{"id":19671241,"url":"https://github.com/cgohlke/dnacurve","last_synced_at":"2026-01-08T19:17:39.478Z","repository":{"id":60667206,"uuid":"242421745","full_name":"cgohlke/dnacurve","owner":"cgohlke","description":"DNA curvature analysis","archived":false,"fork":false,"pushed_at":"2024-06-02T18:23:17.000Z","size":181,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-06-11T18:32:58.909Z","etag":null,"topics":["dna","dna-sequence-analysis","python"],"latest_commit_sha":null,"homepage":"https://pypi.org/project/dnacurve","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cgohlke.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2020-02-22T22:39:03.000Z","updated_at":"2024-06-02T18:23:21.000Z","dependencies_parsed_at":"2022-10-02T23:00:20.211Z","dependency_job_id":"1d0155f5-6d5d-4ae6-be86-cf1562a8df4a","html_url":"https://github.com/cgohlke/dnacurve","commit_stats":{"total_commits":60,"total_committers":2,"mean_commits":30.0,"dds":"0.31666666666666665","last_synced_commit":"b3e5226c698824528fe31601c7729fc41384c9b8"},"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Fdnacurve","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Fdnacurve/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Fdnacurve/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cgohlke%2Fdnacurve/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cgohlke","download_url":"https://codeload.github.com/cgohlke/dnacurve/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224142765,"owners_count":17262884,"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":["dna","dna-sequence-analysis","python"],"created_at":"2024-11-11T17:08:15.493Z","updated_at":"2026-01-08T19:17:39.459Z","avatar_url":"https://github.com/cgohlke.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"..\n  This file is generated by setup.py\n\nDNA curvature analysis\n======================\n\nDnacurve is a Python library, console script, and web application to calculate\nthe global 3D structure of a B-DNA molecule from its nucleotide sequence\naccording to the dinucleotide wedge model. Local bending angles and macroscopic\ncurvature are calculated at each nucleotide.\n\n:Author: `Christoph Gohlke \u003chttps://www.cgohlke.com\u003e`_\n:License: BSD-3-Clause\n:Version: 2026.1.8\n:DOI: `10.5281/zenodo.7135499 \u003chttps://doi.org/10.5281/zenodo.7135499\u003e`_\n\nQuickstart\n----------\n\nInstall the dnacurve package and all dependencies from the\n`Python Package Index \u003chttps://pypi.org/project/dnacurve/\u003e`_::\n\n    python -m pip install -U \"dnacurve[all]\"\n\nPrint the console script usage::\n\n    python -m dnacurve --help\n\nRun the web application::\n\n    python -m dnacurve --web\n\nSee `Examples`_ for using the programming interface.\n\nSource code and support are available on\n`GitHub \u003chttps://github.com/cgohlke/dnacurve\u003e`_.\n\nRequirements\n------------\n\nThis revision was tested with the following requirements and dependencies\n(other versions may work):\n\n- `CPython \u003chttps://www.python.org\u003e`_ 3.11.9, 3.12.10, 3.13.11, 3.14.2 64-bit\n- `NumPy \u003chttps://pypi.org/project/numpy\u003e`_ 2.4.0\n- `Matplotlib \u003chttps://pypi.org/project/matplotlib/\u003e`_ 3.10.8\n- `Flask \u003chttps://pypi.org/project/Flask/\u003e`_ 3.1.2 (optional)\n\nRevisions\n---------\n\n2026.1.8\n\n- Improve code quality.\n\n2025.12.12\n\n- Remove unused overlapping_chunks function.\n- Drop support for Python 3.10, support Python 3.14.\n\n2025.5.8\n\n- Remove deprecated save functions (breaking).\n- Remove doctest command line option.\n\n2025.1.1\n\n- Improve type hints.\n- Drop support for Python 3.9, support Python 3.13.\n\n2024.5.24\n\n- …\n\nRefer to the CHANGES file for older revisions.\n\nNotes\n-----\n\nThe algorithms, plots, and PDB format are not meant to be used with very\nlong sequences. By default, sequences are truncated to 510 nucleotides,\nwhich can be overridden by the user.\n\nThe generated PDB files can be visualized interactively using\n`UCSF Chimera \u003chttps://www.cgl.ucsf.edu/chimera/\u003e`_.\n\nDnacurve.py was derived from DNACG.PAS (c) 1993, and DNACURVE.CPP (c) 1995.\n\nReferences\n----------\n\n1. Bending and curvature calculations in B-DNA.\n   Goodsell DS, Dickerson RE. Nucleic Acids Res 22, 5497-503, 1994.\n   See also http://mgl.scripps.edu/people/goodsell/research/bend/index.html.\n2. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles.\n   Bolshoy A et al. Proc Natl Acad Sci USA 88, 2312-6, 1991.\n3. A comparison of six DNA bending models.\n   Tan RK and Harvey SC. J Biomol Struct Dyn 5, 497-512, 1987.\n4. Curved DNA: design, synthesis, and circularization.\n   Ulanovsky L et al. Proc Natl Acad Sci USA 83, 862-6, 1986.\n5. The ten helical twist angles of B-DNA.\n   Kabsch W, Sander C, and Trifonov EN. Nucleic Acids Res 10, 1097-1104, 1982.\n6. Rod models of DNA: sequence-dependent anisotropic elastic modelling of\n   local bending phenomena.\n   Munteanu MG et al. Trends Biochem Sci 23(9), 341-7, 1998.\n\nExamples\n--------\n\n.. code-block:: python\n\n    \u003e\u003e\u003e from dnacurve import CurvedDNA\n    \u003e\u003e\u003e cdna = CurvedDNA('ATGCAAATTG' * 5, 'trifonov', name='Example')\n    \u003e\u003e\u003e cdna.curvature[:, 18:22]\n    array([[0.58061616, 0.58163338, 0.58277938, 0.583783  ],\n           [0.08029914, 0.11292516, 0.07675816, 0.03166286],\n           [0.57923902, 0.57580064, 0.57367815, 0.57349872]])\n    \u003e\u003e\u003e cdna.write_csv('_test.csv')\n    \u003e\u003e\u003e cdna.write_pdb('_test.pdb')\n    \u003e\u003e\u003e cdna.plot('_test.png', dpi=120)","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcgohlke%2Fdnacurve","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcgohlke%2Fdnacurve","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcgohlke%2Fdnacurve/lists"}