FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway module¶

Classes to represent a KGML Pathway Map.

The KGML definition is as of release KGML v0.7.1 (http://www.kegg.jp/kegg/xml/docs/)

Classes:

Pathway - Specifies graph information for the pathway map
Relation - Specifies a relationship between two proteins or KOs, or protein and compound. There is an implied direction to the relationship in some cases.
Reaction - A specific chemical reaction between a substrate and a product.
Entry - A node in the pathway graph
Graphics - Entry subelement describing its visual representation

class FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Component(parent)[source]¶

Bases: object

An Entry subelement used to represents a complex node.

A subelement of the Entry element, used when the Entry is a complex node, as described in release KGML v0.7.1 (http://www.kegg.jp/kegg/xml/docs/)

The Component acts as a collection (with type ‘group’, and typically its own Graphics subelement), having only an ID.

element¶: Return the Component as a valid KGML element.

id¶: The pathway graph node ID for the Entry

class FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry[source]¶

Bases: object

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/)

Variables:

id - The ID of the entry in the pathway map (-) –
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 (-) –
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

__str__()[source]¶: Return readable descriptive string.

add_component(element)[source]¶

Add an element to the entry.

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

add_graphics(entry)[source]¶: Add the Graphics entry.

bounds¶

Coordinate bounds for all Graphics elements in the Entry.

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

element¶: Return the Entry as a valid KGML element.

id¶: The pathway graph node ID for the Entry.

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

name¶: List of KEGG identifiers for the Entry.

reaction¶: List of reaction KEGG IDs for this Entry.

remove_component(value)[source]¶: Remove the entry with the passed ID from the group.

remove_graphics(entry)[source]¶: Remove the Graphics entry with the passed ID from the group.

class FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics(parent)[source]¶

Bases: object

An Entry subelement used to represents the visual representation.

A subelement of Entry, specifying its visual representation, as described in release KGML v0.7.1 (http://www.kegg.jp/kegg/xml/docs/)

Variables:	name Label for the graphics object (-) – x X-axis position of the object (-) – y Y-axis position of the object (-) – coords polyline co-ordinates, list of (-) – type object shape (-) – width object width (-) – height object height (-) – fgcolor object foreground color (-) – bgcolor object background color (-) –

Some attributes are present only for specific graphics types. For example, line types do not (typically) have a width. We permit non-DTD attributes and attribute settings, such as

dash List of ints, describing an on/off pattern for dashes

bgcolor¶: Background color.

bounds¶

Coordinate bounds for the Graphics element.

Return the bounds of the Graphics object as an [(xmin, ymin), (xmax, ymax)] tuple. Co-ordinates give the centre of the circle, rectangle, roundrectangle elements, so we have to adjust for the relevant width/height.

centre¶: Return the centre of the Graphics object as an (x, y) tuple.

coords¶: Polyline coordinates for the graphics element.

element¶: Return the Graphics as a valid KGML element.

fgcolor¶: Foreground color.

height¶: The height of the graphics element.

width¶: The width of the graphics element.

x¶: The X coordinate for the graphics element.

y¶: The Y coordinate for the graphics element.

class FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway[source]¶

Bases: object

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/)

Variables:

name - KEGGID of the pathway map (-) –
org - ko/ec/[org prefix] (-) –
number - map number (-) –
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.

__str__()[source]¶: Returns a readable summary description string.

add_entry(entry)[source]¶: Add an Entry element to the pathway.

add_reaction(reaction)[source]¶: Add a Reaction element to the pathway.

add_relation(relation)[source]¶: Add a Relation element to the pathway.

bounds¶

Coordinate bounds for all Graphics elements in the Pathway.

Returns the [(xmin, ymin), (xmax, ymax)] coordinates 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()[source]¶: Return the pathway as a string in prettified KGML format.

maps¶: Get a list of entries of type map.

name¶: The KEGGID for the pathway map.

number¶: The KEGG map number.

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(entry)[source]¶: Remove an Entry element from the pathway.

remove_reaction(reaction)[source]¶: Remove a Reaction element from the pathway.

remove_relation(relation)[source]¶: Remove a Relation element from the pathway.

class FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction[source]¶

Bases: object

A specific chemical reaction with substrates and products.

This describes a specific chemical reaction between one or more substrates and one or more products.

Variables:	id Pathway graph node ID of the entry (-) – names List of KEGG identifier (-) – type String (-) – reversible or irreversible substrate Entry object of the substrate (-) – product Entry object of the product (-) –

__str__()[source]¶: Return an informative human-readable string.

add_product(product_id)[source]¶: Add a product, identified by its node ID, to the reaction.

add_substrate(substrate_id)[source]¶: Add a substrate, identified by its node ID, to the reaction.

element¶: Return KGML element describing the Reaction.

entry¶: Return the Entry corresponding to this reaction.

id¶: Node ID for the reaction.

name¶: List of KEGG identifiers for the reaction.

products¶: Return list of product Entry elements.

reactant_ids¶: Return a list of substrate and product reactant IDs.

substrates¶: Return list of substrate Entry elements.

class FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Relation[source]¶

Bases: object

A relationship between to products, KOs, or protein and compound.

This describes a relationship between two products, KOs, or protein and compound, as described in release KGML v0.7.1 (http://www.kegg.jp/kegg/xml/docs/)

Variables:	entry1 - The first Entry object node ID defining the (-) – relation (int) entry2 - The second Entry object node ID defining the (-) – relation (int) type - The relation type (-) – subtypes - List of subtypes for the relation, as a list of (-) – (name, value) tuples

__str__()[source]¶: A useful human-readable string.

element¶: Return KGML element describing the Relation.

entry1¶: Entry1 of the relation.

entry2¶: Entry2 of the relation.

FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway._as_string(s)¶: Turn byte string or unicode string into a unicode string.

FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway._as_unicode(s)[source]¶: Turn byte string or unicode string into a unicode string.

FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway._is_int_or_long(i)[source]¶

Check if the value is an integer.

Note there are no longs on Python 3.