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image:: https://coveralls.io/repos/github/mordred-descriptor/mordred/badge.svg?branch=master\n    :target: https://coveralls.io/github/mordred-descriptor/mordred?branch=master\n\n.. image:: https://codeclimate.com/github/mordred-descriptor/mordred/badges/gpa.svg\n   :target: https://codeclimate.com/github/mordred-descriptor/mordred\n   :alt: Code Climate\n\n.. image:: https://anaconda.org/mordred-descriptor/mordred/badges/version.svg\n    :target: https://anaconda.org/mordred-descriptor/mordred\n\n.. image:: https://img.shields.io/pypi/v/mordred.svg\n    :target: https://pypi.python.org/pypi/mordred\n\n.. image:: https://img.shields.io/badge/doi-10.1186%2Fs13321--018--0258--y-blue.svg\n   :target: https://doi.org/10.1186/s13321-018-0258-y\n\n.. image:: https://img.shields.io/badge/slack-mordred--descriptor-brightgreen.svg\n    :target: https://join.slack.com/t/mordred-descriptor/shared_invite/enQtMzc1MzkyODk1NTY5LTdlYzM4MWUzY2YwZmEwMWYzN2M4YTVkMGRlMDY0ZjU2NjQ1M2RiYzllMzVjZGE4NGZkNWZjODBjODE0YmExNjk\n\nnumber of descriptors\n---------------------\n.. code:: python\n\n    \u003e\u003e\u003e from mordred import Calculator, descriptors\n    \u003e\u003e\u003e n_all = len(Calculator(descriptors, ignore_3D=False).descriptors)\n    \u003e\u003e\u003e n_2D = len(Calculator(descriptors, ignore_3D=True).descriptors)\n    \u003e\u003e\u003e print(\"2D:    {:5}\\n3D:    {:5}\\n------------\\ntotal: {:5}\".format(n_2D, n_all - n_2D, n_all))\n    2D:     1613\n    3D:      213\n    ------------\n    total:  1826\n\nInstallation\n------------\n\nconda(recommended)\n~~~~~~~~~~~~~~~~~~\n#. install conda\n\n       -  `miniconda \u003chttp://conda.pydata.org/miniconda.html\u003e`__\n       -  `anaconda \u003chttps://www.continuum.io/why-anaconda\u003e`__\n\n#. install mordred\n\n       .. code:: console\n\n           $ conda install -c rdkit -c mordred-descriptor mordred\n\npip\n~~~\n\n#. install `rdkit \u003chttp://www.rdkit.org/\u003e`__ python package\n#. install mordred\n\n       .. code:: console\n\n           $ pip install 'mordred[full]'  # install with extra requires\n           # or\n           $ pip install mordred\n           \nTesting the installation\n------------------------\n\n            $ python -m mordred.tests\n\nexamples\n--------\n\nas command\n~~~~~~~~~~\n\ncalculate all descriptors\n\n.. code:: console\n\n    $ python -m mordred example.smi\n    name,ECIndex,WPath,WPol,Zagreb1, (snip)\n    benzene,36,27,3,24.0, (snip)\n    chrolobenzene,45,42,5,30.0, (snip)\n\n\nsave to file (display progress bar)\n\n.. code:: console\n\n    $ python -m mordred example.smi -o example.csv\n    50%|███████████████████████████████████████▌                                       | 1/2 [00:00\u003c00:00,  7.66it/s]\n\n\nstream read (low memory, no number of molecules information)\n\n.. code:: console\n\n    $ python -m mordred example.smi -s -o example.csv\n    0it [00:00, ?it/s]\n\nonly ABCIndex\n\n.. code:: console\n\n    $ python -m mordred example.smi -d ABCIndex\n    name,ABC,ABCGG\n    benzene,4.242640687119286,3.9999999999999996\n    chlorobenzene,5.059137268047012,4.785854275382693\n\nABCIndex and AcidBase\n\n.. code:: console\n\n    $ python -m mordred example.smi -d ABCIndex -d AcidBase\n    name,ABC,ABCGG,nAcid,nBase\n    benzene,4.242640687119286,3.9999999999999996,0,0\n    chlorobenzene,5.059137268047012,4.785854275382693,0,0\n\nmultiple input\n\n.. code:: console\n\n    $ python -m mordred example.smi example2.smi -d ABCIndex\n    name,ABC,ABCGG\n    benzene,4.242640687119286,3.9999999999999996\n    chlorobenzene,5.059137268047012,4.785854275382693\n    pentane,2.8284271247461903,3.1462643699419726\n\nshow help\n\n.. code:: console\n\n    $ python -m mordred --help\n    usage: python -m mordred [-h] [--version] [-t {auto,sdf,mol,smi}] [-o OUTPUT]\n                             [-p PROCESSES] [-q] [-s] [-d DESC] [-3] [-v]\n                             INPUT [INPUT ...]