Index

A

a (rkviewer.config.Color attribute) ABOVE (rkviewer.canvas.data.TextPosition attribute) AbstractNodeSchema (class in rkviewer.iodine) active_tab_fg (rkviewer.config.ThemeSchema attribute) add() (rkviewer.canvas.utils.SetSubject method) add_alias_node() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) add_compartment_g() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) ADD_COMPARTMENTS (rkviewer.canvas.state.InputMode attribute) add_node_g() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) ADD_NODES (rkviewer.canvas.state.InputMode attribute) add_plugin_schema() (in module rkviewer.config) add_reaction_g() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) addAliasNode() (in module rkviewer.iodine) AddButton() (rkviewer.utils.ButtonGroup method) addCompartment() (in module rkviewer.iodine) (rkviewer.iodine.TNetwork method)

addNode() (in module rkviewer.iodine) (rkviewer.iodine.TNetwork method) addReaction() (rkviewer.iodine.TNetwork method) alias_for_reaction() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) aliasForReaction() (in module rkviewer.iodine) AliasSchema (class in rkviewer.iodine) aligned() (rkviewer.canvas.geometry.Rect method) Alignment (class in rkviewer.canvas.canvas) alignment (rkviewer.canvas.data.TextPrim attribute) AlphaToText() (in module rkviewer.forms) append() (rkviewer.events.HandlerChain method) AppSettings (class in rkviewer.config) arrow_adjusted_coords (rkviewer.canvas.data.SpeciesBezier attribute) arrow_tip (rkviewer.canvas.state.CanvasState attribute) arrow_tip_changed() (rkviewer.canvas.data.SpeciesBezier method) ArrowTip (class in rkviewer.canvas.state) as_int() (rkviewer.canvas.geometry.Vec2 method) as_tuple() (rkviewer.canvas.geometry.Rect method) (rkviewer.canvas.geometry.Vec2 method) attach() (rkviewer.canvas.utils.Subject method)

B

b (rkviewer.config.Color attribute) BAD_STOICH (rkviewer.iodine.ErrorCode attribute) base (rkviewer.canvas.data.HandleData attribute), [1] baseNodes (rkviewer.iodine.TNetwork attribute) BELOW (rkviewer.canvas.data.TextPosition attribute) bezier (rkviewer.canvas.elements.ReactionElement attribute) bezier_curves() (in module rkviewer.iodine) bezier_points (rkviewer.canvas.data.SpeciesBezier attribute) bezierCurves (rkviewer.canvas.data.Reaction attribute) (rkviewer.canvas.data.SpeciesBezier attribute), [1] (rkviewer.iodine.TReaction attribute) BezierHandle (class in rkviewer.canvas.elements) bg_color (rkviewer.canvas.data.TextPrim attribute) bhandles (rkviewer.canvas.elements.ReactionElement attribute) bind_controller() (rkviewer.mvc.IView method) bind_error_callback() (rkviewer.plugin_manage.PluginManager method) bind_handler() (in module rkviewer.events) border (rkviewer.canvas.data.Compartment attribute) border_color (rkviewer.canvas.data.CirclePrim attribute) (rkviewer.canvas.data.Node attribute) (rkviewer.canvas.data.PolygonPrim attribute) (rkviewer.canvas.data.RectanglePrim attribute) border_color() (rkviewer.canvas.data.Node property) border_width (rkviewer.canvas.data.CirclePrim attribute) (rkviewer.canvas.data.Compartment attribute) (rkviewer.canvas.data.Node attribute) (rkviewer.canvas.data.PolygonPrim attribute) (rkviewer.canvas.data.RectanglePrim attribute)

border_width() (rkviewer.canvas.data.Node property) BOTTOM (rkviewer.canvas.canvas.Alignment attribute) (rkviewer.canvas.geometry.Direction attribute) bounding_rect (rkviewer.canvas.elements.SelectBox attribute) bounding_rect() (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.CompartmentElt method) (rkviewer.canvas.elements.NodeElement method) (rkviewer.canvas.elements.ReactionCenter method) (rkviewer.canvas.elements.ReactionElement method) bounds (rkviewer.canvas.state.CanvasState attribute) BOUNDS_EPS (in module rkviewer.canvas.canvas) BOUNDS_EPS_VEC (in module rkviewer.canvas.canvas) btn_bg (rkviewer.config.ThemeSchema attribute) btn_border (rkviewer.config.ThemeSchema attribute) btn_fg (rkviewer.config.ThemeSchema attribute) btn_hover_bg (rkviewer.config.ThemeSchema attribute) btn_hover_fg (rkviewer.config.ThemeSchema attribute) ButtonGroup (class in rkviewer.utils) by_user (rkviewer.events.DidChangeCompartmentOfNodesEvent attribute), [1] (rkviewer.events.DidModifyNodesEvent attribute), [1] (rkviewer.events.DidModifyReactionEvent attribute), [1] (rkviewer.events.DidMoveBezierHandleEvent attribute), [1] (rkviewer.events.DidMoveCompartmentsEvent attribute), [1] (rkviewer.events.DidMoveNodesEvent attribute), [1] (rkviewer.events.DidRedoEvent attribute) (rkviewer.events.DidResizeCompartmentsEvent attribute), [1] (rkviewer.events.DidResizeNodesEvent attribute), [1] (rkviewer.events.DidUndoEvent attribute)

