{ "info": { "author": "Daniel Lecina, Joan Francesc Gilabert", "author_email": "danilecina@gmail.com, cescgina@gmail.com", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3" ], "description": "============\nAdaptivePELE\n============\n\n\n|MIT license| |GitHub release| |PyPI release| |DOI|\n\nAdaptivePELE is a Python module to perform enhancing sampling of molecular\nsimulation built around the Protein Energy Landscape Exploration method (`PELE `_) developed in the Electronic and Atomic Protein Modelling grop (`EAPM `_) at the Barcelona Supercomputing Center (`BSC `_).\n\nUsage\n-----\n\nAdaptivePELE is called with a control file as input\nparameter. The control file is a json document that contains 4 sections:\ngeneral parameters, simulation parameters, clustering parameters and spawning\nparameters. The first block refers to general parameters of the adaptive run,\nwhile the other three blocks configure the three steps of an adaptive sampling\nrun, first run a propagation algorithm (simulation), then cluster the\ntrajectories obtained (clustering) and finally select the best point to start\nthe next iteration (spawning).\n\nAn example of usage::\n\n python -m AdaptivePELE.adaptiveSampling controlFile.conf\n\nInstallation\n------------\n\nThere are two methods to install AdaptivePELE, from PyPI (recommended) or\ndirectly from source.\n\nTo install from PyPI simply run::\n\n pip install AdaptivePELE\n\nTo install from source, you need to install and compile cython files in the base folder with::\n\n git clone https://github.com/AdaptivePELE/AdaptivePELE.git\n cd AdaptivePELE\n python setup.py build_ext --inplace\n\nAlso, if AdaptivePELE was not installed in a typical library directory, a common option is to add it to your local PYTHONPATH::\n\n export PYTHONPATH=\"/location/of/AdaptivePELE:$PYTHONPATH\"\n\nDocumentation\n-------------\n\nThe documentation for AdaptivePELE can be found `here `_\n\n\nContributors\n------------\n`Daniel Lecina `_, `Joan Francesc Gilabert `_, `Oriol Gracia `_, `Daniel Soler `_\n\nMantainer\n---------\nJoan Francesc Gilabert (cescgina@gmail.com)\n\nCitation \n--------\n\nAdaptivePELE is research software. If you make use of AdaptivePELE in scientific publications, please cite it. 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