{"id":40129460,"url":"https://github.com/berquist/personal_scripts","last_synced_at":"2026-01-19T13:31:42.156Z","repository":{"id":33589525,"uuid":"37238106","full_name":"berquist/personal_scripts","owner":"berquist","description":"Personal scripts, mostly for computational chemistry analysis.","archived":false,"fork":false,"pushed_at":"2025-12-05T17:17:09.000Z","size":649,"stargazers_count":7,"open_issues_count":0,"forks_count":3,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-12-09T04:48:38.382Z","etag":null,"topics":["computational-chemistry","python"],"latest_commit_sha":null,"homepage":"","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/berquist.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2015-06-11T03:52:28.000Z","updated_at":"2025-10-13T22:40:57.000Z","dependencies_parsed_at":"2024-08-13T17:54:14.230Z","dependency_job_id":null,"html_url":"https://github.com/berquist/personal_scripts","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/berquist/personal_scripts","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/berquist%2Fpersonal_scripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/berquist%2Fpersonal_scripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/berquist%2Fpersonal_scripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/berquist%2Fpersonal_scripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/berquist","download_url":"https://codeload.github.com/berquist/personal_scripts/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/berquist%2Fpersonal_scripts/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28569194,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-19T12:50:50.164Z","status":"ssl_error","status_checked_at":"2026-01-19T12:50:42.704Z","response_time":67,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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":["computational-chemistry","python"],"created_at":"2026-01-19T13:31:42.085Z","updated_at":"2026-01-19T13:31:42.151Z","avatar_url":"https://github.com/berquist.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"All my scripts jumbled together. Subfolders are machine-specific.\n\nWith the `__init__.py`, the directory is a Python module, and the\nfunctions in each Python script can be used elsewhere.\n\n## Python Requirements\n\n### Newish Python standard library modules:\n\n```\nargparse\n```\n\n### External modules:\n\n```\ndocopt\nmatplotlib\nnumpy\npandas\n```\n\n### External quantum chemistry modules:\n\n```\ncclib\n```\n\n### Personal repositories:\n\n```\norcaparse\n```\n\n# Plotting in VMD\n\nInteractive/graphical:\n\n``` bash\n# in normal terminal:\nvmd_pretty_cubes.py --nsurf=1\nvmd \u003cparent XYZ filename\u003e -e vmd.load_all_plt.vmd\n# in VMD terminal:\nsource vmd.plot_all.vmd\n# shell command, in either terminal:\n./vmd.convert.bash\n```\n\nText-only with no repositioning of the scene:\n\n``` bash\n# in normal terminal:\nvmd_pretty_cubes.py --nsurf=1\ncat vmd.load_all_plt.vmd vmd.plot_all.vmd \u003e vmd.do_all.vmd\necho \"quit\" \u003e\u003e vmd.do_all.vmd\nvmd \u003cparent XYZ filename\u003e -e vmd.do_all.vmd -dispdev text\n./vmd.convert.bash\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fberquist%2Fpersonal_scripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fberquist%2Fpersonal_scripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fberquist%2Fpersonal_scripts/lists"}