Metadata-Version: 1.2
Name: Cathub
Version: 0.1.7
Summary: Python API for the Surface Reactions database on Catalysis-Hub.org
Home-page: https://github.com/SUNCAT-Center/CatHub
Author: Kirsten Winther
Author-email: winther@stanford.edu
License: GPL-3.0
Description: ## Introduction
        
        CatHub provides an interface to the Surface Reactions database on [Catalysis-Hub.org](http://www.catalysis-hub.org).
        
        The module includes a command line interface that can be used to access and upload data. A short guide is given below. We refer to the [catalysis-hub documentation](http://docs.catalysis-hub.org/en/latest/tutorials/upload.html) for details on how to submit data.
        
        ## Using the cathub cli
        
        Run `cathub` from the command line:
        
            cathub --help
        
        or with any of its sub-commands:
        
            cathub reactions --help
        
        ## Examples
        
        Querying the Surface Reactions database in Python:
        
            from cathub.cathubsql import CathubSQL
        
            # To get data on catalysis-hub.org
            db = CathubSQL()
        
            # Data from local cathub .db file
            db = CathubSQL('filename.db')
        
        Get reactions in pandas dataframe:
        
            dataframe = db.get_dataframe(pub_id='PengRole2020',
                                         include_atoms=False,
                                         include_atoms=True,  # include atoms in dataframe
                                         #include_atoms='PengRole2020.db',  # save atoms to local db
                                         reactants=['COgas'],
                                         products=['COstar'],
                                         elements=['Cu', 'Al'],
                                         #surface_composition='Cu', # match specific composition
                                         facet = '100'
                                         )
        
        Get atomic structure seperately:
        
            # Get atoms for one reaction_id taken from dataframe
            atoms_list = db.get_atoms_for_reaction(reaction_id)
        
            # Get atoms for entire dataset
            atoms_list = db.get_atoms_for_publication(pub_id='PengRole2020')
        
        
        Quick view of atomic structures on Catalysis Hub with ase db CLI:
        
            cathub ase 'CuAg pub_id=PengRole2020'
        
        ## Uploading data
        
        Organizing a general folder into a structured folder:
        
            cathub organize <folderame> -a <ads1,ads2> -c <dft-code> -x <xc-functional> -f <facet> -S <crystal structure>
        
        As an alternative to cathub organize, create an empty organized folderstructure for dropping files yourself. First create a template and edit it, then create the folders.
        
            cathub make_folders --create-template <template>
            cathub make_folders <template>
        
        Reading folders into a local .db file:
        
            cathub folder2db <foldername>
        
        Sending the data to the Catalysis Hub server:
        
            cathub db2server <dbfile>
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.5