C

calc_node_dimensions() (in module rkviewer.canvas.geometry) Callback (rkviewer.canvas.overlays.Minimap attribute), [1] (rkviewer.utils.ButtonGroup attribute), [1] callbacks (rkviewer.plugin_manage.PluginManager attribute) canvas (rkviewer.canvas.elements.NodeElement attribute) (rkviewer.canvas.elements.ReactionElement attribute) canvas_bg (rkviewer.config.ThemeSchema attribute) canvas_height (rkviewer.config.ThemeSchema attribute) canvas_outside_bg (rkviewer.config.ThemeSchema attribute) canvas_width (rkviewer.config.ThemeSchema attribute) CanvasDidUpdateEvent (class in rkviewer.events) CanvasElement (class in rkviewer.canvas.elements) CanvasEvent (class in rkviewer.events) CanvasOverlay (class in rkviewer.canvas.overlays) CanvasState (class in rkviewer.canvas.state) CENTER (rkviewer.canvas.canvas.Alignment attribute) (rkviewer.canvas.data.TextAlignment attribute) center_el (rkviewer.canvas.elements.ReactionElement attribute) center_moved() (rkviewer.canvas.data.ReactionBezier method) center_point() (rkviewer.canvas.geometry.Rect property) center_pos (rkviewer.canvas.data.Reaction attribute) CENTER_RATIO (rkviewer.canvas.data.ReactionBezier attribute) centerHandlePos (rkviewer.iodine.TReaction attribute) centerPos (rkviewer.iodine.TReaction attribute) centroid_handle (rkviewer.canvas.data.SpeciesBezier attribute) change_opacity() (in module rkviewer.utils) ChangePairValue() (in module rkviewer.forms) ChoiceField (class in rkviewer.iodine) ChoiceItem (class in rkviewer.canvas.data) CIRCLE (rkviewer.canvas.data.ModifierTipStyle attribute) circle_bounds() (in module rkviewer.canvas.geometry) CirclePrim (class in rkviewer.canvas.data) CircleSchema (class in rkviewer.iodine) clamp_point() (in module rkviewer.canvas.geometry) clamp_point_outside() (in module rkviewer.canvas.geometry) clamp_rect_pos() (in module rkviewer.canvas.geometry) clamp_rect_size() (in module rkviewer.canvas.geometry) clear_network() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) clearNetwork() (in module rkviewer.iodine) clearNetworks() (in module rkviewer.iodine) clearReactions() (in module rkviewer.iodine) CLOCKWISE (rkviewer.canvas.geometry.Orientation attribute) clone() (rkviewer.canvas.state.ArrowTip method) cnetroid_handle (rkviewer.canvas.data.SpeciesBezier attribute) COLINEAR (rkviewer.canvas.geometry.Orientation attribute) Color (class in rkviewer.config) color (rkviewer.config.Font attribute) (rkviewer.iodine.FontSchema attribute) ColorField (class in rkviewer.config)

colorToRGB() (in module rkviewer.iodine) comb() (in module rkviewer.canvas.data) commit_node_pos() (rkviewer.canvas.elements.ReactionElement method) comp_border (rkviewer.config.ThemeSchema attribute) comp_border_width (rkviewer.config.ThemeSchema attribute) comp_fill (rkviewer.config.ThemeSchema attribute) comp_idx (rkviewer.canvas.data.Node attribute) comp_indices (rkviewer.canvas.elements.SelectBox attribute) comp_min_ratio (rkviewer.canvas.elements.SelectBox attribute) COMP_ONLY (rkviewer.canvas.elements.SelectBox.SMode attribute) Compartment (class in rkviewer.canvas.data) compartment (rkviewer.events.DidAddCompartmentEvent attribute) compartment_indices (rkviewer.events.DidDeleteEvent attribute), [1] (rkviewer.events.DidMoveCompartmentsEvent attribute), [1] (rkviewer.events.DidResizeCompartmentsEvent attribute), [1] (rkviewer.events.SelectionDidUpdateEvent attribute), [1] CompartmentElt (class in rkviewer.canvas.elements) CompartmentIndexError compartments (rkviewer.canvas.elements.SelectBox attribute) (rkviewer.iodine.TNetwork attribute) CompartmentSchema (class in rkviewer.iodine) compi (rkviewer.iodine.TAbstractNode attribute) (rkviewer.iodine.TAliasNode attribute) (rkviewer.iodine.TNode attribute) COMPI_NOT_FOUND (rkviewer.iodine.ErrorCode attribute) composite_shape (rkviewer.canvas.data.Node attribute) CompositeShape (class in rkviewer.canvas.data) CompositeShapeFactory (class in rkviewer.canvas.data) CompositeShapeSchema (class in rkviewer.iodine) compute_centroid() (in module rkviewer.canvas.data) compute_min_ratio() (rkviewer.canvas.elements.SelectBox method) concentration (rkviewer.canvas.data.Node attribute) (rkviewer.iodine.TNode attribute) CONTAINED (rkviewer.canvas.elements.SelectBox.SMode attribute) contains() (rkviewer.canvas.geometry.Rect method) (rkviewer.canvas.utils.SetSubject method) Controller (class in rkviewer.controller) controller (rkviewer.canvas.elements.ReactionElement attribute) convert_position() (in module rkviewer.utils) corner_radius (rkviewer.canvas.data.RectanglePrim attribute) COUNTERCLOCKWISE (rkviewer.canvas.geometry.Orientation attribute) create_dialog() (rkviewer.plugin_manage.PluginManager method) create_install_dialog() (rkviewer.plugin_manage.PluginManager method) CreateBiBi() (in module rkviewer.iodine) CreateBiUni() (in module rkviewer.iodine) createReaction() (in module rkviewer.iodine) CreateUniBi() (in module rkviewer.iodine) createUniUni() (in module rkviewer.iodine) CURSOR_TYPES (rkviewer.canvas.elements.SelectBox attribute), [1] CURVE_SLACK (in module rkviewer.canvas.data)

