{ "info": { "author": "James Collier", "author_email": "james@thecolliers.xyz", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)", "Operating System :: OS Independent", "Programming Language :: C", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "[![Donate](https://liberapay.com/assets/widgets/donate.svg)](https://liberapay.com/JamesCollier/donate) to me on Liberapay.\n\n**Master:** [![build status](https://gitlab.com/structural-fragment-search/super/badges/master/build.svg)](https://gitlab.com/structural-fragment-search/super/commits/master)\n[![coverage report](https://gitlab.com/structural-fragment-search/super/badges/master/coverage.svg)](https://gitlab.com/structural-fragment-search/super/commits/master)\n\n**Latest 0.2 release:** [![build status](https://gitlab.com/structural-fragment-search/super/badges/0.2_series/build.svg)](https://gitlab.com/structural-fragment-search/super/commits/0.2_series)\n[![coverage report](https://gitlab.com/structural-fragment-search/super/badges/0.2_series/coverage.svg)](https://gitlab.com/structural-fragment-search/super/commits/0.2_series)\n\n# Super -- Information for users and developers\n*Super* is able to rapidly search of 3D structural databases. Given a query fragment, *Super* searches through a database of 3D structures for the query\nwithin a tolerence threshold (measured by RMSD).\n\n## Releases\n* [Current stable version: 0.2](https://gitlab.com/structural-fragment-search/super/tags/v0.2)\n* [Curret development version: 0.3]()\n\n## Dependencies\nThere are a few dependencies required to build and run Super:\n1. python2 (https://www.python.org/) script is used to pre-process PDB text datafiles into an efficient binary database format\n2. prody (http://prody.csb.pitt.edu/) is used to parse PDB files\n3. check (https://libcheck.github.io/check/) is used for unit testing and can be disabled by passing --disable-check to the configure script.\n4. lcov is used for code coverage. It is not necessary by default, but passing --enable-code-coverage to the configure script will search for the lcov program.\n\n## Compile\n```bash\n./configure --prefix=${HOME}/some/install/path\n```\nI say ${HOME} so that I don't have to install as superuser. I often use --prefix=${HOME}/install\n\n```bash\nmake && make install\n```\n\n## Running Super\nin ${prefix}/bin directory:\n$ LD_LIBRARY_PATH=../lib ./super [OPTIONS...] ${pdb_path}/pdb.db\n\n```\nOptions listing from ./super --help:\nUsage: super [OPTION...] DATABASE\nsuper -- A 3D protein pattern search program.\n\n -c, --thread-count=COUNT Concurrently process the database with COUNT\n threads of control\n -d, --defaults Keep default arguments.\n -g, --disable-gershgorin Disable use of gershgorin circles for Jacobi\n diagonalisation\n -l, --lowerbounds=BOUNDS Comma separated list of lower bound checks to use\n -n, --disable-rmsd Disable the full (Kearsley) RMSD calculation, just\n use the LB\n -o, --output=OUTPUT Output to OUTPUT instead of stdout\n --quiet Produce no output\n -q, --query=QUERY Query database\n -r, --disable-mmap Disable use of memory mapped databases to speed up\n calculations\n -t, --threshold=THRESHOLD Pattern matching threshold measured in Angstrom\n -?, --help Give this help list\n --usage Give a short usage message\n -V, --version Print program version\n\nMandatory or optional arguments to long options are also mandatory or optional\nfor any corresponding short options.