libsbml_draw.model.sbml_layout.SBMLlayout Class Reference

Public Member Functions
def	__init__ (self, sbml_source=None, layout_alg_options=None, layout_number=0, fitToWindow=tuple(), autoComputeLayout=False)
def	loadSBMLFile (self, sbml_file)
def	loadSBMLString (self, sbml_string)
def	setLayoutAlgorithmOptions (self, k=None, grav=None, baryx=None, baryy=None, autobary=None, padding=None)
def	setLayoutAlgorithm_k (self, k)
def	setLayoutAlgorithm_grav (self, gravity)
def	setLayoutAlgorithm_baryx (self, baryx)
def	setLayoutAlgorithm_baryy (self, baryy)
def	setLayoutAlgorithm_autobary (self, autobary)
def	setLayoutAlgorithm_padding (self, padding)
def	getLayoutAlgorithmOptions (self)
def	showLayoutAlgorithmOptions (self)
def	regenerateLayoutAndResetRenderInfo (self)
def	regenerateLayout (self)
def	getNumberOfCompartments (self)
def	getNumberOfNodes (self)
def	getNumberOfReactions (self)
def	setModelNamespace (self, level, version)
def	aliasNode (self, node_id)
def	getIsNodeAliased (self, node_id)
def	getIsNodeLocked (self, node_id)
def	lockNode (self, node_id)
def	unlockNode (self, node_id)
def	getNodeCentroid (self, node_id)
def	setNodeCentroid (self, node_id, x, y)
def	getReactionCentroid (self, reaction_id)
def	writeSBMLFile (self, out_file_name)
def	getCompartmentIds (self)
def	setCompartmentEdgeColor (self, compartment_id, edge_color)
def	getCompartmentEdgeColor (self, compartment_id)
def	setCompartmentFillColor (self, compartment_id, fill_color)
def	getCompartmentFillColor (self, compartment_id)
def	getCompartmentLineWidth (self, compartment_id)
def	setCompartmentLineWidth (self, compartment_id, line_width)
def	getNodeIds (self)
def	getNodeColor (self, node_id)
def	getNodeKeywordIds (self, node_keyword)
def	setNodeColor (self, node_id, node_color)
def	getNodeFillColor (self, node_id)
def	setNodeFillColor (self, node_id, fill_color)
def	getNodeEdgeColor (self, node_id)
def	setNodeEdgeColor (self, node_id, edge_color)
def	getNodeEdgeWidth (self, node_id)
def	setNodeEdgeWidth (self, node_id, edge_width)
def	getNodeFontSize (self, node_id)
def	setNodeFontSize (self, node_id, font_size)
def	getNodeFontName (self, node_id)
def	setNodeFontName (self, node_id, font_name)
def	getNodeFontFamily (self, node_id)
def	setNodeFontFamily (self, node_id, font_family)
def	getNodeFontColor (self, node_id)
def	setNodeFontColor (self, node_id, font_color)
def	getNodeFontStyle (self, node_id)
def	setNodeFontStyle (self, node_id, font_style)
def	getNodeWidth (self, node_id)
def	getNodeHeight (self, node_id)
def	getNodeName (self, node_id)
def	getNodeLowerLeftPoint (self, node_id)
def	getBoundarySpeciesIds (self)
def	getFloatingSpeciesIds (self)
def	getReactionIds (self)
def	setReactionColor (self, reaction_id, reaction_color)
def	getReactionEdgeColor (self, reaction_id)
def	setReactionEdgeColor (self, reaction_id, edge_color)
def	getReactionFillColor (self, reaction_id)
def	setReactionFillColor (self, reaction_id, fill_color)
def	getReactionCurveWidth (self, reaction_id)
def	setReactionCurveWidth (self, reaction_id, curve_width)
def	getArrowheadStyle (self, role)
def	setArrowheadStyle (self, role, style)
def	getArrowheadNumVerts (self, style)
def	getArrowheadVert (self, style, vertex_number)
def	getArrowheadNumStyles (self)
def	drawNetwork (self, save_file_name=None, show=True, dpi=72, width_shift=.25, height_shift=.25, scaling_factor=1)
def	getSBMLString (self)
def	setArrowheadScale (self, role, arrowhead_scale)
def	getArrowheadScale (self, role)
def	getNumberOfRoles (self)
def	getReactionBezierPoints (self, reaction_id)

Static Public Attributes
	LIBSBML_DRAW_VERSION = sbnw.getCurrentLibraryVersion()
dictionary	NODE_KEYWORDS = {"all", "boundary", "floating"}
int	WIDTH_PADDING = 2
int	HEIGHT_PADDING = 1

Detailed Description

SBMLlayout represents the model in an SBML file.

