Substituents

Represents non-saccharide units that are found attached to saccharide residues. They also posses graph node-like properties.

class glypy.structure.substituent.Substituent(name, links=None, composition=None, id=None, can_nh_derivatize=None, is_nh_derivatizable=None, derivatize=False, attachment_composition=None)

Bases: glypy.structure.base.SubstituentBase

Represents a non-saccharide molecule commonly found bound to saccharide units.

Attributes

name: str	The name of the substituent, used to uniquely identify it.
links: OrderedMultiMap	All links to all molecules connected to this one.
composition: Composition	The chemical makeup of this molecule.
attachment_composition: Composition	The default cost of attaching this substituent to a Monosaccharide
id: int	A unique identifier number for this molecule.
can_nh_derivatize: bool	Whether this substituent will derivatize at an amine group.
is_nh_derivatizable: bool	Whether this substituent contains a derivatizable amine group.
_derivatize: bool	Whether this substituent was added by a derivatization process.
_order: int	The number of connections to this molecule. Mutated internally by Link objects, not for external use. See order().

add_substituent(substitent, position=2, max_occupancy=1, child_position=1, parent_loss=None, child_loss=None)

Adds a Substituent and associated Link to links at the site given by position. This new substituent is included when calculating mass with substituents included

Parameters:

substituent: str or Substituent

The substituent to add. If passed a str, it will be translated into an instance of Substituent

position: int or ‘x’

The location to add the Substituent link to links. Defaults to 2

child_position: int

The location to add the link to in substituent‘s links. Defaults to 1. Substituent indices are currently not checked.

max_occupancy: int, optional

The maximum number of items acceptable at position. Defaults to 1

parent_loss: Composition or str

The elemental composition removed from self. Defaults to H1.

child_loss: Composition or str

The elemental composition removed from substituent. Defaults to H1.

Raises:

ValueError:

position is occupied by more than max_occupancy elements

children()

Returns an iterator over the Monosaccharide`s which are considered the descendants of ``self`.

clone(prop_id=True)

Duplicates this Substituent object, recursively copying all children as well.

Parameters:

prop_id: bool

Whether or not to propagate id to the clone.

Returns:

Substituent

See also

structure.Monosaccharide.clone()

is_occupied(position)

Check to see if position is occupied. Unlike Monosaccharide, Substituent objects can only have two attachment sites at this time.

Parameters:

position: int

Returns:

int:

Number of links at position

Raises:

IndexError:

If position > 2 or < 1

mass(average=False, charge=0, mass_data=None)

Calculates the total mass of self and all nodes returned by children().

Parameters:

average: bool, optional, defaults to False

Whether or not to use the average isotopic composition when calculating masses. When average == False, masses are calculated using monoisotopic mass.

charge: int, optional, defaults to 0

If charge is non-zero, m/z is calculated, where m is the theoretical mass, and z is charge

mass_data: dict, optional, defaults to `None`

If mass_data is None, standard NIST mass and isotopic abundance data are used. Otherwise the contents of mass_data are assumed to contain elemental mass and isotopic abundance information.

Returns:

float

See also

glypy.composition.composition.calculate_mass()

parents()

Returns an iterator over the objects which are considered the ancestors of self.

static register(name, composition, can_nh_derivatize=None, is_nh_derivatizable=None, attachment_composition=None)

Register common information about a Substituent group to be used during initialization of instances of Substituent which share that name.

Parameters:

name : str

The name to be registered

composition : Composition

The shared base composition that will be initialized for each instance

can_nh_derivatize : None, optional

Passed to DerivatizePathway.register

is_nh_derivatizable : None, optional

Passed to DerivatizePathway.register

attachment_composition : None, optional

The shared composition that will be lost from the parent molecule when forming a bond with substituents of this type.

total_composition()

Computes the sum of the composition of self and each of its linked :class:`~.substituent.Substituent`s

Returns:Composition

static unregister(name)

Removes all information about the Substituent group denoted by name from the shared indices.

Parameters:

name : str

The name to un-register

glypy.structure.substituent.register(name, composition, can_nh_derivatize=None, is_nh_derivatizable=None, attachment_composition=None)

Register common information about a Substituent group to be used during initialization of instances of Substituent which share that name.

Parameters:

name : str

The name to be registered

composition : Composition

The shared base composition that will be initialized for each instance

can_nh_derivatize : None, optional

Passed to DerivatizePathway.register

is_nh_derivatizable : None, optional

Passed to DerivatizePathway.register

attachment_composition : None, optional

The shared composition that will be lost from the parent molecule when forming a bond with substituents of this type.

glypy.structure.substituent.unregister(name)

Removes all information about the Substituent group denoted by name from the shared indices.

Parameters:

name : str

The name to un-register