\n```\n\nI usually run with:\n```bash\nLD_LIBRARY_PATH=${HOME}/install/lib ./super --lowerbounds=arithmetic --threshold=1.0 --query=qry.db pdb.db\n```\n\nOR ON Mac OSX:\n```bash\nDYLD_LIBRARY_PATH=${HOME}/install/lib ./super -t 1.0 -q qry.db pdb.db\n```\n\n## Databases\nAn up-to-date pre-processed version of the entire PDB is available for download from http://lcb.infotech.monash.edu.au/super/pdb.db\n\nTo generate a query:\n```bash\npython pdb_pp.py --query [YOUR PDB FRAGMENT FILE].pdb --output myquery.qry\n```\n\nTo generate a searchable database from a directory containing PDB files (pdb/):\n```bash\npython pdb_pp.py -o pdb.db pdb/\n```\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://gitlab.com/structural-fragment-search/super", "keywords": "", "license": "", "maintainer": "", "maintainer_email": "", "name": "pysuper", "package_url": "https://pypi.org/project/pysuper/", "platform": "", "project_url": "https://pypi.org/project/pysuper/", "project_urls": { "Homepage": "https://gitlab.com/structural-fragment-search/super" }, "release_url": "https://pypi.org/project/pysuper/0.2.91/", "requires_dist": [ "cffi (>=1.0.0)" ], "requires_python": "", "summary": "Search for oligopeptide fragments", "version": "0.2.91" }, "last_serial": 4119098, "releases": { "0.2.91": [ { "comment_text": "", "digests": { "md5": "6c4e23e638479816ee357cf0805767fc", "sha256": "d08e4924da5e12f8f2859c283b10b2d28fce477bf7e79a710480b850fedcf608" }, "downloads": -1, "filename": "pysuper-0.2.91-cp36-cp36m-linux_armv7l.whl", "has_sig": false, "md5_digest": "6c4e23e638479816ee357cf0805767fc", "packagetype": "bdist_wheel", "python_version": "cp36", "requires_python": null, "size": 13268, "upload_time": "2018-07-31T07:00:03", "url": "https://files.pythonhosted.org/packages/45/62/018df359821b9848553279fdf867d58ef4ec1328e2f755e08a2805c4f2ba/pysuper-0.2.91-cp36-cp36m-linux_armv7l.whl" }, { "comment_text": "", "digests": { "md5": "78f8992a7ba43133ffc410260000eae4", "sha256": "1cf8d57419f4c9ef2be14d93c513f74e0c95f50654bb86d4fe35ddb7ec78e539" }, "downloads": -1, "filename": "pysuper-0.2.91.tar.gz", "has_sig": false, "md5_digest": "78f8992a7ba43133ffc410260000eae4", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4824, "upload_time": "2018-07-31T07:00:04", "url": "https://files.pythonhosted.org/packages/3f/dd/c6440b2ea3085862bf663b6365ec5e2b18e8e06d937fc1e44a3d3fc173ee/pysuper-0.2.91.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "6c4e23e638479816ee357cf0805767fc", "sha256": "d08e4924da5e12f8f2859c283b10b2d28fce477bf7e79a710480b850fedcf608" }, "downloads": -1, "filename": "pysuper-0.2.91-cp36-cp36m-linux_armv7l.whl", "has_sig": false, "md5_digest": "6c4e23e638479816ee357cf0805767fc", "packagetype": "bdist_wheel", "python_version": "cp36", "requires_python": null, "size": 13268, "upload_time": "2018-07-31T07:00:03", "url": "https://files.pythonhosted.org/packages/45/62/018df359821b9848553279fdf867d58ef4ec1328e2f755e08a2805c4f2ba/pysuper-0.2.91-cp36-cp36m-linux_armv7l.whl" }, { "comment_text": "", "digests": { "md5": "78f8992a7ba43133ffc410260000eae4", "sha256": "1cf8d57419f4c9ef2be14d93c513f74e0c95f50654bb86d4fe35ddb7ec78e539" }, "downloads": -1, "filename": "pysuper-0.2.91.tar.gz", "has_sig": false, "md5_digest": "78f8992a7ba43133ffc410260000eae4", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4824, "upload_time": "2018-07-31T07:00:04", "url": "https://files.pythonhosted.org/packages/3f/dd/c6440b2ea3085862bf663b6365ec5e2b18e8e06d937fc1e44a3d3fc173ee/pysuper-0.2.91.tar.gz" } ] }