The Protein Class¶

class ionize.Protein(name=None, ids=None, sequences=None, members=None)[source]¶

Protein represents an ion composed of a complex of peptides.

Parameters:	name – Name of the protein. ids – Names of the peptide members. sequences – Sequences of the peptide members. members – An iterable of the peptide members.

If members and sequences are not provided, the name will be searched in the Protein DataBase (PDB). If a protein of the same name is available, the sequences of the peptides will be gathered from the PDB.

charge(pH=None, ionic_strength=None, temperature=None, moment=1)¶: Return the net charge for the complex.

context(context=False)¶

Control the context of the ion.

Complex contexts works by setting the context of the members of the complex. The Complex has on context of its own.

See the context method for the members for additional information.

diffusivity(pH=None, ionic_strength=None, temperature=None)¶: The diffusivity of the ion, in meter^2/second.

members¶: Name of the peptide members.

mobility(pH=None, ionic_strength=None, temperature=None)¶: Return the mobility of the complex, in m^2/V/s.

molar_conductivity(pH=None, ionic_strength=None, temperature=None)¶: The molar conductivity of the ion, in Seimens/meter/Molar.

name¶: Protein name.

reference_temperature¶: The temperature at which ion properties were measured.

save(filename)¶: Save a serialized Ion to a file.

separability(other, pH=None, ionic_strength=None, temperature=None)¶

Return the separability between this ion and the other ion.

Separabillity is a normalized difference between this ion and the other ion, defined as:

abs((self.mobility - other.mobility)/ self.mobility)

Parameters:	other – The other ion for comparison. Must have valid context

and mobility methods.

The context from this ion is used to override the context of the other ion.

serialize(nested=False, compact=False)¶

Returns a JSON serialized string representation of the ion. This representation can be returned to an Ion object using deserialize.

Parameters:	nested – If True, skips JSON serialization and returns a python

dictionary.

Parameters:	compact – If True, returns a JSON representation with minimal

characters. Otherwise, whitespace is introduced for readability.

class ionize.Peptide(name=None, sequence=None)[source]¶

Peptide represents single protein chains in solution.

Peptides properties are based entirely on analysis of the sequence of the peptide.

charge(pH=None, ionic_strength=None, temperature=None, moment=1)[source]¶

Return the time-averaged charge of the peptide.

:param pH :param ionic_strength :param temperature

context(context=False)¶

Control the context in which ion properties are calculated.

The context is used as a convenience to specify what values of pH, ionic strength, and temperature are used to compute ion properties.

Example::

``water = ionize.Solution()

my_ion.mobility() # Raises without a pH for calculation

with my_ion.context(water):: my_ion.mobility() # Uses water pH

my_ion.context(water) my_ion.mobility() # Uses water pH my_ion.context() # Returns water my_ion.context(None)``

There are multiple sources from which pH, ionic strength, and temperature can be drawn. They are, in order of priority:

Method parameters. Manually setting a value when calling an ion
method always has the highest priority.

Context.

Default values. The default temperature is the package reference
temperature, 25 degrees C. This is assumed throughout the package
if temperature is not specified. The default ionic strength is the
solvent ionic strength. This ionic strength is calculated from the
pH if available. Otherwise, it is calculated as the minimum ionic
strength associated with the solvent dissociation constant. There
is no default value for the pH.

Parameters:	context – The new context to use for ion calculations. If context

is False, the current context is returned. Context can be None (to erase the current context) or a Solution object.

density()[source]¶: Return the approximate density of the folded peptide in kg/L.

diffusivity(pH=None, ionic_strength=None, temperature=None)¶: The diffusivity of the ion, in meter^2/second.

isoelectric_point(ionic_strength=None, temperature=None)[source]¶: Return the isoelectric point of the peptide.

mobility(pH=None, ionic_strength=None, temperature=None)[source]¶

Return the effective mobility of the ion in m^2/V/s.

If a context solution is available, mobility uses the full Onsager-Fuoss correction to mobility. Otherwise, the Robinson-Stokes model is used.