{ "info": { "author": "Hirotomo Moriwaki", "author_email": "philopon.dependence@gmail.com", "bugtrack_url": null, "classifiers": [], "description": "mordred\n=======\nmolecular descriptor calculator.\n\n.. image:: https://travis-ci.org/mordred-descriptor/mordred.svg?branch=master\n :target: https://travis-ci.org/mordred-descriptor/mordred\n\n.. 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 >>> from mordred import Calculator, descriptors\n >>> n_all = len(Calculator(descriptors, ignore_3D=False).descriptors)\n >>> n_2D = len(Calculator(descriptors, ignore_3D=True).descriptors)\n >>> 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 `__\n - `anaconda `__\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 `__ 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%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 1/2 [00:00<00:00, 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 >>> from rdkit import Chem\n >>> from mordred import Calculator, descriptors\n\n # create descriptor calculator with all descriptors\n >>> calc = Calculator(descriptors, ignore_3D=True)\n\n >>> len(calc.descriptors)\n 1613\n\n >>> len(Calculator(descriptors, ignore_3D=True, version=\"1.0.0\"))\n 1612\n\n # calculate single molecule\n >>> mol = Chem.MolFromSmiles('c1ccccc1')\n >>> calc(mol)[:3]\n [4.242640687119286, 3.9999999999999996, 0]\n\n # calculate multiple molecule\n >>> mols = [Chem.MolFromSmiles(smi) for smi in ['c1ccccc1Cl', 'c1ccccc1O', 'c1ccccc1N']]\n\n # as pandas\n >>> df = calc.pandas(mols)\n >>> df['SLogP']\n 0 2.3400\n 1 1.3922\n 2 1.2688\n Name: SLogP, dtype: float64\n\nsee `examples `_\n\nCitation\n--------\nMoriwaki H, Tian Y-S, Kawashita N, Takagi T (2018) Mordred: a molecular descriptor calculator. 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