# Bio.KEGG.KGML.KGML_pathway module

Classes to represent a KGML Pathway Map.

The KGML definition is as of release KGML v0.7.2 (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 Bio.KEGG.KGML.KGML_pathway.Pathway

  Bases: `object`

  Represents a KGML pathway from KEGG.

  Specifies graph information for the pathway map, as described in release KGML v0.7.2 (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.

  __init__()

    Initialize the class.

  get_KGML()

    Return the pathway as a string in prettified KGML format.

  add_entry(entry)

    Add an Entry element to the pathway.

  remove_entry(entry)

    Remove an Entry element from the pathway.

  add_reaction(reaction)

    Add a Reaction element to the pathway.

  remove_reaction(reaction)

    Remove a Reaction element from the pathway.

  add_relation(relation)

    Add a Relation element to the pathway.

  remove_relation(relation)

    Remove a Relation element from the pathway.

  __str__()

    Return a readable summary description string.

  property name

    The KEGGID for the pathway map.

  property number

    The KEGG map number.

  property compounds

    Get a list of entries of type compound.

  property maps

    Get a list of entries of type map.

  property orthologs

    Get a list of entries of type ortholog.

  property genes

    Get a list of entries of type gene.

  property reactions

    Get a list of reactions in the pathway.

  property reaction_entries

    List of entries corresponding to each reaction in the pathway.

  property relations

    Get a list of relations in the pathway.

  property element

    Return the Pathway as a valid KGML element.

  property bounds

    Coordinate bounds for all Graphics elements in the Pathway.

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

  __firstlineno__ = 32
  __static_attributes__ = ('_name', '_number', '_reactions', '_relations', 'entries', 'image', 'link', 'org', 'title')

class Bio.KEGG.KGML.KGML_pathway.Entry

  Bases: `object`

  Represent an Entry from KGML.

  Each Entry element is a node in the pathway graph, as described in release KGML v0.7.2 (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

  __init__()

    Initialize the class.

  __str__()

    Return readable descriptive string.

  add_component(element)

    Add an element to the entry.

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

  remove_component(value)

    Remove the entry with the passed ID from the group.

  add_graphics(entry)

    Add the Graphics entry.

  remove_graphics(entry)

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

  property name

    List of KEGG identifiers for the Entry.

  property reaction

    List of reaction KEGG IDs for this Entry.

  property id

    The pathway graph node ID for the Entry.

  property element

    Return the Entry as a valid KGML element.

  property bounds

    Coordinate bounds for all Graphics elements in the Entry.

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

  property is_reactant

    Return true if this Entry participates in any reaction in its parent pathway.

  __firstlineno__ = 259
  __static_attributes__ = ('_id', '_names', '_pathway', '_reactions', 'alt', 'components', 'graphics', 'image', 'link', 'type')

class Bio.KEGG.KGML.KGML_pathway.Component(parent)

  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 v0.7.2 (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.

  __init__(parent)

    Initialize the class.

  property id

    The pathway graph node ID for the Entry

  property element

    Return the Component as a valid KGML element.

  __firstlineno__ = 419
  __static_attributes__ = ('_id', '_parent')

class Bio.KEGG.KGML.KGML_pathway.Graphics(parent)

  Bases: `object`

  An Entry subelement used to represents the visual representation.

  A subelement of Entry, specifying its visual representation, as described in release KGML v0.7.2 (http://www.kegg.jp/kegg/xml/docs/)

  Attributes:

    - name Label for the graphics object

    - x X-axis position of the object (int)

    - y Y-axis position of the object (int)

    - coords polyline coordinates, list of (int, int) tuples

    - type object shape

    - width object width (int)

    - height object height (int)

    - fgcolor object foreground color (hex RGB)

    - bgcolor object background color (hex RGB)

  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

  __init__(parent)

    Initialize the class.

  property x

    The X coordinate for the graphics element.

  property y

    The Y coordinate for the graphics element.

  property width

    The width of the graphics element.

  property height

    The height of the graphics element.

  property coords

    Polyline coordinates for the graphics element.

  property fgcolor

    Foreground color.

  property bgcolor

    Background color.

  property element

    Return the Graphics as a valid KGML element.

  property bounds

    Coordinate bounds for the Graphics element.

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

  property centre

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

  __firstlineno__ = 457
  __static_attributes__ = ('_bgcolor', '_coords', '_fgcolor', '_height', '_parent', '_width', '_x', '_y', 'bgcolor', 'fgcolor', 'name', 'type')

class Bio.KEGG.KGML.KGML_pathway.Reaction

  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.

  Attributes:

    - id Pathway graph node ID of the entry

    - names List of KEGG identifier(s) from the REACTION database

    - type String: reversible or irreversible

    - substrate Entry object of the substrate

    - product Entry object of the product

  __init__()

    Initialize the class.

  __str__()

    Return an informative human-readable string.

  add_substrate(substrate_id)

    Add a substrate, identified by its node ID, to the reaction.

  add_product(product_id)

    Add a product, identified by its node ID, to the reaction.

  property id

    Node ID for the reaction.

  property name

    List of KEGG identifiers for the reaction.

  property substrates

    Return list of substrate Entry elements.

  property products

    Return list of product Entry elements.

  property entry

    Return the Entry corresponding to this reaction.

  property reactant_ids

    Return a list of substrate and product reactant IDs.

  property element

    Return KGML element describing the Reaction.

  __firstlineno__ = 653
  __static_attributes__ = ('_id', '_names', '_pathway', '_products', '_substrates', 'type')

class Bio.KEGG.KGML.KGML_pathway.Relation

  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 v0.7.2 (http://www.kegg.jp/kegg/xml/docs/)

  Attributes:

    - 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

  __init__()

    Initialize the class.

  __str__()

    Return a useful human-readable string.

  property entry1

    Entry1 of the relation.

  __firstlineno__ = 777
  __static_attributes__ = ('_entry1', '_entry2', '_pathway', 'subtypes', 'type')
  property entry2

    Entry2 of the relation.

  property element

    Return KGML element describing the Relation.

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