chemistry_tools

chemistry_tools.cas

chemistry_tools.cas.cas_int_to_string(cas_no)[source]

Converts an integer CAS number to a hyphenated string

Parameters:cas_no (int) –
Returns:
Return type:str
chemistry_tools.cas.cas_string_to_int(cas_no)[source]

Converts a hyphenated string CAS number to a integer

Parameters:cas_no (str) –
Returns:
Return type:int
chemistry_tools.cas.check_cas_number(cas_no)[source]

Checks the CAS number to ensure the check digit is valid with respect to the rest of the number.

If the CAS number is valid 0 is returned. If there is a problem the difference between the computed check digit and that given as part of the CAS number is returned.

Parameters:cas_no (int) –
Returns:
Return type:int

chemistry_tools.constants

class chemistry_tools.constants.Constant[source]
as_quantity()[source]

Returns the constant as a quantities.quantity.Quantity object.

Return type:quantities.quantity.Quantity

chemistry_tools.lookup

Lookup properties for compound by name or CAS number Uses data from PubChem and toxnet

chemistry_tools.lookup.get_assays(identifier, namespace='aid', **kwargs)[source]

Retrieve the specified assay records from PubChem.

Parameters:
  • identifier – The assay identifier to use as a search query.
  • namespace – (optional) The identifier type.
chemistry_tools.lookup.get_compounds(identifier, namespace='cid', searchtype=None, as_dataframe=False, **kwargs)[source]

Retrieve the specified compound records from PubChem.

Parameters:
  • identifier – The compound identifier to use as a search query.
  • namespace – (optional) The identifier type, one of cid, name, smiles, sdf, inchi, inchikey or formula.
  • searchtype – (optional) The advanced search type, one of substructure, superstructure or similarity.
  • as_dataframe – (optional) Automatically extract the Compound properties into a pandas DataFrame and return that.
chemistry_tools.lookup.get_substances(identifier, namespace='sid', as_dataframe=False, **kwargs)[source]

Retrieve the specified substance records from PubChem.

Parameters:
  • identifier – The substance identifier to use as a search query.
  • namespace – (optional) The identifier type, one of sid, name or sourceid/<source name>.
  • as_dataframe – (optional) Automatically extract the Substance properties into a pandas DataFrame and return that.

chemistry_tools.names

Lookup properties for compound by name or CAS number Uses data from PubChem and toxnet

chemistry_tools.lookup.get_assays(identifier, namespace='aid', **kwargs)[source]

Retrieve the specified assay records from PubChem.

Parameters:
  • identifier – The assay identifier to use as a search query.
  • namespace – (optional) The identifier type.
chemistry_tools.lookup.get_compounds(identifier, namespace='cid', searchtype=None, as_dataframe=False, **kwargs)[source]

Retrieve the specified compound records from PubChem.

Parameters:
  • identifier – The compound identifier to use as a search query.
  • namespace – (optional) The identifier type, one of cid, name, smiles, sdf, inchi, inchikey or formula.
  • searchtype – (optional) The advanced search type, one of substructure, superstructure or similarity.
  • as_dataframe – (optional) Automatically extract the Compound properties into a pandas DataFrame and return that.
chemistry_tools.lookup.get_substances(identifier, namespace='sid', as_dataframe=False, **kwargs)[source]

Retrieve the specified substance records from PubChem.

Parameters:
  • identifier – The substance identifier to use as a search query.
  • namespace – (optional) The identifier type, one of sid, name or sourceid/<source name>.
  • as_dataframe – (optional) Automatically extract the Substance properties into a pandas DataFrame and return that.

chemistry_tools.property_format

Format Physical Properties for Chemicals

chemistry_tools.property_format.scientific(string)[source]

TODO: Finish :param string: :return:

chemistry_tools.spectrum_similarity

chemistry_tools.spectrum_similarity.SpectrumSimilarity(spec_top, spec_bottom, t=0.25, b=10, top_label=None, bottom_label=None, xlim=(50, 1200), x_threshold=0, print_alignment=False, print_graphic=True, output_list=False)[source]
Parameters:
  • spec_top (numpy.array) – Array containing the experimental spectrum’s peak list with the m/z values in the first column and corresponding intensities in the second
  • spec_bottom (numpy.array) – Array containing the reference spectrum’s peak list with the m/z values in the first column and corresponding intensities in the second
  • t (float) – numeric value specifying the tolerance used to align the m/z values of the two spectra.
  • b (float) – numeric value specifying the baseline threshold for peak identification. Expressed as a percent of the maximum intensity.
  • top_label (str) – string to label the top spectrum.
  • bottom_label (str) – string to label the bottom spectrum.
  • xlim (tuple of int) – tuple of length 2, defining the beginning and ending values of the x-axis.
  • x_threshold (float) – numeric value specifying
  • print_alignment (bool) – whether the intensities should be printed
  • print_graphic (bool) –
  • output_list (bool) – whether the intensities should be returned
Returns:
Return type:

chemistry_tools.toxnet

Read data from National Library of Medicine TOXNET

chemistry_tools.utils

General utilities.

chemistry_tools.utils.defaultnamedtuple(typename, field_names, defaults=())[source]

Generates a new subclass of tuple with default values.

typename : string
The name of the class.
field_names : str or iterable
An iterable of splitable string.
defaults : iterable
Default values for field_names, counting [-len(defaults):].
>>> Body = defaultnamedtuple('Body', 'x y z density', (1.0,))
>>> Body.__doc__
'Body(x, y, z, density)'
>>> b = Body(10, z=3, y=5)
>>> b._asdict() == dict(x=10, y=5, z=3, density=1.0)
True

A new tuple subclass named typename