biopython

v1.71.0

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

Represents a KGML pathway from KEGG.

Specifies graph information for the pathway map, as described in release KGML v0.7.1 (http://www.kegg.jp/kegg/xml/docs/)

Attributes:

  • name - KEGGID of the pathway map
  • org - ko/ec/[org prefix]
  • number - map number (integer)
  • title - the map title
  • image - URL of the image map for the pathway
  • link - URL of information about the pathway
  • entries - Dictionary of entries in the pathway, keyed by node ID
  • reactions - Set of reactions in the pathway

The name attribute has a restricted format, so we make it a property and enforce the formatting.

The Pathway object is the only allowed route for adding/removing Entry, Reaction, or Relation elements.

Entries are held in a dictionary and keyed by the node ID for the pathway graph - this allows for ready access via the Reaction/Relation etc. elements. Entries must be added before reference by any other element.

Reactions are held in a dictionary, keyed by node ID for the path. The elements referred to in the reaction must be added before the reaction itself.

Link to this section Summary

Functions

__init__()

Initialize the class

__str__()

Returns a readable summary description string

add_entry()

Add an Entry element to the pathway

add_reaction()

Add a Reaction element to the pathway

add_relation()

Add a Relation element to the pathway

bounds()

Coordinate bounds for all Graphics elements in the Pathway

compounds()

Get a list of entries of type compound

element()

Return the Pathway as a valid KGML element

genes()

Get a list of entries of type gene

get_KGML()

Return the pathway as a string in prettified KGML format

maps()

Get a list of entries of type map

orthologs()

Get a list of entries of type ortholog

reaction_entries()

List of entries corresponding to each reaction in the pathway

reactions()

Get a list of reactions in the pathway

relations()

Get a list of relations in the pathway

remove_entry()

Remove an Entry element from the pathway

remove_reaction()

Remove a Reaction element from the pathway

remove_relation()

Remove a Relation element from the pathway

Link to this section Functions

Link to this function __init__()

Initialize the class.

Link to this function __str__()

Returns a readable summary description string.

Link to this function add_entry()

Add an Entry element to the pathway.

Link to this function add_reaction()

Add a Reaction element to the pathway.

Link to this function add_relation()

Add a Relation element to the pathway.

Link to this function bounds()

Coordinate bounds for all Graphics elements in the Pathway.

Returns the [(xmin, ymin), (xmax, ymax)] coordinates for all Graphics elements in the Pathway

Link to this function compounds()

Get a list of entries of type compound.

Link to this function element()

Return the Pathway as a valid KGML element.

Link to this function genes()

Get a list of entries of type gene.

Link to this function get_KGML()

Return the pathway as a string in prettified KGML format.

Link to this function maps()

Get a list of entries of type map.

Link to this function orthologs()

Get a list of entries of type ortholog.

Link to this function reaction_entries()

List of entries corresponding to each reaction in the pathway.

Link to this function reactions()

Get a list of reactions in the pathway.

Link to this function relations()

Get a list of relations in the pathway.

Link to this function remove_entry()

Remove an Entry element from the pathway.

Link to this function remove_reaction()

Remove a Reaction element from the pathway.

Link to this function remove_relation()

Remove a Relation element from the pathway.