\n\n    positional arguments:\n      INPUT\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --version             input molecular file\n      -t {auto,sdf,mol,smi}, --type {auto,sdf,mol,smi}\n                            input filetype (default: auto)\n      -o OUTPUT, --output OUTPUT\n                            output file path (default: stdout)\n      -p PROCESSES, --processes PROCESSES\n                            number of processes (default: number of logical\n                            processors)\n      -q, --quiet           hide progress bar\n      -s, --stream          stream read\n      -d DESC, --descriptor DESC\n                            descriptors to calculate (default: all)\n      -3, --3D              use 3D descriptors (require sdf or mol file)\n      -v, --verbosity       verbosity\n\n    descriptors: ABCIndex AcidBase AdjacencyMatrix Aromatic AtomCount\n    Autocorrelation BalabanJ BaryszMatrix BCUT BertzCT BondCount CarbonTypes Chi\n    Constitutional CPSA DetourMatrix DistanceMatrix EccentricConnectivityIndex\n    EState ExtendedTopochemicalAtom FragmentComplexity Framework GeometricalIndex\n    GravitationalIndex HydrogenBond InformationContent KappaShapeIndex Lipinski\n    McGowanVolume MoeType MolecularDistanceEdge MolecularId MomentOfInertia MoRSE\n    PathCount Polarizability RingCount RotatableBond SLogP TopologicalCharge\n    TopologicalIndex TopoPSA VdwVolumeABC VertexAdjacencyInformation WalkCount\n    Weight WienerIndex ZagrebIndex\n\nas library\n^^^^^^^^^^\n\n.. code:: python\n\n    \u003e\u003e\u003e from rdkit import Chem\n    \u003e\u003e\u003e from mordred import Calculator, descriptors\n\n    # create descriptor calculator with all descriptors\n    \u003e\u003e\u003e calc = Calculator(descriptors, ignore_3D=True)\n\n    \u003e\u003e\u003e len(calc.descriptors)\n    1613\n\n    \u003e\u003e\u003e len(Calculator(descriptors, ignore_3D=True, version=\"1.0.0\"))\n    1612\n\n    # calculate single molecule\n    \u003e\u003e\u003e mol = Chem.MolFromSmiles('c1ccccc1')\n    \u003e\u003e\u003e calc(mol)[:3]\n    [4.242640687119286, 3.9999999999999996, 0]\n\n    # calculate multiple molecule\n    \u003e\u003e\u003e mols = [Chem.MolFromSmiles(smi) for smi in ['c1ccccc1Cl', 'c1ccccc1O', 'c1ccccc1N']]\n\n    # as pandas\n    \u003e\u003e\u003e df = calc.pandas(mols)\n    \u003e\u003e\u003e df['SLogP']\n    0    2.3400\n    1    1.3922\n    2    1.2688\n    Name: SLogP, dtype: float64\n\nsee `examples \u003chttps://github.com/mordred-descriptor/mordred/tree/develop/examples\u003e`_\n\nCitation\n--------\nMoriwaki H, Tian Y-S, Kawashita N, Takagi T (2018) Mordred: a molecular descriptor calculator. Journal of Cheminformatics 10:4 . doi: `10.1186/s13321-018-0258-y \u003chttps://doi.org/10.1186/s13321-018-0258-y\u003e`__\n\nDocumentation\n-------------\n\n-  `master \u003chttp://mordred-descriptor.github.io/documentation/master\u003e`__\n-  `develop \u003chttp://mordred-descriptor.github.io/documentation/develop\u003e`__\n\n-  `v1.1.0 \u003chttp://mordred-descriptor.github.io/documentation/v1.1.1\u003e`__\n-  `v1.0.0 \u003chttp://mordred-descriptor.github.io/documentation/v1.0.0\u003e`__\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmordred-descriptor%2Fmordred","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmordred-descriptor%2Fmordred","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmordred-descriptor%2Fmordred/lists"}