Metadata-Version: 2.1
Name: mordred
Version: 1.2.0
Summary: molecular descriptor calculator
Home-page: https://github.com/mordred-descriptor/mordred
Author: Hirotomo Moriwaki
Author-email: philopon.dependence@gmail.com
License: BSD-3-Clause
Description: mordred
        =======
        molecular descriptor calculator.
        
        .. image:: https://travis-ci.org/mordred-descriptor/mordred.svg?branch=master
            :target: https://travis-ci.org/mordred-descriptor/mordred
        
        .. image:: https://coveralls.io/repos/github/mordred-descriptor/mordred/badge.svg?branch=master
            :target: https://coveralls.io/github/mordred-descriptor/mordred?branch=master
        
        .. image:: https://codeclimate.com/github/mordred-descriptor/mordred/badges/gpa.svg
           :target: https://codeclimate.com/github/mordred-descriptor/mordred
           :alt: Code Climate
        
        .. image:: https://anaconda.org/mordred-descriptor/mordred/badges/version.svg
            :target: https://anaconda.org/mordred-descriptor/mordred
        
        .. image:: https://img.shields.io/pypi/v/mordred.svg
            :target: https://pypi.python.org/pypi/mordred
        
        .. image:: https://img.shields.io/badge/doi-10.1186%2Fs13321--018--0258--y-blue.svg
           :target: https://doi.org/10.1186/s13321-018-0258-y
        
        .. image:: https://img.shields.io/badge/slack-mordred--descriptor-brightgreen.svg
            :target: https://join.slack.com/t/mordred-descriptor/shared_invite/enQtMzc1MzkyODk1NTY5LTdlYzM4MWUzY2YwZmEwMWYzN2M4YTVkMGRlMDY0ZjU2NjQ1M2RiYzllMzVjZGE4NGZkNWZjODBjODE0YmExNjk
        
        number of descriptors
        ---------------------
        .. code:: python
        
            >>> from mordred import Calculator, descriptors
            >>> n_all = len(Calculator(descriptors, ignore_3D=False).descriptors)
            >>> n_2D = len(Calculator(descriptors, ignore_3D=True).descriptors)
            >>> print("2D:    {:5}\n3D:    {:5}\n------------\ntotal: {:5}".format(n_2D, n_all - n_2D, n_all))
            2D:     1613
            3D:      213
            ------------
            total:  1826
        
        Installation
        ------------
        
        conda(recommended)
        ~~~~~~~~~~~~~~~~~~
        #. install conda
        
               -  `miniconda <http://conda.pydata.org/miniconda.html>`__
               -  `anaconda <https://www.continuum.io/why-anaconda>`__
        
        #. install mordred
        
               .. code:: console
        
                   $ conda install -c rdkit -c mordred-descriptor mordred
        
        pip
        ~~~
        
        #. install `rdkit <http://www.rdkit.org/>`__ python package
        #. install mordred
        
               .. code:: console
        
                   $ pip install 'mordred[full]'  # install with extra requires
                   # or
                   $ pip install mordred
                   
        Testing the installation
        ------------------------
        
                    $ python -m mordred.tests
        
        examples
        --------
        
        as command
        ~~~~~~~~~~
        
        calculate all descriptors
        
        .. code:: console
        
            $ python -m mordred example.smi
            name,ECIndex,WPath,WPol,Zagreb1, (snip)
            benzene,36,27,3,24.0, (snip)
            chrolobenzene,45,42,5,30.0, (snip)
        
        
        save to file (display progress bar)
        
        .. code:: console
        
            $ python -m mordred example.smi -o example.csv
            50%|███████████████████████████████████████▌                                       | 1/2 [00:00<00:00,  7.66it/s]
        
        
        stream read (low memory, no number of molecules information)
        
        .. code:: console
        
            $ python -m mordred example.smi -s -o example.csv
            0it [00:00, ?it/s]
        
        only ABCIndex
        
        .. code:: console
        
            $ python -m mordred example.smi -d ABCIndex
            name,ABC,ABCGG
            benzene,4.242640687119286,3.9999999999999996
            chlorobenzene,5.059137268047012,4.785854275382693
        