Member Function Documentation

aliasNode()

def libsbml_draw.model.sbml_layout.SBMLlayout.aliasNode	(		self,
			node_id
	)

Creates an alias of this node for each incoming and outgoing
reaction.

Args:
    node_id (str):

Returns: None

drawNetwork()

def libsbml_draw.model.sbml_layout.SBMLlayout.drawNetwork	(		self,
			save_file_name = None,
			show = True,
			dpi = 72,
			width_shift = .25,
			height_shift = .25,
			scaling_factor = 1
	)

Draws the network to screen.  The figure can be saved.

Args:
    save_file_name (optional, str): save figure to this file
    show (optional, bool): if True, display the network on screen
    dpi (optional, int): desired dots-per-inch for the figure
    width_shift (optional, float): size in inches of the left and right
borders
    height_shift (optional, float): size in inches of the bottom and
top borders
    scaling_factor (option, float): decrease or increase the size of
the figure using this factor; example, 0.5 results in reducing
the figure size by one-half    

Returns: matplotlib.figure.Figure

getArrowheadNumStyles()

def libsbml_draw.model.sbml_layout.SBMLlayout.getArrowheadNumStyles

(

self

)

Returns the number of arrowhead styles available.

Args: None

Returns: int

getArrowheadNumVerts()

def libsbml_draw.model.sbml_layout.SBMLlayout.getArrowheadNumVerts	(		self,
			style
	)

Returns the number of vertices in the arrowhead of the given style.

Args:
    style (int): which arrowhead style

Returns:int

getArrowheadScale()

def libsbml_draw.model.sbml_layout.SBMLlayout.getArrowheadScale	(		self,
			role
	)

Returns the arrowhead scale for the given role.  Bigger values
result in bigger arrowheads.

Args: role(int)

Returns: int

getArrowheadStyle()

def libsbml_draw.model.sbml_layout.SBMLlayout.getArrowheadStyle	(		self,
			role
	)

Returns the arrowhead style for the given role.

Args:
    role (int): which role

Returns: int

getArrowheadVert()

def libsbml_draw.model.sbml_layout.SBMLlayout.getArrowheadVert	(		self,
			style,
			vertex_number
	)

Returns a point for the given vertex_number, given an arrowhead
style.

Args:
    style (int): which arrowhead style
    vertex_number (int): specify the vertex in the arrowhead

Returns: point with fields x and y

getBoundarySpeciesIds()

def libsbml_draw.model.sbml_layout.SBMLlayout.getBoundarySpeciesIds

(

self

)

Gets the id values of the Species who have boundaryCondition set to
True.

Args:
    None

Returns: list of Species ids

getCompartmentEdgeColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.getCompartmentEdgeColor	(		self,
			compartment_id
	)

Returns the color id for the compartment edge color.

Args:
    compartment_id(str): id for the compartment

Returns: str

getCompartmentFillColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.getCompartmentFillColor	(		self,
			compartment_id
	)

Returns the color id for the compartment fill color.

Args:
    compartment_id(str): id for the compartment

Returns: str

getCompartmentIds()

def libsbml_draw.model.sbml_layout.SBMLlayout.getCompartmentIds

(

self

)

Returns a list of compartment ids.

Args: None

Returns: list of str

getCompartmentLineWidth()

def libsbml_draw.model.sbml_layout.SBMLlayout.getCompartmentLineWidth	(		self,
			compartment_id
	)

Returns the line width for the given compartment.

Args: compartment_id (str): id for the compartment

Returns: int

getFloatingSpeciesIds()

def libsbml_draw.model.sbml_layout.SBMLlayout.getFloatingSpeciesIds

(

self

)

Gets the id values of the Species who have boundaryCondition set to
False.

