mordred package

modred descriptor calculator.

class mordred.Result(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
drop_missing()[source]

Delete missing value.

Returns:Result
items()[source]

Get items.

Returns:Iterable[(Descriptor, value)]
keys()[source]

Get descriptors instances.

Returns:Iterable[Descriptor]
values()[source]

Get descriptor values.

Returns:Iterable[value]
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
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
class mordred.Descriptor[source]

Abstract base class of descriptors.

mol

rdkit.Mol – target molecule

classmethod preset()[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:tuple
to_json()[source]

Convert to json serializable dictionary.

Returns:dictionary of descriptor
Return type:dict
calculate()[source]

[abstractmethod] calculate descriptor value.

Returns:rtype
dependencies()[source]

Descriptor dependencies.

Returns:dict[str, Descriptor or None] or None
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]
fail(exception)[source]

Raise known exception and return missing value.

Raises:MissingValueException
rethrow_zerodiv()[source]

[contextmanager] treat zero div as known exception.

rethrow_na(exception)[source]

[contextmanager] treat any exceptions as known exception.

classmethod from_json(obj)

Create Descriptor instance from json dict.

Parameters:obj (dict) – descriptor dict
Returns:descriptor
Return type:Descriptor
class mordred.Calculator(descs=None, ignore_3D=False)[source]

descriptor calculator.

Parameters:
  • descs – see Calculator.register() method
  • ignore_3D – see Calculator.register() method
classmethod from_json(obj)[source]

Create Calculator from json descriptor objects.

Parameters:obj (list or dict) – descriptors to register
Returns:calculator
Return type:Calculator
register_json(obj)[source]

Register Descriptors from json descriptor objects.

Parameters:obj (list or dict) – descriptors to register
to_json()[source]

Convert descriptors to json serializable data.

Returns:descriptors
Return type:list
descriptors

All descriptors.

you can get/set/delete descriptor.

Returns:registered descriptors
Return type:tuple[Descriptor]
register(desc, 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
Parameters:
  • desc (Descriptor-like) – descriptors to register
  • ignore_3D (bool) – ignore 3D descriptors
echo(s, file=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, end='\n')[source]

Output message.

Parameters:
  • s (str) – message to output
  • file (file-like) – output to
  • end (str) – end mark of message
Returns:

None
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]]
pandas(mols, nproc=None, nmols=None, quiet=False, ipynb=False, id=-1)[source]

Calculate descriptors over mols.

Returns:pandas.DataFrame
mordred.get_descriptors_from_module(mdl, submodule=False)[source]

Get descriptors from module.

Parameters:mdl (module) – module to search
Returns:[Descriptor]