{ "info": { "author": "The Research Software Company", "author_email": "itay@chelem.co.il", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 3.5", "Topic :: Scientific/Engineering :: Chemistry" ], "description": "# ProteinCSM\n\n## INTRODUCTION\n\nThe ProteinCSM program calculates continuous symmetry and chirality measures of protein homomers in pdb format.\nPlease note that pdb files should be cleaned prior to calculation. Our code pdb_prep can be used for this purpose (https://sagivba.github.io/pdb_prep).\n\n## USAGE\n\nAfter installation, the program can be called from the command line. For example:\n\n`proteincsm c2 inputmol.pdb output.pdb --optional-args`\n\nYou can access a help menu with a list of all available options via `proteincsm -h`\n\n## INSTALLATION\n\nproteincsm can be installed on Windows and Linux machines.\n\n### REQUIREMENTS\n\nBefore installing CSM, please install:\n\n* Openbabel (http://openbabel.org/wiki/Category:Installation), \nversion 2.4.0 or later.\n* openbabel's python bindings (`pip install openbabel`) \n* numpy (`pip install numpy`)\n\nBecause installing openbabel correctly is a delicate and bug-prone process, an alternative method of installing \nProteinCSM is available using Conda, and is described in the file conda_install_instructions.txt\n\n### INSTALLATION \n\nProteinCSM can be installed using:\n\n`pip install proteincsm`\n\nYou can also install ProteinCSM from the source. \n\n## CITATIONS \n\nPlease cite ProteinCSM using the following:\n\nproteincsm:\n\n> Tuvi-Arad I. and Alon G., \"Improved Algorithms for Quantifying the Near Symmetry of Proteins: Complete Side Chains Analysis\" (submitted). \n> Dryzun C., Zait A. and Avnir D., \"Quantitative Symmetry and Chirality - A Fast Computational Algorithm for Large Structures: Proteins, Macromolecules, Nanotubes, and Unit Cells\", J. Comput. Chem., 32, 2526-2538 (2011). \n\n\nExact Algorithm for calculating the CSM of molecules:\n\n> Alon G. and Tuvi-Arad I., \"Improved algorithms for symmetry analysis: Structure preserving permutations\", J. Math. Chem., 56(1), 193-212 (2018).\n\nOriginal Code by Avnir and coworkers:\n\n> Pinsky M., Dryzun C., Casanova D., Alemany P., Avnir D., \"Analytical Methods for Calculating Continuous Symmetry Measures and the Chirality Measure\", Journal of Computational Chemistry 29(16): 2712-2721 (2008).\n\n> Zabrodsky H., Peleg S., Avnir D., \"Continuous symmetry measures\", Journal of the American Chemical Society 114(20): 7843-7851 (1992).\n\n\n\n## CREDITS\n\n**Science/Math:**\n\nDr. Inbal Tuvi-Arad, Department of Natural Sciences, The Open University of Israel\n\nDr. Gil Alon, Department of Mathematics and Computer Science, The Open University of Israel\n\nProf. David Avnir, Institute of Chemistry, The Hebrew University of Jerusalem\n\n**Programming:**\n\nThe Research Software Company (www.chelem.co.il)\n\n**Testing, scripts and additional technical support:**\n\nSagiv Barhoom,The Open University of Israel\n\n**Intensive testing:**\n\nYaffa Shalit, The Open University of Israel\n\nThe code for the hungarian algorithm is copyright (c) 2012, Jacob Frelinger\n\n\n## CONTACT\n\nDr. Inbal Tuvi-Arad, Department of Natural Sciences, The Open University of Israel, E-mail: inbaltu@openu.ac.il\n\n\n\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/continuous-symmetry/proteincsm/tree/v1.0.1", "keywords": "", "license": "GPL2", "maintainer": "", "maintainer_email": "", "name": "proteincsm", "package_url": "https://pypi.org/project/proteincsm/", "platform": "", "project_url": "https://pypi.org/project/proteincsm/", "project_urls": { "Homepage": "https://github.com/continuous-symmetry/proteincsm/tree/v1.0.1" }, "release_url": "https://pypi.org/project/proteincsm/1.0.1/", "requires_dist": [ "numpy (>=1.10)", "openbabel (>=2.4.0)" ], "requires_python": "", "summary": "The Continuous Symmetry Measure for Proteins", "version": "1.0.1" }, "last_serial": 5110786, 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