libSBNW Documentation

Contents:

Example 1: Basic Usage

Import the module

>>> import sbnw

Load an SBML model

>>> model = sbnw.loadsbml('BorisEJB.xml') # included in the test cases

Shrink or enlarge a network so that it fits within a window

>>> model.network.fitwindow(0,0,300,300)

Access the node coordinates

>>> for node in model.network.nodes:
>>>   print(node.centroid)

Example 2: Add layout information to an SBML model

Import the module

>>> import sbnw

Load an SBML model

>>> model = sbnw.loadsbml('ant_power_law_sbml.xml') # included in the test cases

Randomize the initial configuration and run the FR algorithm

>>> model.network.randomize(0,0,300,300)
>>> model.network.autolayout()

Shrink or enlarge a network so that it fits within a window

>>> model.network.fitwindow(0,0,300,300)

Override SBML level/version if desired

>>> model.level = 3
>>> model.version = 1

Save the model to an SBML file

>>> model.save('output.xml')

Example 3: Render network as a TikZ

Import the module

>>> import sbnw

Load an SBML model

>>> model = sbnw.loadsbml('GlycolysisOriginal.xml') # included in the test cases

Render the model to a TikZ file

>>> model.savetikz('GlycolysisOriginal_Render.tikz')

Example 4: Curves

Import the module

>>> import sbnw

Load an SBML model

>>> model = sbnw.loadsbml('BorisEJB.xml') # included in the test cases

Access the curve control points:

>>> for reaction in model.network.rxns:
>>>   for curve in reaction.curves:
>>>   print('Curve: Start {}, End {}, CP1 {}, CP2 {}'.format(curve[0], curve[3], curve[1], curve[2]))

Access endcap polygon:

>>>   if len(curve) > 5 and len(curve[5]) > 0:
>>>     print('Endcap poly: {}'.format(curve[5]))

Set endcap (a.k.a. arrowhead styles):

>>> sbnw.get_arrow_style('SUBSTRATE') # Other values are PRODUCT, MODIFIER, ACTIVATOR, INHIBITOR
>>> sbnw.set_arrow_style('SUBSTRATE', 3)

Example 5: Version

Get the version information

>>> import sbnw
>>> print(sbnw.__version__)

API Documentation

Functions

loadsbml
arrowpoly
arrowpoly_filled
narrow_styles
get_arrow_style
set_arrow_style

Classes

sbmlmodel
point
network
node
compartment
reaction
transform

Indices and tables

Table Of Contents

This Page