Dependencies¶

This module requres lxml and sqlalchemy.

class pyteomics.mass.unimod.AlternativeName(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	alt_name id modification_id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.AminoAcid(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base, pyteomics.mass.unimod.HasFullNameMixin

Attributes:	full_name id num_C num_H num_N num_O num_S one_letter three_letter

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Brick(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base, pyteomics.mass.unimod.HasFullNameMixin

Attributes:	brick composition elements full_name id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.BrickToElement(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	brick_id count element element_obj id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Classification(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	classification id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Crossreference(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	id modification_id source source_id text url

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.CrossreferenceSource(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	id source

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Element(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base, pyteomics.mass.unimod.HasFullNameMixin

Attributes:	average_mass element full_name id monoisotopic_mass

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Fragment(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	composition id modification_id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.FragmentComposition(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	brick_string count fragment_id id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.HasFullNameMixin[source]¶

Bases: object

A simple mixin to standardize equality operators for models with a full_name attribute.

__init__¶

x.__init__(…) initializes x; see help(type(x)) for signature

class pyteomics.mass.unimod.MiscNotesModifications(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	id modification_id text

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Modification(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base, pyteomics.mass.unimod.HasFullNameMixin

Attributes:	approved average_mass bricks code_name ex_code_name full_name id monoisotopic_mass notes specificities username_of_poster

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.ModificationToBrick(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	brick_string count id modification_id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.NeutralLoss(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	brick_string count id specificity_id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Position(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	id position

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Specificity(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	amino_acid classification classification_id group hidden id modification_id neutral_losses position_id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.SpecificityToNeutralLoss(**kwargs)[source]¶

Bases: sqlalchemy.ext.declarative.api.Base

Attributes:	average_mass id is_peptide_neutral_loss is_required_peptide_neutral_loss is_slave monoisotopic_mass specificity specificity_id

Methods

from_tag

__init__(self, **kwargs)¶

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

class pyteomics.mass.unimod.Unimod(path=None)[source]¶

Bases: object

Main class representing the relational Unimod database.

Attributes:	mods

Methods

by_name(self, identifier[, strict])	Get a modification matching identifier.
by_title(self, identifier[, strict])	Get a modification matching identifier.
get(self, identifier[, strict])	Get a modification matching identifier.

__init__(self, path=None)[source]¶

Initialize the object from a database file.

Parameters:	path : str or None, optional If str, should point to a database. Use a dialect-specific prefix, like 'sqlite://'. If None (default), a relational XML file will be downloaded from default location.

by_name(self, identifier, strict=True)¶

Get a modification matching identifier. Replaces both by_name and by_title methods in the old class.

Parameters:	identifier : str strict : bool, optional Defaults to True.
Returns:	out : Modification

by_title(self, identifier, strict=True)¶

Get a modification matching identifier. Replaces both by_name and by_title methods in the old class.

Parameters:	identifier : str strict : bool, optional Defaults to True.
Returns:	out : Modification

get(self, identifier, strict=True)[source]¶

Get a modification matching identifier. Replaces both by_name and by_title methods in the old class.

Parameters:	identifier : str strict : bool, optional Defaults to True.
Returns:	out : Modification

pyteomics.mass.unimod.has_composition(attr_name)[source]¶

A decorator to simplify flagging a Model with a column to be treated as a formula for parsing. Calls _composition_listener() internally.

pyteomics.mass.unimod.load(doc_path, output_path='sqlite://')[source]¶

Parse the relational table-like XML file provided by http://www.unimod.org/downloads.html and convert each <tag>_row into an equivalent database entry.

By default the table will be held in memory.

pyteomics.mass.unimod.preprocess_xml(doc_path)[source]¶

Parse and drop namespaces from an XML document.

Parameters:	doc_path : str
Returns:	out : etree.ElementTree

pyteomics.mass.unimod.remove_namespace(doc, namespace)[source]¶

Remove namespace in the passed document in place.