biopython

v1.71.0

biopython v1.71.0 Bio.KEGG.KGML.KGML_pathway.Entry

Represent an Entry from KGML.

Each Entry element is a node in the pathway graph, as described in release KGML v0.7.1 (http://www.kegg.jp/kegg/xml/docs/)

Attributes:

  • id - The ID of the entry in the pathway map (integer)
  • names - List of KEGG IDs for the entry
  • type - The type of the entry
  • link - URL of information about the entry
  • reaction - List of KEGG IDs of the corresponding reactions (integer)
  • graphics - List of Graphics objects describing the Entry’s visual representation
  • components - List of component node ID for this Entry (‘group’)
  • alt - List of alternate names for the Entry

NOTE: The alt attribute represents a subelement of the substrate and product elements in the KGML file

Link to this section Summary

Functions

__init__()

Initialize the class

__str__()

Return readable descriptive string

add_component()

Add an element to the entry

add_graphics()

Add the Graphics entry

bounds()

Coordinate bounds for all Graphics elements in the Entry

element()

Return the Entry as a valid KGML element

is_reactant()

Does this Entry participate in any reaction in parent pathway?

remove_component()

Remove the entry with the passed ID from the group

remove_graphics()

Remove the Graphics entry with the passed ID from the group

Link to this section Functions

Link to this function __init__()

Initialize the class.

Link to this function __str__()

Return readable descriptive string.

Link to this function add_component()

Add an element to the entry.

If the Entry is already part of a pathway, make sure the component already exists.

Link to this function add_graphics()

Add the Graphics entry.

Link to this function bounds()

Coordinate bounds for all Graphics elements in the Entry.

Return the [(xmin, ymin), (xmax, ymax)] co-ordinates for the Entry Graphics elements.

Link to this function element()

Return the Entry as a valid KGML element.

Link to this function is_reactant()

Does this Entry participate in any reaction in parent pathway?

Returns True if the Entry participates in any reaction of its parent Pathway

Link to this function remove_component()

Remove the entry with the passed ID from the group.

Link to this function remove_graphics()

Remove the Graphics entry with the passed ID from the group.