Args:
    None

Returns: list of Species ids

getIsNodeAliased()

def libsbml_draw.model.sbml_layout.SBMLlayout.getIsNodeAliased	(		self,
			node_id
	)

Returns True if this node is an alias of earlier node.

Args:
    node_id (str):

Returns: None

getIsNodeLocked()

def libsbml_draw.model.sbml_layout.SBMLlayout.getIsNodeLocked	(		self,
			node_id
	)

Returns True if this node is locked.

Args:
    node_id(str): id for the node

Returns: bool

getLayoutAlgorithmOptions()

def libsbml_draw.model.sbml_layout.SBMLlayout.getLayoutAlgorithmOptions

(

self

)

Get the Fruchterman-Reingold layout algorithm parameter values.

Args: None

Returns: instance of the fr_alg_options class

getNodeCentroid()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeCentroid	(		self,
			node_id
	)

Returns the center point of the node.

Args:
    node_id (str): id for the node

Returns: tuple, with x and y

getNodeColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeColor	(		self,
			node_id
	)

Returns the id of the fill color for this node.

Args:
    node_id (str): id for the node

Returns: str

getNodeEdgeColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeEdgeColor	(		self,
			node_id
	)

Returns the color id for the node edge color.

Args:
    node_id(str): id for the node

Returns: str

getNodeEdgeWidth()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeEdgeWidth	(		self,
			node_id
	)

Returns the line width for the node edge.

Args:
    node_id(str): id for the node

Returns: float

getNodeFillColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeFillColor	(		self,
			node_id
	)

Returns the color id for the node fill color.

Args: node_id(str): id of the node

Returns: str

getNodeFontColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeFontColor	(		self,
			node_id
	)

Returns the color of the node's text.

Args:
    node_id (str): id for the node

Returns: str

getNodeFontFamily()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeFontFamily	(		self,
			node_id
	)

Returns the font family value, which can be the font family or
font name.

getNodeFontName()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeFontName	(		self,
			node_id
	)

Returns the font family value, which can be the font family or
font name.

Args:
    node_id (str): id for the node

Returns: str, eg. "Arial" or "serif"

getNodeFontSize()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeFontSize	(		self,
			node_id
	)

Returns the font size of the node text.

Args:
    node_id (str): id for the node

Returns: int

getNodeFontStyle()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeFontStyle	(		self,
			node_id
	)

Returns the style of the font for the given node.

Args:
    node_id (str): id for the node

Returns: str, "italic", "normal", or "oblique"

getNodeHeight()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeHeight	(		self,
			node_id
	)

Returns the height of the node.

Args:
    node_id (str): id for the node

Returns: float

getNodeIds()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeIds

(

self

)

Returns a list of node ids.

Args: None

Returns: list of str

getNodeKeywordIds()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeKeywordIds	(		self,
			node_keyword
	)

Returns a list of node ids corresponding to the given keyword.

Args:
    node_keyword(str): 'all', 'boundary', or 'floating'

Returns: list of str

getNodeLowerLeftPoint()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeLowerLeftPoint	(		self,
			node_id
	)

Returns the point for the node's lower left corner.

Args:
    node_id (str): id for the node

Returns: point which has fields x and y

getNodeName()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeName	(		self,
			node_id
	)

Returns the name of the node.

Args:
    node_id (str): id for the node

Returns: str

getNodeWidth()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNodeWidth	(		self,
			node_id
	)

Returns the width of the node.

Args:
    node_id (str): id for the node

Returns: float

getNumberOfCompartments()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNumberOfCompartments

(

self

)

Returns the number of compartments in the model.

Args: None
Returns: None

getNumberOfNodes()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNumberOfNodes

(

self

)

Returns the number of nodes in the model.

Args: None
Returns: None

getNumberOfReactions()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNumberOfReactions

(

self

)

Returns the number of reactions in the model.

Args: None
Returns: None

getNumberOfRoles()

def libsbml_draw.model.sbml_layout.SBMLlayout.getNumberOfRoles

(

self

)

Args: None

Returns: int

getReactionBezierPoints()

def libsbml_draw.model.sbml_layout.SBMLlayout.getReactionBezierPoints	(		self,
			reaction_id
	)

Returns a list of Bezier points (start, end, control1, control2) for
each curve in the reaction.