D

data (rkviewer.canvas.elements.BezierHandle attribute), [1] default_handle_positions() (in module rkviewer.canvas.utils) delete_compartment() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) delete_node() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) delete_reaction() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) deleteCompartment() (in module rkviewer.iodine) deleteNetwork() (in module rkviewer.iodine) deleteNode() (in module rkviewer.iodine) deleteReaction() (in module rkviewer.iodine) dest_beziers (rkviewer.canvas.data.ReactionBezier attribute), [1] dest_c_handle (rkviewer.canvas.data.Reaction attribute) (rkviewer.canvas.data.ReactionBezier attribute) dest_handle_moved() (rkviewer.canvas.data.ReactionBezier method) destMap (rkviewer.iodine.TNetwork attribute) destroy() (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.ReactionElement method) destroyed (rkviewer.canvas.elements.CanvasElement attribute), [1] (rkviewer.canvas.elements.CompartmentElt attribute) detach() (rkviewer.canvas.utils.Subject method) determinant() (in module rkviewer.canvas.geometry) device_pos (rkviewer.canvas.overlays.Minimap attribute), [1] DidAddCompartmentEvent (class in rkviewer.events) DidAddNodeEvent (class in rkviewer.events) DidAddReactionEvent (class in rkviewer.events) DidChangeCompartmentOfNodesEvent (class in rkviewer.events) DidCommitDragEvent (class in rkviewer.events) DidDeleteEvent (class in rkviewer.events) DidModifyCompartmentsEvent (class in rkviewer.events) DidModifyNodesEvent (class in rkviewer.events) DidModifyReactionEvent (class in rkviewer.events) DidMoveBezierHandleEvent (class in rkviewer.events) DidMoveCompartmentsEvent (class in rkviewer.events) DidMoveNodesEvent (class in rkviewer.events)

DidMoveReactionCenterEvent (class in rkviewer.events) DidNewNetworkEvent (class in rkviewer.events) DidPaintCanvasEvent (class in rkviewer.events) DidRedoEvent (class in rkviewer.events) DidResizeCompartmentsEvent (class in rkviewer.events) DidResizeNodesEvent (class in rkviewer.events) DidUndoEvent (class in rkviewer.events) Dim (class in rkviewer.config) Dim2 (class in rkviewer.config) direct (rkviewer.events.DidMoveBezierHandleEvent attribute), [1] Direction (class in rkviewer.canvas.geometry) do_paint() (rkviewer.canvas.data.ReactionBezier method) (rkviewer.canvas.data.SpeciesBezier method) DoPaint() (rkviewer.canvas.overlays.CanvasOverlay method) (rkviewer.canvas.overlays.Minimap method) dot() (rkviewer.canvas.geometry.Vec2 method) drag_border (rkviewer.config.ThemeSchema attribute) drag_border_width (rkviewer.config.ThemeSchema attribute) drag_fill (rkviewer.config.ThemeSchema attribute) dragged (rkviewer.events.DidMoveCompartmentsEvent attribute), [1] (rkviewer.events.DidMoveNodesEvent attribute), [1] (rkviewer.events.DidMoveReactionCenterEvent attribute), [1] (rkviewer.events.DidResizeCompartmentsEvent attribute), [1] (rkviewer.events.DidResizeNodesEvent attribute), [1] dragging() (rkviewer.canvas.overlays.Minimap property) draw_circle_to_gc() (in module rkviewer.canvas.elements) draw_composite_shape() (in module rkviewer.canvas.elements) draw_polygon_to_gc() (in module rkviewer.canvas.elements) draw_rect() (in module rkviewer.canvas.utils) draw_rect_to_gc() (in module rkviewer.canvas.elements) draw_text_to_gc() (in module rkviewer.canvas.elements) dump_network() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) dumpNetwork() (in module rkviewer.iodine) DUPLICATE_RATIO (rkviewer.canvas.data.ReactionBezier attribute) DUPLICATE_ROT (rkviewer.canvas.data.ReactionBezier attribute)

E

elem_abs() (rkviewer.canvas.geometry.Vec2 method) elem_div() (rkviewer.canvas.geometry.Vec2 method) elem_mul() (rkviewer.canvas.geometry.Vec2 method) elements (rkviewer.canvas.overlays.Minimap attribute), [1] enable_plugins (rkviewer.config.RuntimeVariables attribute)

enabled (rkviewer.canvas.elements.CanvasElement attribute), [1] (rkviewer.canvas.elements.CompartmentElt attribute) endGroup() (in module rkviewer.iodine) EnumField (class in rkviewer.iodine) ErrorCode (class in rkviewer.iodine) even_round() (in module rkviewer.utils)

F

family (rkviewer.iodine.FontSchema attribute) FILE_ERROR (rkviewer.iodine.ErrorCode attribute) FileError fill (rkviewer.canvas.data.Compartment attribute) fill_color (rkviewer.canvas.data.CirclePrim attribute) (rkviewer.canvas.data.Node attribute) (rkviewer.canvas.data.PolygonPrim attribute) (rkviewer.canvas.data.Reaction attribute) (rkviewer.canvas.data.RectanglePrim attribute) fill_color() (rkviewer.canvas.data.Node property)

fillColor (rkviewer.iodine.TCompartment attribute) (rkviewer.iodine.TReaction attribute) floating (rkviewer.iodine.TNode attribute) floatingNode (rkviewer.canvas.data.Node attribute) Font (class in rkviewer.config) font_color (rkviewer.canvas.data.TextPrim attribute) font_size (rkviewer.canvas.data.TextPrim attribute) FontField (class in rkviewer.config) FontSchema (class in rkviewer.iodine) from_rgb() (rkviewer.config.Color class method)

