, add the path of the directory you created in step 2 and click save.\n\n4 - Download the [latest version](https://github.com/insilichem/gaudiview/archive/master.zip) of **GaudiView** and place it inside that directory.\n\n    cd ~/insilichem\n    wget https://github.com/insilichem/gaudiview/archive/master.zip\n    unzip master.zip\n    mv gaudiview-master gaudiview\n\nYou can also use `git clone` inside `~/insilichem`:\n\n    git clone https://github.com/insilichem/gaudiview.git\n\n5 - Install the dependencies in-place with any Python 2 `pip`:\n\n    pip install -t . tkintertable pyyaml https://github.com/insilichem/libtangram/archive/master.zip\n\n\n### Alternative A\n\nIf `pip` is not available in your system, you can install it with Chimera's own Python:\n\n    wget https://bootstrap.pypa.io/get-pip.py\n    chimera --nogui --script get-pip.py # run it twice if it segfaults\n    chimera --nogui --script `chimera --root`\"/bin/pip install -t . tkintertable pyyaml https://github.com/insilichem/libtangram/archive/master.zip\"\n\n### Alternative B\n\nDownload [tkintertable](https://pypi.python.org/pypi/tkintertable) source package and extract the `*tar.gz` file. Open Chimera display and click on `Favorites\u003e Command Line`. This will bring in an input field at the bottom of the GUI, in which you need to type the following commands. Press `Enter` after each line.\n\n    cd /path/to/where/tkintertable/was/extracted/\n    runscript setup.py install\n\nRepeat with [PyYaml](https://pypi.python.org/pypi/PyYAML) source package and [libtangram](https://github.com/insilichem/libtangram/archive/master.zip).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsilichem%2Fgaudiview","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finsilichem%2Fgaudiview","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsilichem%2Fgaudiview/lists"}