Args:
    reaction_id(str): id for the reaction

Returns: list, of BezierPoints named tuple of tuples

getReactionCentroid()

def libsbml_draw.model.sbml_layout.SBMLlayout.getReactionCentroid	(		self,
			reaction_id
	)

Returns the centroid of the reaction.

Args:
    reaction_id (str): id of the reaction

Returns: tuple, with x and y

getReactionCurveWidth()

def libsbml_draw.model.sbml_layout.SBMLlayout.getReactionCurveWidth	(		self,
			reaction_id
	)

Returns the curve width for the given reaction.

Args: reaction_id (str): id for the reaction

Returns: int

getReactionEdgeColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.getReactionEdgeColor	(		self,
			reaction_id
	)

Returns the color id for the edge color of the reaction.

Args:
    reaction_id (str): id for the reaction

Returns: str

getReactionFillColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.getReactionFillColor	(		self,
			reaction_id
	)

Returns the fill color for the reaction.

Args:
    reaction_id (str): id for the reaction

Returns: str

getReactionIds()

def libsbml_draw.model.sbml_layout.SBMLlayout.getReactionIds

(

self

)

Gets the ids of the reactions in the model.

Args: None

Returns: list of Reaction ids

getSBMLString()

def libsbml_draw.model.sbml_layout.SBMLlayout.getSBMLString

(

self

)

Returns the SBML string for the model.

Args: None

Returns: str

loadSBMLFile()

def libsbml_draw.model.sbml_layout.SBMLlayout.loadSBMLFile	(		self,
			sbml_file
	)

Loads the SBML model into SBMLlayout.

Args:
    sbml_string(str): name of file containing an SBML model

Returns: None

loadSBMLString()

def libsbml_draw.model.sbml_layout.SBMLlayout.loadSBMLString	(		self,
			sbml_string
	)

Loads the SBML model into SBMLlayout.

Args:
    sbml_string(str): SBML model in string format

Returns: None

lockNode()

def libsbml_draw.model.sbml_layout.SBMLlayout.lockNode	(		self,
			node_id
	)

Locks the node so that a new layout can be generated w/o moving
this node.

Args:
    node_id (str): id for the node

Returns: None

regenerateLayout()

def libsbml_draw.model.sbml_layout.SBMLlayout.regenerateLayout

(

self

)

Use this to generate a new layout, and update the network's node
reaction, and compartment layout values.

Args: None

Returns: None

regenerateLayoutAndResetRenderInfo()

def libsbml_draw.model.sbml_layout.SBMLlayout.regenerateLayoutAndResetRenderInfo

(

self

)

Use this to generate a new layout, and reset the network's node
and reaction layout and render values.

Args: None

Returns: None

setArrowheadScale()

def libsbml_draw.model.sbml_layout.SBMLlayout.setArrowheadScale	(		self,
			role,
			arrowhead_scale
	)

Set a value for matplotlib's mutation_scale to change the
size of the arrowhead for a given role.  The default value is 10.
Bigger values result in bigger arrowheads.

Args:
    arrowhead_scale(int): passed on to matplotlib
    role(int): role of the reaction

Returns: None

setArrowheadStyle()

def libsbml_draw.model.sbml_layout.SBMLlayout.setArrowheadStyle	(		self,
			role,
			style
	)

Set the arrowhead style for the given role.

Args:
    role (int): which role
    style (int): which style

Returns: None

setCompartmentEdgeColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setCompartmentEdgeColor	(		self,
			compartment_id,
			edge_color
	)

Sets the compartment edge color.

Args:
    compartment_id (str): id of the compartment to change the color of
one compartment, or 'all' to change the color of all the
compartments
    edge_color (str): id of the color

Returns: None

setCompartmentFillColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setCompartmentFillColor	(		self,
			compartment_id,
			fill_color
	)

Sets the compartment fill color.

Args:
    compartment_id (str): id of the compartment to change the color of
one compartment, or 'all' to change the color of all the
compartments
    fill_color (str): id of the color

Returns: None

setCompartmentLineWidth()

def libsbml_draw.model.sbml_layout.SBMLlayout.setCompartmentLineWidth	(		self,
			compartment_id,
			line_width
	)

Sets the line width of the compartment.