G

g (rkviewer.config.Color attribute) gc (rkviewer.events.DidPaintCanvasEvent attribute), [1] gchain() (in module rkviewer.utils) gen_polygon_pts() (in module rkviewer.canvas.data) get_application_position() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_bounding_rect() (in module rkviewer.canvas.geometry) (rkviewer.canvas.data.ReactionBezier method) (rkviewer.canvas.data.SpeciesBezier method) get_center_handle() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_compartment_by_index() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_compartment_indices() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_compartment_of_node() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_composite_shape_at() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_composite_shape_list() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_default_raw_settings() (in module rkviewer.config) get_dest_node_handle() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_dest_node_stoich() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_list_of_compartments() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_list_of_dest_indices() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_list_of_node_ids() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_list_of_nodes() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_list_of_reactions() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_list_of_src_indices() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_local_path() (in module rkviewer.utils) get_modifier_tip_style() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_network_parameters() (rkviewer.controller.Controller method) get_node_by_index() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_node_id() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_node_index() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_node_indices() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_node_shape() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_node_shape_index() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_nodes_by_ident() (in module rkviewer.canvas.utils) get_nodes_by_idx() (in module rkviewer.canvas.utils) get_nodes_in_compartment() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_plugins_by_category() (rkviewer.plugin_manage.PluginManager method) get_reaction_by_index() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_reaction_index() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_reaction_indices() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_reaction_modifiers() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_reactions_as_product() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_reactions_as_reactant() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_rxns_by_idx() (in module rkviewer.canvas.utils) get_setting() (in module rkviewer.config) get_src_node_handle() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) get_src_node_stoich() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method)

get_theme() (in module rkviewer.config) get_theme_fn() (in module rkviewer.iodine) getCompartmentFillColor() (in module rkviewer.iodine) getCompartmentID() (in module rkviewer.iodine) getCompartmentOfNode() (in module rkviewer.iodine) getCompartmentOutlineColor() (in module rkviewer.iodine) getCompartmentOutlineThickness() (in module rkviewer.iodine) getCompartmentPosition() (in module rkviewer.iodine) getCompartmentSize() (in module rkviewer.iodine) getCompartmentVolume() (in module rkviewer.iodine) getCompositeShapeAt() (in module rkviewer.iodine) GetConfigDir() (in module rkviewer.config) getDestReactions() (in module rkviewer.iodine) getErrorCode() (in module rkviewer.iodine) getListOfCompartmentIndices() (in module rkviewer.iodine) getListOfCompartments() (in module rkviewer.iodine) getListOfCompositeShapes() (in module rkviewer.iodine) getListOfNetworks() (in module rkviewer.iodine) getListOfNodeIDs() (in module rkviewer.iodine) getListOfNodeIndices() (in module rkviewer.iodine) getListOfReactionDestNodes() (in module rkviewer.iodine) getListOfReactionDestStoich() (in module rkviewer.iodine) getListOfReactionIDs() (in module rkviewer.iodine) getListOfReactionIndices() (in module rkviewer.iodine) getListOfReactionSrcNodes() (in module rkviewer.iodine) getListOfReactionSrcStoich() (in module rkviewer.iodine) getModifierTipStyle() (in module rkviewer.iodine) GetMultiColor() (in module rkviewer.forms) GetMultiEnum() (in module rkviewer.forms) GetMultiFloatText() (in module rkviewer.forms) GetMultiInt() (in module rkviewer.forms) getNetworkID() (in module rkviewer.iodine) getNetworkIndex() (in module rkviewer.iodine) getNodeBorderColor() (in module rkviewer.iodine) getNodeBorderColorAlpha() (in module rkviewer.iodine) getNodeBorderColorRGB() (in module rkviewer.iodine) getNodeBorderWidth() (in module rkviewer.iodine) getNodeCenter() (in module rkviewer.iodine) getNodeConcentration() (in module rkviewer.iodine) getNodeCoordinateAndSize() (in module rkviewer.iodine) getNodeFillColor() (in module rkviewer.iodine) getNodeFillColorAlpha() (in module rkviewer.iodine) getNodeFillColorRGB() (in module rkviewer.iodine) getNodeID() (in module rkviewer.iodine) getNodeIndex() (in module rkviewer.iodine) getNodeName() (in module rkviewer.iodine) getNodeSBO() (in module rkviewer.iodine) getNodeShape() (in module rkviewer.iodine) getNodeShapeIndex() (in module rkviewer.iodine) getNodesInCompartment() (in module rkviewer.iodine) getNumberOfDestNodes() (in module rkviewer.iodine) getNumberOfNetworks() (in module rkviewer.iodine) getNumberOfNodes() (in module rkviewer.iodine) getNumberOfReactions() (in module rkviewer.iodine) getNumberOfSrcNodes() (in module rkviewer.iodine) getOriginalIndex() (in module rkviewer.iodine) getParameters() (in module rkviewer.iodine) getReactionCenterHandlePosition() (in module rkviewer.iodine) getReactionCenterPos() (in module rkviewer.iodine) getReactionDestNodeHandlePosition() (in module rkviewer.iodine) getReactionDestNodeStoich() (in module rkviewer.iodine) getReactionFillColor() (in module rkviewer.iodine) getReactionFillColorAlpha() (in module rkviewer.iodine) getReactionFillColorRGB() (in module rkviewer.iodine) getReactionID() (in module rkviewer.iodine) getReactionIndex() (in module rkviewer.iodine) getReactionLineThickness() (in module rkviewer.iodine) getReactionModifiers() (in module rkviewer.iodine) getReactionRateLaw() (in module rkviewer.iodine) getReactionSrcNodeHandlePosition() (in module rkviewer.iodine) getReactionSrcNodeStoich() (in module rkviewer.iodine) getSrcReactions() (in module rkviewer.iodine) GetThemeSettingsPath() (in module rkviewer.config) GRID (rkviewer.canvas.canvas.Alignment attribute) group_action() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method)

