{ "info": { "author": "Oskar Weser", "author_email": "oskar.weser@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", "Natural Language :: English", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX", "Operating System :: Unix", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Physics" ], "description": "# chemcoord: A python module for coordinates of molecules\n\n\n\n \n \n\n \n \n\n\n \n \n\n\n \n \n\n\n \n \n\n\n \n \n\n
Latest Release\n \n \"latest\n \n
Package Status\n \n \"status\"\n \n
License\n \n \"license\"\n \n
Build Status\n \n \"travis\n \n
Code Quality\n \n \"Code\n \n
Coverage\n \n \"Codecov\"\n \n
\n\n## Website\n\nThe project's website with documentation is: http://chemcoord.readthedocs.org/\n\n\n## Features\n\n* Molecules are reliably transformed between cartesian space and\n non redundant internal coordinates (Zmatrices).\n Dummy atoms are inserted and removed automatically on the fly if necessary.\n* The created Zmatrix is not only a structure expressed in internal coordinates,\n it is a \"chemical\" Zmatrix.\n \"Chemical\" Zmatrix means, that e.g. distances are along bonds\n or dihedrals are defined as they are drawn in chemical textbooks\n (Newman projections).\n* Analytical gradients for the transformations between the different\n coordinate systems are implemented.\n* Performance intensive functions/methods are implemented\n with Fortran/C like speed using [numba](http://numba.pydata.org/).\n* Geometries may be defined with symbolic expressions using\n [sympy](http://www.sympy.org/en/index.html).\n* Built on top of [pandas](http://pandas.pydata.org/) with very similar syntax.\n This allows for example distinct label or row based indexing.\n* It derived from my own work and I heavily use it during the day.\n So all functions are tested and tailored around the work flow in\n theoretical chemistry.\n* The classes are safe to inherit from and can easily be customized.\n* [It as a python module ;)](https://xkcd.com/353/)\n\n\n## Installation guide\nA working python installation is required (2.7 and >=3.5 are possible).\n\nIt is highly recommended to use this module in combination with\n [Ipython](http://ipython.org/) and [jupyter](http://jupyter.org/).\nThey come shipped by default with the\n [anaconda3 installer](https://www.continuum.io/downloads/)\n\n### Unix\n\n\nFor the packaged versions, the following commands have to be executed in the\n terminal:\n```\nconda install -c mcocdawc chemcoord\n```\nor\n```\npip install chemcoord\n```\nFor the up to date development version (experimental):\n```\ngit clone https://github.com/mcocdawc/chemcoord.git\ncd chemcoord\npip install .\n```\n\n### Windows\n\nNeither installation nor running the module are tested on windows.\nTo the best of my knowledge it should work there as well.\nJust use the same steps as for UNIX.\n\n### Changelog\n\nThe changelog can be found\n[here](https://github.com/mcocdawc/chemcoord/blob/v2.0.4/CHANGELOG.md).\n\n\n\n### Citation and mathematical background\n\nIf chemcoord is used in a project that leads to a scientific publication,\nplease acknowledge this fact by citing Oskar Weser (2017) using this ready-made BibTeX entry:\n\n```\n@mastersthesis{OWeser2017,\nauthor = {Oskar Weser},\ntitle = {An efficient and general library for the definition and use of internal coordinates in large molecular systems},\nschool = {Georg August Universit\u00e4t G\u00f6ttingen},\nyear = {2017},\nmonth = {November},\n}\n```\n\nThe master thesis including the derivation of implemented equations\nand the mathematical background can be found\n[here](https://github.com/mcocdawc/chemcoord/blob/v2.0.4/docs/source/files/master_thesis_oskar_weser_chemcoord.pdf).\n\n\n", "description_content_type": null, "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/mcocdawc/chemcoord", "keywords": "chemcoord,transformation,cartesian,internal,chemistry,zmatrix,xyz,zmat,coordinates,coordinate system", "license": "LGPLv3", "maintainer": "", "maintainer_email": "", "name": "chemcoord", "package_url": "https://pypi.org/project/chemcoord/", "platform": "", "project_url": "https://pypi.org/project/chemcoord/", "project_urls": { "Homepage": "https://github.com/mcocdawc/chemcoord" }, "release_url": "https://pypi.org/project/chemcoord/2.0.4/", "requires_dist": [ "numba (>=0.35)", "numpy", "pandas (>=0.20)", "pymatgen", "scipy", "six", "sortedcontainers", "sympy" ], "requires_python": "", "summary": "Python module for dealing with chemical coordinates.", 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