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        "author": "Damien Coupry",
        "author_email": "damien.coupry@uni-leipzig.de",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: Implementation :: CPython"
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        "description": "\nAuToGraFS\n=========\n\nOriginal publication: `\"Automatic Topological Generator for Framework Structures\"`__.\n\n.. _here: http://pubs.acs.org/doi/abs/10.1021/jp507643v \n\n__ here_\n\n*This version is under active development*. Bug hunting is very much going on, and there are still some old funtionalities that are not yet reimplemented.\n\nTODO:\n-----\n\nMedium priority:\n- offer an isotropic scaling option\n- the symmetry axes detection has trouble with planar shapes\n- more robust mmanalysis module\n\nLow priority:\n\n- unit testing coverage is non-existant\n- documentation writing\n- better handling of the databases:\n  + precomputing sbu-topologies correspondance\n  + use better format than pickle\n\nInstall:\n--------\n\n.. highlight:: bash\n\n$ pip install --user --upgrade AuToGraFS\n\n\nFor a manual install, first install the dependencies,\n\n1. python >=3.4\n2. ase, scipy, numpy<1.15.0\n\n\nthen clone this repository and add it to you pythonpath::\n\n\t$ cd $HOME\n\t$ git clone https://github.com/DCoupry/autografs.git\n\t$ export PYTHONPATH=$HOME/autografs:$PYTHONPATH`\n\n\nExamples:\n---------\n\nFrom any python script or command line:\n\n.. highlight:: python\n\n>>> from autografs import Autografs\n>>> mofgen = Autografs()\n>>> mof = mofgen.make(topology_name=\"pcu\", \n>>>                   sbu_names=[\"Zn_mof5_octahedral\", \"Benzene_linear\"])\n>>> mof.write()\n\nCustom databases can be accessed by passing the path during instanciation\n\n>>> mofgen = Autografs(topology_path=\"my_topo_path\",sbu_path=\"my_sbu_path\")\n>>> mof = mofgen.set_topology(topology_name=custom_topology_name,sbu_name=custom_sbu_names)\n\nWhen looping over both SBU and topologies, it is better to set the topology directly\n(here, my_topologies and my_sbu_names are appropriate dummy colletions)\n\n>>> for topologi_name in my_topology_names:\n>>>     mofgen.set_topology(topology_name=topology_name)\n>>>     for sbu_names in my_sbu_names:\n>>>          mof = mofgen.make(sbu_names=sbu_names)\n\nIt is possible to pass more than one SBU of each shape, optionally with an associated probabilistic weight.\nThis weight defaults to 1.0/(number of similar sbu).\n\n>>> mof = mofgen.make(topology_name=\"pcu\", \n>>>                   sbu_names=[\"Zn_mof5_octahedral\", (\"Benzene_linear\",2.0),(\"Acetylene_linear\",0.5)])\n>>> mof.write()\n\nThis is particularly helpful in combination with an initial supercell for statistically introducing defects.\n\n>>> mof = mofgen.make(topology_name=\"pcu\", \n>>>                   sbu_names=[(\"Zn_mof5_octahedral\",2.0),(\"defect_octahedral\",0.5), \"Benzene_linear\"],\n>>>                   supercell=(3,3,3))\n>>> mof.write()\n\nSupercell can also be generated post-alignement, carrying everything done before.\n\n>>> supercell_6x6x6 = mof.get_supercell(m=2)\n>>> supercell_6x6x6.write()\n\nDefects and modifications can be introduced at any time directly:\n\n>>> # get the site directly\n>>> sbu = mof[7]\n>>> # change all hydrogens to Fluorine\n>>> atoms = sbu.atoms.copy()\n>>> symbols = atoms.get_chemical_symbols()\n>>> symbols = [s if s!=\"H\" else \"F\" for s in symbols]\n>>> atoms.set_chemical_symbols(symbols)\n>>> # by setting the atoms back, \n>>> # mmtypes and bonding are updated.\n>>> sbu.set_atoms(atoms=atoms,analyze=True)\n>>> # delete another sbu. H will cap the dangling bits.\n>>> del mof[8]\n>>> mof.write()\n\nMethods are also available for the rotation, functionalization and flipping.\n\n>>> # rotate the sbu 7 buy 45 degrees\n>>> mof.rotate(index=7,angle=45.0)\n>>> # if a C* axis or reflection plane is detected\n>>> # in the sbu 8 , flip around it\n>>> mof.flip(index=8)\n>>> # replace all functionalizable H sites with NH2\n>>> nh2 = mofgen.sbu[\"NH2_point_group\"]\n>>> sites = mof.list_functionalizable_sites(self,symbol=\"H\")\n>>> for site in sites:\n>>>     mof.functionalize(where=site,fg=nh2)\n>>> mof.write()\n\nAt any moment, we can monitor the bonding matrix and mmtypes, or get a cleaned version without dummies.\n\n>>> from ase.visualize import view\n>>> # with the dummies included\n>>> mmtypes = mof.get_mmtypes()\n>>> bonds = mof.get_bonds()\n>>> # without the dummies\n>>> atoms,bonds,mmtypes = mof.get_atoms(dummies=False)\n>>> view(atoms)\n\nIf you know the shape of each slot and its index within the topology, it is possible to directly pass a dictionary mapping\nthe SBU to a particular slot.\n\n>>> # method to investigate the topology shapes and slots\n>>> topology = mofgen.get_topology(topology_name=\"pcu\")\n>>> sbu_dict = {}\n>>> for slot_index,slot_shape in topology.shapes.items():\n>>>     # do something to choose an sbu\n>>>     ...\n>>>     sbu_dict[slot_index] = \"chosen_sbu_name\"\n>>> # now pass it directly\n>>> mof = mofgen.make(topology_name=\"pcu\", sbu_dict=sbu_dict)\n>>> mof.write()\n\nYou can access the databases as dictionaries using the following:\n\n>>> sbudict  = mofgen.sbu\n>>> topodict = mofgen.topologies\n\nOr using tools to find compatible objects:\n\n>>> sbu_list = mofgen.list_available_sbu(topology_name=\"pcu\")\n>>> topology_list = mofgen.list_available_topologies(sbu_names=[\"Zn_mof5_octahedral\", \"Benzene_linear\"])\n\nAAuToGraFS is also aware of topologically equivalent positions, and can generate multi components frameworks\nwith minimal effort.\n\n>>> sbu_dicts = mofgen.list_available_frameworks()\n>>> for sbu_dict in sbu_dicts:\n>>>     mof = mofgen.make(sbu_dict=sbu_dict)\n>>>     mof.view()\n\nA useful utility is the Atom typer, which assigns bond orders and UFF atom types to a structure:\n\n>>> from autografs.mmanalysis import analyze_mm\n>>> bonds, types = analyze_mm(sbu=mofgen.sbu[\"Zn_mof5_octahedral\"])\n\n\n\n",
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