H

handle (rkviewer.canvas.data.SpeciesBezier attribute), [1] handle_color (rkviewer.config.ThemeSchema attribute) HANDLE_MULT (rkviewer.canvas.elements.SelectBox attribute) HANDLE_RADIUS (rkviewer.canvas.elements.BezierHandle attribute), [1] HandleData (class in rkviewer.canvas.data) handlePos (rkviewer.iodine.TSpeciesNode attribute) handler (rkviewer.events.HandlerNode attribute) HandlerChain (class in rkviewer.events) HandlerNode (class in rkviewer.events)

handles (rkviewer.canvas.data.Reaction attribute) (rkviewer.canvas.data.ReactionBezier attribute) head (rkviewer.events.HandlerChain attribute) HexagonPrim (class in rkviewer.canvas.data) HexagonSchema (class in rkviewer.iodine) hgap (rkviewer.config.ThemeSchema attribute) highlight_paint() (rkviewer.canvas.elements.CompartmentElt method) highlighted_handle_color (rkviewer.config.ThemeSchema attribute) HORIZONTAL (rkviewer.canvas.canvas.Alignment attribute) hovering (rkviewer.canvas.overlays.CanvasOverlay attribute), [1]

I

IController (class in rkviewer.mvc) id (rkviewer.canvas.data.Compartment attribute) (rkviewer.canvas.data.Node attribute), [1] (rkviewer.canvas.data.Reaction attribute) (rkviewer.iodine.TCompartment attribute) (rkviewer.iodine.TNetwork attribute) (rkviewer.iodine.TNode attribute) (rkviewer.iodine.TReaction attribute) ID_NOT_FOUND (rkviewer.iodine.ErrorCode attribute) ID_REPEAT (rkviewer.iodine.ErrorCode attribute) IDLE (rkviewer.canvas.elements.SelectBox.Mode attribute) IDNotFoundError IDRepeatError in_group() (rkviewer.controller.Controller method) IN_NODE (rkviewer.canvas.data.TextPosition attribute) index (rkviewer.canvas.data.Compartment attribute) (rkviewer.canvas.data.Node attribute), [1] (rkviewer.canvas.data.Reaction attribute) (rkviewer.events.DidAddCompartmentEvent attribute) (rkviewer.events.DidAddReactionEvent attribute) (rkviewer.iodine.TAbstractNode attribute) (rkviewer.iodine.TAliasNode attribute) (rkviewer.iodine.TNode attribute)

index_to_bz (rkviewer.canvas.elements.ReactionElement attribute) indices (rkviewer.events.DidModifyCompartmentsEvent attribute), [1] (rkviewer.events.DidModifyNodesEvent attribute) (rkviewer.events.DidModifyReactionEvent attribute), [1] init_bezier() (in module rkviewer.canvas.data) INITIALIZED (in module rkviewer.canvas.data) input_mode() (rkviewer.canvas.state.CanvasState property) input_mode_changed() (rkviewer.canvas.state.CanvasState method) InputMode (class in rkviewer.canvas.state) int_round() (in module rkviewer.utils) intersect() (rkviewer.canvas.utils.SetSubject method) iod_setter() (in module rkviewer.controller) is_mouse_on() (rkviewer.canvas.data.ReactionBezier method) is_on_curve() (rkviewer.canvas.data.SpeciesBezier method) is_source (rkviewer.canvas.data.SpeciesBezier attribute), [1] IsBoundaryNode() (in module rkviewer.iodine) isEmpty() (rkviewer.iodine.TStack method) IsFloatingNode() (in module rkviewer.iodine) IsNodeLocked() (in module rkviewer.iodine) item_copy() (rkviewer.canvas.utils.SetSubject method) items (rkviewer.canvas.data.CompositeShape attribute) (rkviewer.iodine.TStack attribute) IView (class in rkviewer.mvc)

J

JSON_ERROR (rkviewer.iodine.ErrorCode attribute)

JSONError

L

lastCompartmentIdx (rkviewer.iodine.TNetwork attribute) lastNodeIdx (rkviewer.iodine.TNetwork attribute) lastReactionIdx (rkviewer.iodine.TNetwork attribute) layer_above() (in module rkviewer.canvas.elements) layers (rkviewer.canvas.elements.CanvasElement attribute), [1] (rkviewer.canvas.elements.CompartmentElt attribute) LEFT (rkviewer.canvas.canvas.Alignment attribute) (rkviewer.canvas.data.TextAlignment attribute) (rkviewer.canvas.geometry.Direction attribute) linear_coefficients() (in module rkviewer.canvas.geometry)

LinePrim (class in rkviewer.canvas.data) LineSchema (class in rkviewer.iodine) list_field (rkviewer.config.ColorField attribute) load_appSettings() (rkviewer.config.AppSettings method) load_from() (rkviewer.plugin_manage.PluginManager method) load_network() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) load_theme_settings() (in module rkviewer.config) loadNetwork() (in module rkviewer.iodine) lockNode (rkviewer.canvas.data.Node attribute)