Args:
    compartment_id (str): id of the compartment to change the width of
one compartment, or 'all' to change the width of all the
compartments
    line_width (int): numeric value representing the line width

Returns: None

setLayoutAlgorithm_autobary()

def libsbml_draw.model.sbml_layout.SBMLlayout.setLayoutAlgorithm_autobary	(		self,
			autobary
	)

Set the Fruchterman-Reingold layout algorithm parameter 'autobary'.

Args:
    autobary (int):

Returns: None

setLayoutAlgorithm_baryx()

def libsbml_draw.model.sbml_layout.SBMLlayout.setLayoutAlgorithm_baryx	(		self,
			baryx
	)

Set the Fruchterman-Reingold layout algorithm parameter 'baryx'.

Args:
    baryx (float):

Returns: None

setLayoutAlgorithm_baryy()

def libsbml_draw.model.sbml_layout.SBMLlayout.setLayoutAlgorithm_baryy	(		self,
			baryy
	)

Set the Fruchterman-Reingold layout algorithm parameter 'baryy'.

Args:
    baryy (float):

Returns: None

setLayoutAlgorithm_grav()

def libsbml_draw.model.sbml_layout.SBMLlayout.setLayoutAlgorithm_grav	(		self,
			gravity
	)

Set the Fruchterman-Reingold layout algorithm parameter 'grav'.

Args:
    gravity (float):

Returns: None

setLayoutAlgorithm_k()

def libsbml_draw.model.sbml_layout.SBMLlayout.setLayoutAlgorithm_k	(		self,
			k
	)

Set the Fruchterman-Reingold layout algorithm parameter 'k'.

Args:
    k (float):

Returns: None

setLayoutAlgorithm_padding()

def libsbml_draw.model.sbml_layout.SBMLlayout.setLayoutAlgorithm_padding	(		self,
			padding
	)

Set the Fruchterman-Reingold layout algorithm parameter 'padding'.

Args:
    padding (float):

Returns: None

setLayoutAlgorithmOptions()

def libsbml_draw.model.sbml_layout.SBMLlayout.setLayoutAlgorithmOptions	(		self,
			k = None,
			grav = None,
			baryx = None,
			baryy = None,
			autobary = None,
			padding = None
	)

Set values for the Fruchterman-Reingold layout algorithm parameters.

Args:
    k (float):
    gravity (float):
    baryx (float):
    baryy (float):
    autobary (int):
    padding (float):

Returns: None

setModelNamespace()

def libsbml_draw.model.sbml_layout.SBMLlayout.setModelNamespace	(		self,
			level,
			version
	)

Specify the Model level and version.

Args:
    level (int): model level
    version (int): model version

Returns: None

setNodeCentroid()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeCentroid	(		self,
			node_id,
			x,
			y
	)

Sets the center point of the node.

Args:
    node_id (str): id for the node
    x (float): new x coordinate
    y (float): new y coordinate

Returns: None

setNodeColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeColor	(		self,
			node_id,
			node_color
	)

Sets the node edge color and fill color to the same value.

Args:
    node_id (str or list of str): id of the node to change,
or keyword 'all', 'boundary', or 'floating' to change the color
of all the nodes of that type, or a list of node ids to change.
    node_color (str): id of the color

Returns: None

setNodeEdgeColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeEdgeColor	(		self,
			node_id,
			edge_color
	)

Sets the node edge color.

Args:
    node_id (str or list of str): id of the node to change,
or keyword 'all', 'boundary', or 'floating' to change the color
of all the nodes of that type, or a list of node ids to change.
    edge_color (str): id of the color

Returns: None

setNodeEdgeWidth()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeEdgeWidth	(		self,
			node_id,
			edge_width
	)

Sets the line width of the node edge.

Args:
    node_id (str or list of str): id of the node to change,
or keyword 'all', 'boundary', or 'floating' to change the color
of all the nodes of that type, or a list of node ids to change.
    edge_width (float): line width of the edge

Returns: None

setNodeFillColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeFillColor	(		self,
			node_id,
			fill_color
	)

Sets the node fill color.

