mordred package¶
modred descriptor calculator.
-
class
mordred.
Result
(mol, r, d)[source]¶ Result type.
-
fill_missing
(value=nan)[source]¶ Replace missing value to “value”.
- Parameters
value – value that missing value is replaced
- Returns
Result
-
asdict
(rawkey=False)[source]¶ Convert Result to dict.
- Parameters
rawkey (bool) –
True: dict key is Descriptor instance
False: dict key is str
- Returns
dict
-
ix
¶ Access descriptor value by index.
>>> from mordred import Calculator, Lipinski >>> from rdkit import Chem >>> result = Calculator(Lipinski.Lipinski)(Chem.MolFromSmiles("C1CCCCC1")) >>> result.ix[0] True
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name
¶ Access descriptor value by descriptor name or instance.
>>> from mordred import Calculator, descriptors >>> from rdkit import Chem >>> result = Calculator(descriptors)(Chem.MolFromSmiles("C1CCCCC1")) >>> result.name["C2SP3"] 6
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-
class
mordred.
Descriptor
[source]¶ Abstract base class of descriptors.
-
mol
¶ target molecule
- Type
rdkit.Mol
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classmethod
preset
(version)[source]¶ Generate preset descriptor instances.
- Returns
preset descriptors
- Return type
Iterable[Descriptor]
-
parameters
()[source]¶ [abstractmethod] get __init__ arguments of this descriptor instance.
this method used in pickling and identifying descriptor instance.
- Returns
tuple of __init__ arguments
- Return type
-
to_json
()[source]¶ Convert to json serializable dictionary.
- Returns
dictionary of descriptor
- Return type
-
as_argument
¶ Argument representation of descriptor.
- Returns
any
-
mol
Get molecule.
- Returns
rdkit.Mol
-
coord
¶ Get 3D coordinate.
- Returns
coordinate matrix
- Return type
numpy.array[3, N]
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fail
(exception)[source]¶ Raise known exception and return missing value.
- Raises
MissingValueException –
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-
class
mordred.
Calculator
(descs=None, version=None, ignore_3D=False, config=None)[source]¶ descriptor calculator.
- Parameters
descs – see Calculator.register() method
ignore_3D – see Calculator.register() method
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classmethod
from_json
(obj)[source]¶ Create Calculator from json descriptor objects.
- Parameters
- Returns
calculator
- Return type
-
descriptors
¶ All descriptors.
you can get/set/delete descriptor.
- Returns
registered descriptors
- Return type
-
register
(desc, version=None, ignore_3D=False)[source]¶ Register descriptors.
- Descriptor-like:
Descriptor instance: self
Descriptor class: use Descriptor.preset() method
module: use Descriptor-likes in module
Iterable: use Descriptor-likes in Iterable
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echo
(s, file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, end='\n')[source]¶ Output message.
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map
(mols, nproc=None, nmols=None, quiet=False, ipynb=False, id=-1)[source]¶ Calculate descriptors over mols.
- Parameters
mols (Iterable[rdkit.Mol]) – moleculars
nproc (int) – number of process to use. default: multiprocessing.cpu_count()
nmols (int) – number of all mols to use in progress-bar. default: mols.__len__()
quiet (bool) – don’t show progress bar. default: False
ipynb (bool) – use ipython notebook progress bar. default: False
id (int) – conformer id to use. default: -1.
- Returns
Iterator[Result[scalar]]
-
mordred.
get_descriptors_in_module
(mdl, submodule=True)[source]¶ Get descriptors in module.
- Parameters
mdl (module) – module to search
submodule (bool) – search recursively
- Returns
Iterator[Descriptor]
-
mordred.
get_descriptors_from_module
(mdl, submodule=False)[source]¶ [DEPRECATED] Get descriptors from module.
- Parameters
mdl (module) – module to search
- Returns
[Descriptor]
- Subpackages
- Submodules
- mordred.ABCIndex module
- mordred.AcidBase module
- mordred.AdjacencyMatrix module
- mordred.Aromatic module
- mordred.AtomCount module
- mordred.Autocorrelation module
- mordred.BCUT module
- mordred.BalabanJ module
- mordred.BaryszMatrix module
- mordred.BertzCT module
- mordred.BondCount module
- mordred.CPSA module
- mordred.CarbonTypes module
- mordred.Chi module
- mordred.Constitutional module
- mordred.DetourMatrix module
- mordred.DistanceMatrix module
- mordred.EState module
- mordred.EccentricConnectivityIndex module
- mordred.ExtendedTopochemicalAtom module
- mordred.FragmentComplexity module
- mordred.Framework module
- mordred.GeometricalIndex module
- mordred.GravitationalIndex module
- mordred.HydrogenBond module
- mordred.InformationContent module
- mordred.KappaShapeIndex module
- mordred.Lipinski module
- mordred.LogS module
- mordred.McGowanVolume module
- mordred.MoRSE module
- mordred.MoeType module
- mordred.MolecularDistanceEdge module
- mordred.MolecularId module
- mordred.MomentOfInertia module
- mordred.PBF module
- mordred.PathCount module
- mordred.Polarizability module
- mordred.RingCount module
- mordred.RotatableBond module
- mordred.SLogP module
- mordred.TopoPSA module
- mordred.TopologicalCharge module
- mordred.TopologicalIndex module
- mordred.VdwVolumeABC module
- mordred.VertexAdjacencyInformation module
- mordred.WalkCount module
- mordred.Weight module
- mordred.WienerIndex module
- mordred.ZagrebIndex module