M

main_loop() (rkviewer.mvc.IView method) make_command_callback() (rkviewer.plugin_manage.PluginManager method) make_drop_handle_func() (rkviewer.canvas.elements.ReactionElement method) make_handle_moved_func() (rkviewer.canvas.data.ReactionBezier method) make_notify() (rkviewer.plugin_manage.PluginManager method) make_windowed_callback() (rkviewer.plugin_manage.PluginManager method) map() (rkviewer.canvas.geometry.Vec2 method) map_rel_pos() (rkviewer.canvas.elements.SelectBox method) MIDDLE (rkviewer.canvas.canvas.Alignment attribute) Minimap (class in rkviewer.canvas.overlays) mode (rkviewer.canvas.elements.SelectBox attribute) mode() (rkviewer.canvas.elements.SelectBox property) mode_panel_width (rkviewer.config.ThemeSchema attribute) ModelError modifier_tip_style (rkviewer.canvas.data.Reaction attribute) modifiers (rkviewer.canvas.data.Reaction attribute) (rkviewer.iodine.TReaction attribute) ModifierTipStyle (class in rkviewer.canvas.data) module rkviewer rkviewer.canvas rkviewer.canvas.canvas rkviewer.canvas.data rkviewer.canvas.elements rkviewer.canvas.geometry rkviewer.canvas.overlays rkviewer.canvas.state rkviewer.canvas.utils rkviewer.config rkviewer.controller rkviewer.events rkviewer.forms rkviewer.iodine rkviewer.mvc rkviewer.plugin_manage rkviewer.utils

move_compartment() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) move_node() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) move_offset() (rkviewer.canvas.elements.SelectBox method) moved_handler_id (rkviewer.canvas.elements.ReactionElement attribute) MOVING (rkviewer.canvas.elements.SelectBox.Mode attribute) multi_select (rkviewer.canvas.state.CanvasState attribute) multi_select() (rkviewer.canvas.state.CanvasState property)

N

name (rkviewer.canvas.data.CirclePrim attribute) (rkviewer.canvas.data.CompositeShape attribute) (rkviewer.canvas.data.HexagonPrim attribute) (rkviewer.canvas.data.LinePrim attribute) (rkviewer.canvas.data.PolygonPrim attribute) (rkviewer.canvas.data.Primitive attribute) (rkviewer.canvas.data.RectanglePrim attribute) (rkviewer.canvas.data.TextPrim attribute) (rkviewer.canvas.data.TrianglePrim attribute) (rkviewer.iodine.FontSchema attribute) net_index (rkviewer.canvas.data.Compartment attribute) (rkviewer.canvas.data.Node attribute), [1] (rkviewer.canvas.data.Reaction attribute) (rkviewer.events.DidMoveBezierHandleEvent attribute), [1] (rkviewer.events.DidMoveReactionCenterEvent attribute), [1] NETI_NOT_FOUND (rkviewer.iodine.ErrorCode attribute) NetIndexError NetworkSchema (class in rkviewer.iodine) new_compi (rkviewer.events.DidChangeCompartmentOfNodesEvent attribute), [1] new_network() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) newNetwork() (in module rkviewer.iodine) next_ (rkviewer.events.HandlerNode attribute) NEXT_TO (rkviewer.canvas.data.TextPosition attribute) no_rzeros() (in module rkviewer.utils) Node (class in rkviewer.canvas.data) node (rkviewer.canvas.data.SpeciesBezier attribute) (rkviewer.canvas.elements.NodeElement attribute) (rkviewer.events.DidAddNodeEvent attribute), [1] node_border (rkviewer.config.ThemeSchema attribute) node_border_width (rkviewer.config.ThemeSchema attribute) node_fill (rkviewer.config.ThemeSchema attribute) node_font_color (rkviewer.config.ThemeSchema attribute) node_font_size (rkviewer.config.ThemeSchema attribute) node_height (rkviewer.config.ThemeSchema attribute) node_idx (rkviewer.canvas.data.SpeciesBezier attribute) (rkviewer.canvas.elements.BezierHandle attribute), [1] node_index (rkviewer.events.DidMoveBezierHandleEvent attribute), [1]

node_indices (rkviewer.canvas.elements.SelectBox attribute) (rkviewer.events.DidChangeCompartmentOfNodesEvent attribute), [1] (rkviewer.events.DidDeleteEvent attribute), [1] (rkviewer.events.DidMoveNodesEvent attribute), [1] (rkviewer.events.DidResizeNodesEvent attribute), [1] (rkviewer.events.SelectionDidUpdateEvent attribute), [1] (rkviewer.iodine.TCompartment attribute) node_intersection (rkviewer.canvas.data.SpeciesBezier attribute), [1] node_min_ratio (rkviewer.canvas.elements.SelectBox attribute) node_name (rkviewer.canvas.data.Node attribute) (rkviewer.iodine.TNode attribute) NODE_NOT_FREE (rkviewer.iodine.ErrorCode attribute) node_or_alias_dump() (in module rkviewer.iodine) node_or_alias_load() (in module rkviewer.iodine) node_SBO (rkviewer.canvas.data.Node attribute) (rkviewer.iodine.TNode attribute) node_width (rkviewer.config.ThemeSchema attribute) NodeElement (class in rkviewer.canvas.elements) nodei (rkviewer.forms.StoichInfo attribute) NODEI_NOT_FOUND (rkviewer.iodine.ErrorCode attribute) NodeIndexError nodeLocked (rkviewer.iodine.TAbstractNode attribute) (rkviewer.iodine.TAliasNode attribute) (rkviewer.iodine.TNode attribute) NodeNotFreeError nodes (rkviewer.canvas.data.Compartment attribute) (rkviewer.canvas.elements.SelectBox attribute), [1] (rkviewer.events.DidModifyNodesEvent attribute) (rkviewer.iodine.TNetwork attribute) NODES_IN_ONE (rkviewer.canvas.elements.SelectBox.SMode attribute) nodes_moved() (rkviewer.canvas.data.ReactionBezier method) (rkviewer.canvas.elements.ReactionElement method) NodeSchema (class in rkviewer.iodine) norm() (rkviewer.canvas.geometry.Vec2 property) norm_sq() (rkviewer.canvas.geometry.Vec2 property) normalized() (rkviewer.canvas.geometry.Vec2 method) NOT_CONTAINED (rkviewer.canvas.elements.SelectBox.SMode attribute) notify() (rkviewer.canvas.utils.Subject method) nth_vertex() (rkviewer.canvas.geometry.Rect method)