Args:
    node_id (str or list of str): id of the node to change,
or keyword 'all', 'boundary', or 'floating' to change the color
of all the nodes of that type, or a list of node ids to change.
    fill_color (str): id of the color

Returns: None

setNodeFontColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeFontColor	(		self,
			node_id,
			font_color
	)

Sets the node font color.

Args:
    node_id (str or list of str): id of the node to change,
or keyword 'all', 'boundary', or 'floating' to change the color
of all the nodes of that type, or a list of node ids to change.
    font_color (str): id of the color

Returns: None

setNodeFontFamily()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeFontFamily	(		self,
			node_id,
			font_family
	)

Sets the font family for the node, which can be a value for either
the family or name of the font.

Args:
    node_id (str): id for the node
    font_family (str): value for font family (eg. 'serif')
    or font name (eg. 'Arial')

Returns: None

setNodeFontName()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeFontName	(		self,
			node_id,
			font_name
	)

Sets the font family for the node, which can be a value for the
family or name of the font.

Args:
    node_id (str): id for the node
    font_name (str): value for font family (eg. 'serif')
    or font name (eg. 'Arial')

Returns: None

setNodeFontSize()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeFontSize	(		self,
			node_id,
			font_size
	)

Set the font size for the node.

Args:
    node_id (str): id for the node
    font_size (int or str): matplotlib acceptable values, which are:
{size in points, 'xx-small', 'x-small', 'small', 'medium',
'large', 'x-large', 'xx-large'}

Returns: None

setNodeFontStyle()

def libsbml_draw.model.sbml_layout.SBMLlayout.setNodeFontStyle	(		self,
			node_id,
			font_style
	)

Sets the node font style.

Args:
    node_id (str or list of str): id of the node to change,
or keyword 'all', 'boundary', or 'floating' to change the color
of all the nodes of that type, or a list of node ids to change.
    font_style (str): Available font styles are normal, italic, and
oblique.

Returns: None

setReactionColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setReactionColor	(		self,
			reaction_id,
			reaction_color
	)

Sets the reaction edge color and fill color to the same value.

Args:
    reaction_id (str): id of the reaction to change the color of one
reaction, or 'all' to change the color of all the reactions
    reaction_color (str): id of the color

Returns: None

setReactionCurveWidth()

def libsbml_draw.model.sbml_layout.SBMLlayout.setReactionCurveWidth	(		self,
			reaction_id,
			curve_width
	)

Sets the width of the reaction curve.

Args:
    reaction_id (str): id of the reaction to change the width of one
reaction, or 'all' to change the width of all the reactions
    curve_width (int): numeric value representing the line width

Returns: None

setReactionEdgeColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setReactionEdgeColor	(		self,
			reaction_id,
			edge_color
	)

Sets the reaction edge color.

Args:
    reaction_id (str): id of the reaction to change the color of one
reaction, or 'all' to change the color of all the reactions
    edge_color (str): id of the color

Returns: None

setReactionFillColor()

def libsbml_draw.model.sbml_layout.SBMLlayout.setReactionFillColor	(		self,
			reaction_id,
			fill_color
	)

Sets the reaction fill color.

Args:
    reaction_id (str): id of the reaction to change the color of one
reaction, or 'all' to change the color of all the reactions
    fill_color (str): id of the color

Returns: None

showLayoutAlgorithmOptions()

def libsbml_draw.model.sbml_layout.SBMLlayout.showLayoutAlgorithmOptions

(

self

)

Prints out the values of the Fruchterman-Reingold algorithm
paramters, which are: k, grav, baryx, baryy, autobary, and padding.

Args: None

Returns: None

unlockNode()

def libsbml_draw.model.sbml_layout.SBMLlayout.unlockNode	(		self,
			node_id
	)

Unlocks a previously locked node.

Args:
    node_id (str): id for the node

Returns: None

writeSBMLFile()

def libsbml_draw.model.sbml_layout.SBMLlayout.writeSBMLFile	(		self,
			out_file_name
	)

Writes the model as an SBML file.

Args:
    out_file_name (str): name of the file to write

Returns: None

---

The documentation for this class was generated from the following file:

• C:/Users/nrhaw/Documents/repos/libsbml-draw/src/python/libsbml_draw/model/sbml_layout.py