{"id":23991600,"url":"https://github.com/aslozada/kanon","last_synced_at":"2025-04-14T17:05:26.407Z","repository":{"id":181898845,"uuid":"323647920","full_name":"aslozada/kanon","owner":"aslozada","description":"Program to compute chirality indices and assess molecular symmetry","archived":false,"fork":false,"pushed_at":"2024-07-12T14:44:32.000Z","size":1158,"stargazers_count":6,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-14T17:04:01.479Z","etag":null,"topics":["chemistry","chirality","hausdorff","molecule","quaternions","symmetry"],"latest_commit_sha":null,"homepage":"","language":"Fortran","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/aslozada.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":"2020-12-22T14:24:36.000Z","updated_at":"2025-04-08T14:20:52.000Z","dependencies_parsed_at":"2024-07-12T16:51:44.236Z","dependency_job_id":null,"html_url":"https://github.com/aslozada/kanon","commit_stats":null,"previous_names":["aslozada/kanon"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aslozada%2Fkanon","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aslozada%2Fkanon/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aslozada%2Fkanon/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aslozada%2Fkanon/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aslozada","download_url":"https://codeload.github.com/aslozada/kanon/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248923767,"owners_count":21183953,"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":["chemistry","chirality","hausdorff","molecule","quaternions","symmetry"],"created_at":"2025-01-07T19:57:16.678Z","updated_at":"2025-04-14T17:05:26.385Z","avatar_url":"https://github.com/aslozada.png","language":"Fortran","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Program to compute chirality indices and assess molecular symmetry \n\nThis is the official repository of the `kanon` program developed by Asdrubal Lozada-Blanco in the Laboratory of Theoretical Chemistry (Federal University of São Carlos - Brazil)\n\n\u003cdiv align=\"center\"\u003e\n\u003cimg src=\"https://github.com/aslozada/kanon/blob/main/tests/logo_kanon.png\" width=\"35%\" height=\"35%\"\u003e\n\u003c/div\u003e\n\n\n\n## Installation\n\n### Building from source\n\nTo build kanon from source code you need to have:\n- a Fortran compiler\n- build systems: make or fpm\n- [fpm](https://github.com/fortran-lang/fpm) version 0.2.0 or newer\n\n#### Building with make\n\n```\ncp app/kanon.f90 src/\ncp Makefile src/\ncd src/\nmake clean\nmake\nmake clean\n```\n\n#### Building with fpm\n\n```\nfpm build\n```\n\n#### How to use kanon?\n\nkanon uses a XYZFile as input\n\n```\nnatom\ncomment\nlabel1 xcoor1 ycoord1 zcoord1\nlabel2 xcoor2 ycoord2 zcoord2\n...\n```\n\nExamples\n```\n3\nWater H2O.xyz\nO     0.000000     0.000000     0.000000\nH     0.000000     0.000000     0.947000\nH     0.895670     0.000000    -0.316663\n\n```\n\n```\nkanon --pattern H2O.xyz\n\n---------------------------------------------------------------------------------\nCartesian coordinates input file: H2O.xyz\nNumber atoms:     3\n O    0.00000   0.00000   0.00000\n H    0.00000   0.00000   0.94700\n H    0.89567   0.00000  -0.31666\n\n-----------------------------------------------------------------------------\nDiameter of molecule:    1.54889 ang.\n--------------------------------------------------------------------------------\nCenter of masses\n   0.05011   0.00000   0.03527\n--------------------------------------------------------------------------------\n--------------------------------------------------------------------------------\nPrincipal moments of inertia\n     Ia           Ib           Ic\n   0.53688      1.20907      1.74595\n--------------------------------------------------------------------------------\nInertia axis\n   0.00000   0.81430  -0.58045\n   1.00000   0.00000   0.00000\n   0.00000   0.58045   0.81430\n--------------------------------------------------------------------------------\nSymmetry elements. Tolerance:    0.05000\n--------------------------------------------------------------------------------\n\n```\n```\nkanon --single \u003cH2O\u003e.xyz\n\n-----------------------------------------------------------------------------\nDiameter of molecule:    1.54889 ang.\n-----------------------------------------------------------------------------\nCenter of masses:    0.05011   0.00000   0.03527\n------------------------------------------------------------------------------\nMoments of inertia:       1.74595      1.20907      0.53688\nEigenvectors\n     0.000     0.814    -0.580\n     1.000     0.000     0.000\n     0.000     0.580     0.814\n---------------------------------------------------------------------------------\nSymmetrical matrix in Diamond`s method to optimal rotation: B\n---------------------------------------------------------------------------------\n     0.000     0.000     0.000     0.000\n     0.000     3.353    -0.000    -0.000\n     0.000    -0.000     2.399    -0.001\n     0.000    -0.000    -0.001     0.954\n---------------------------------------------------------------------------------\n Eigenvalues   -   Eigenvectors\n---------------------------------------------------------------------------------\n     0.954     0.000     0.000     0.000     1.000\n     0.000     1.000     0.000     0.000     0.000\n     3.353     0.000     1.000    -0.000    -0.000\n     2.399     0.000     0.000     1.000    -0.000\n--------------------------------------------------------------------------------\nCheck files: Pattern.xyz / Rotate_image.xyz\n---------------------------------------------------------------------------------\nRoot-mean-square deviation\nRMSD:   0.00000000\n--------------------------------------------------------------------------------\nHausdorff-derived chirality Index\nCHI:    0.00000000\n--------------------------------------------------------------------------------\n```\n\nComparing an object with any image\n\n```\nkanon --pattern \u003cobject\u003e.xyz --image \u003cimage\u003e.xyz\n\n```\n\nDelaunay triangulation of surfaces\n\n```\nkanon --pattern \u003cfile\u003e.xyz --delaunay \u003coutput_grid\u003e.dat\n\n```\n\n```\noutput_grid.dat\n\nGRID       1286\nREF  6 2 1\n            6         2         1\n            6         3         2\n            4        70         3\n            4        69        70\n           70        69        74\n           71        70        74\n...\n\n```\nWith openmp\n```\nexport OMP_NUM_THREADS=#\n```\n\n\nExample: Hausdorff Chirality Measure for biphenyl\n\n\u003cimg src=\"https://github.com/aslozada/kanon/blob/main/tests/HCM_bf.png\" width=\"50%\" height=\"50%\"\u003e\n\n\n Grid's effects\n\n\nElectron density: Isovalue 0.05\n\n\u003cimg src=\"https://github.com/aslozada/kanon/blob/main/tests/grid.png\" width=\"50%\" height=\"50%\"\u003e\n\nSurface\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faslozada%2Fkanon","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faslozada%2Fkanon","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faslozada%2Fkanon/lists"}