O

Observer (class in rkviewer.canvas.utils) offset (rkviewer.events.DidMoveCompartmentsEvent attribute), [1] (rkviewer.events.DidMoveNodesEvent attribute), [1] (rkviewer.events.DidMoveReactionCenterEvent attribute), [1] OK (rkviewer.iodine.ErrorCode attribute) old_compi (rkviewer.events.DidChangeCompartmentOfNodesEvent attribute), [1] on_dropped (rkviewer.canvas.elements.BezierHandle attribute), [1] on_left_down() (rkviewer.canvas.elements.BezierHandle method) (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.CompartmentElt method) (rkviewer.canvas.elements.NodeElement method) (rkviewer.canvas.elements.ReactionCenter method) (rkviewer.canvas.elements.ReactionElement method) (rkviewer.canvas.elements.SelectBox method) on_left_up() (rkviewer.canvas.elements.BezierHandle method) (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.ReactionCenter method) (rkviewer.canvas.elements.SelectBox method) on_mouse_drag() (rkviewer.canvas.elements.BezierHandle method) (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.ReactionCenter method) (rkviewer.canvas.elements.SelectBox method) on_mouse_enter() (rkviewer.canvas.elements.BezierHandle method) (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.ReactionCenter method) (rkviewer.canvas.elements.ReactionElement method) (rkviewer.canvas.elements.SelectBox method) on_mouse_leave() (rkviewer.canvas.elements.BezierHandle method) (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.ReactionCenter method) (rkviewer.canvas.elements.SelectBox method) on_mouse_move() (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.SelectBox method) on_moved (rkviewer.canvas.elements.BezierHandle attribute), [1] on_msw() (in module rkviewer.utils) on_paint() (rkviewer.canvas.elements.BezierHandle method) (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.CompartmentElt method) (rkviewer.canvas.elements.NodeElement method) (rkviewer.canvas.elements.ReactionCenter method) (rkviewer.canvas.elements.ReactionElement method) (rkviewer.canvas.elements.SelectBox method)

on_paint_cue() (rkviewer.canvas.elements.BezierHandle method) (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.ReactionCenter method) OnLeftDown() (rkviewer.canvas.overlays.CanvasOverlay method) (rkviewer.canvas.overlays.Minimap method) OnLeftUp() (rkviewer.canvas.overlays.CanvasOverlay method) (rkviewer.canvas.overlays.Minimap method) OnMotion() (rkviewer.canvas.overlays.CanvasOverlay method) (rkviewer.canvas.overlays.Minimap method) opacity_mul() (in module rkviewer.utils) opts (rkviewer.config.RootSchema attribute) (rkviewer.config.ThemeSchema attribute) (rkviewer.iodine.AbstractNodeSchema attribute) (rkviewer.iodine.AliasSchema attribute) (rkviewer.iodine.CircleSchema attribute) (rkviewer.iodine.CompartmentSchema attribute) (rkviewer.iodine.CompositeShapeSchema attribute) (rkviewer.iodine.FontSchema attribute) (rkviewer.iodine.HexagonSchema attribute) (rkviewer.iodine.LineSchema attribute) (rkviewer.iodine.NetworkSchema attribute) (rkviewer.iodine.NodeSchema attribute) (rkviewer.iodine.PolygonSchema attribute) (rkviewer.iodine.PrimitiveSchema attribute) (rkviewer.iodine.ReactionSchema attribute) (rkviewer.iodine.RectangleSchema attribute) (rkviewer.iodine.SpeciesNode attribute) (rkviewer.iodine.TextSchema attribute) (rkviewer.iodine.TransformSchema attribute) (rkviewer.iodine.TriangleSchema attribute) Orientation (class in rkviewer.canvas.geometry) orientation() (in module rkviewer.canvas.geometry) original_index (rkviewer.canvas.data.Node attribute) originalIdx (rkviewer.iodine.TAliasNode attribute) OTHER (rkviewer.iodine.ErrorCode attribute) OUT_OF_RANGE (rkviewer.iodine.ErrorCode attribute) outline_rect() (rkviewer.canvas.elements.SelectBox method) outlineColor (rkviewer.iodine.TCompartment attribute) outlineThickness (rkviewer.iodine.TCompartment attribute) overall_bg (rkviewer.config.ThemeSchema attribute)