        ABCIndex and AcidBase
        
        .. code:: console
        
            $ python -m mordred example.smi -d ABCIndex -d AcidBase
            name,ABC,ABCGG,nAcid,nBase
            benzene,4.242640687119286,3.9999999999999996,0,0
            chlorobenzene,5.059137268047012,4.785854275382693,0,0
        
        multiple input
        
        .. code:: console
        
            $ python -m mordred example.smi example2.smi -d ABCIndex
            name,ABC,ABCGG
            benzene,4.242640687119286,3.9999999999999996
            chlorobenzene,5.059137268047012,4.785854275382693
            pentane,2.8284271247461903,3.1462643699419726
        
        show help
        
        .. code:: console
        
            $ python -m mordred --help
            usage: python -m mordred [-h] [--version] [-t {auto,sdf,mol,smi}] [-o OUTPUT]
                                     [-p PROCESSES] [-q] [-s] [-d DESC] [-3] [-v]
                                     INPUT [INPUT ...]
        
            positional arguments:
              INPUT
        
            optional arguments:
              -h, --help            show this help message and exit
              --version             input molecular file
              -t {auto,sdf,mol,smi}, --type {auto,sdf,mol,smi}
                                    input filetype (default: auto)
              -o OUTPUT, --output OUTPUT
                                    output file path (default: stdout)
              -p PROCESSES, --processes PROCESSES
                                    number of processes (default: number of logical
                                    processors)
              -q, --quiet           hide progress bar
              -s, --stream          stream read
              -d DESC, --descriptor DESC
                                    descriptors to calculate (default: all)
              -3, --3D              use 3D descriptors (require sdf or mol file)
              -v, --verbosity       verbosity
        
            descriptors: ABCIndex AcidBase AdjacencyMatrix Aromatic AtomCount
            Autocorrelation BalabanJ BaryszMatrix BCUT BertzCT BondCount CarbonTypes Chi
            Constitutional CPSA DetourMatrix DistanceMatrix EccentricConnectivityIndex
            EState ExtendedTopochemicalAtom FragmentComplexity Framework GeometricalIndex
            GravitationalIndex HydrogenBond InformationContent KappaShapeIndex Lipinski
            McGowanVolume MoeType MolecularDistanceEdge MolecularId MomentOfInertia MoRSE
            PathCount Polarizability RingCount RotatableBond SLogP TopologicalCharge
            TopologicalIndex TopoPSA VdwVolumeABC VertexAdjacencyInformation WalkCount
            Weight WienerIndex ZagrebIndex
        
        as library
        ^^^^^^^^^^
        
        .. code:: python
        
            >>> from rdkit import Chem
            >>> from mordred import Calculator, descriptors
        
            # create descriptor calculator with all descriptors
            >>> calc = Calculator(descriptors, ignore_3D=True)
        
            >>> len(calc.descriptors)
            1613
        
            >>> len(Calculator(descriptors, ignore_3D=True, version="1.0.0"))
            1612
        
            # calculate single molecule
            >>> mol = Chem.MolFromSmiles('c1ccccc1')
            >>> calc(mol)[:3]
            [4.242640687119286, 3.9999999999999996, 0]
        
            # calculate multiple molecule
            >>> mols = [Chem.MolFromSmiles(smi) for smi in ['c1ccccc1Cl', 'c1ccccc1O', 'c1ccccc1N']]
        
            # as pandas
            >>> df = calc.pandas(mols)
            >>> df['SLogP']
            0    2.3400
            1    1.3922
            2    1.2688
            Name: SLogP, dtype: float64
        
        see `examples <https://github.com/mordred-descriptor/mordred/tree/develop/examples>`_
        
        Citation
        --------
        Moriwaki 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 <https://doi.org/10.1186/s13321-018-0258-y>`__
        
        Documentation
        -------------
        
        -  `master <http://mordred-descriptor.github.io/documentation/master>`__
        -  `develop <http://mordred-descriptor.github.io/documentation/develop>`__
        
        -  `v1.1.0 <http://mordred-descriptor.github.io/documentation/v1.1.1>`__
        -  `v1.0.0 <http://mordred-descriptor.github.io/documentation/v1.0.0>`__
        
Keywords: QSAR chemoinformatics
Platform: any
Provides-Extra: full