P

padded_rect() (in module rkviewer.canvas.geometry) paint_arrow_tip() (rkviewer.canvas.data.SpeciesBezier method) paint_handle() (in module rkviewer.canvas.data) pairwise() (in module rkviewer.utils) parameters (rkviewer.iodine.TNetwork attribute) parent (rkviewer.canvas.elements.ReactionCenter attribute) parse_num_pair() (in module rkviewer.forms) parse_precisions() (in module rkviewer.forms) peripheral_nodes (rkviewer.canvas.elements.SelectBox attribute) Pixel (class in rkviewer.config) PluginManager (class in rkviewer.plugin_manage) plugins (rkviewer.plugin_manage.PluginManager attribute) points (rkviewer.canvas.data.HexagonPrim attribute) (rkviewer.canvas.data.LinePrim attribute) (rkviewer.canvas.data.PolygonPrim attribute) (rkviewer.canvas.data.TrianglePrim attribute) (rkviewer.canvas.state.ArrowTip attribute) pointSize (rkviewer.config.Font attribute) PolygonPrim (class in rkviewer.canvas.data) PolygonSchema (class in rkviewer.iodine) pop() (rkviewer.iodine.TStack method) pop_settings_err() (in module rkviewer.config) pos_inside() (rkviewer.canvas.elements.BezierHandle method) (rkviewer.canvas.elements.CanvasElement method) (rkviewer.canvas.elements.CompartmentElt method) (rkviewer.canvas.elements.NodeElement method) (rkviewer.canvas.elements.ReactionCenter method) (rkviewer.canvas.elements.ReactionElement method) (rkviewer.canvas.elements.SelectBox method) position (rkviewer.canvas.data.Compartment attribute) (rkviewer.canvas.data.Node attribute), [1] (rkviewer.canvas.data.RectData attribute) (rkviewer.canvas.data.TextPrim attribute) (rkviewer.iodine.TAbstractNode attribute) (rkviewer.iodine.TAliasNode attribute) (rkviewer.iodine.TCompartment attribute) (rkviewer.iodine.TNode attribute)

position() (rkviewer.canvas.overlays.CanvasOverlay property) post_dump() (rkviewer.iodine.AbstractNodeSchema method) (rkviewer.iodine.NetworkSchema method) post_event() (in module rkviewer.events) post_load() (rkviewer.iodine.AliasSchema method) (rkviewer.iodine.CircleSchema method) (rkviewer.iodine.CompartmentSchema method) (rkviewer.iodine.CompositeShapeSchema method) (rkviewer.iodine.HexagonSchema method) (rkviewer.iodine.LineSchema method) (rkviewer.iodine.NetworkSchema method) (rkviewer.iodine.NodeSchema method) (rkviewer.iodine.ReactionSchema method) (rkviewer.iodine.RectangleSchema method) (rkviewer.iodine.SpeciesNode method) (rkviewer.iodine.TextSchema method) (rkviewer.iodine.TransformSchema method) (rkviewer.iodine.TriangleSchema method) pre_load() (rkviewer.iodine.NetworkSchema method) prev (rkviewer.events.HandlerNode attribute) Primitive (class in rkviewer.canvas.data) primitive_brush() (in module rkviewer.canvas.elements) primitive_dump() (in module rkviewer.iodine) primitive_load() (in module rkviewer.iodine) primitive_peninfo() (in module rkviewer.canvas.elements) PrimitiveFactory (class in rkviewer.canvas.data) PrimitiveSchema (class in rkviewer.iodine) printReactionInfo() (in module rkviewer.iodine) produce() (rkviewer.canvas.data.CompositeShapeFactory method) (rkviewer.canvas.data.PrimitiveFactory method) product_border (rkviewer.config.ThemeSchema attribute) products (rkviewer.iodine.TReaction attribute) props_equal() (rkviewer.canvas.data.Node method) pt_in_circle() (in module rkviewer.canvas.geometry) pt_in_rect() (in module rkviewer.canvas.geometry) pt_on_line() (in module rkviewer.canvas.geometry) pt_on_rect_sides() (in module rkviewer.canvas.geometry) push() (rkviewer.iodine.TStack method)

R

r (rkviewer.config.Color attribute) radius (rkviewer.canvas.data.PolygonPrim attribute) range_validate (rkviewer.config.ColorField attribute) rate_law (rkviewer.canvas.data.Reaction attribute) rateLaw (rkviewer.iodine.TReaction attribute) ratio (rkviewer.events.DidResizeCompartmentsEvent attribute), [1] (rkviewer.events.DidResizeNodesEvent attribute), [1] react_node_border_width (rkviewer.config.ThemeSchema attribute) react_node_padding (rkviewer.config.ThemeSchema attribute) reactant_border (rkviewer.config.ThemeSchema attribute) reactants (rkviewer.iodine.TReaction attribute) Reaction (class in rkviewer.canvas.data) reaction (rkviewer.canvas.elements.BezierHandle attribute), [1] (rkviewer.canvas.elements.ReactionElement attribute) (rkviewer.events.DidAddReactionEvent attribute) reaction_fill (rkviewer.config.ThemeSchema attribute) reaction_index (rkviewer.events.DidMoveBezierHandleEvent attribute), [1] (rkviewer.events.DidMoveReactionCenterEvent attribute), [1] reaction_indices (rkviewer.events.DidDeleteEvent attribute), [1] (rkviewer.events.SelectionDidUpdateEvent attribute), [1] reaction_line_thickness (rkviewer.config.ThemeSchema attribute) reaction_radius (rkviewer.config.ThemeSchema attribute) ReactionBezier (class in rkviewer.canvas.data) ReactionCenter (class in rkviewer.canvas.elements) ReactionElement (class in rkviewer.canvas.elements) ReactionIndexError reactions (rkviewer.iodine.TNetwork attribute) ReactionSchema (class in rkviewer.iodine) REAI_NOT_FOUND (rkviewer.iodine.ErrorCode attribute) real_canvas_height (rkviewer.config.ThemeSchema attribute) real_canvas_width (rkviewer.config.ThemeSchema attribute) real_center (rkviewer.canvas.data.SpeciesBezier attribute) real_center() (rkviewer.canvas.data.ReactionBezier property) realsize() (rkviewer.canvas.overlays.Minimap property) Rect (class in rkviewer.canvas.geometry) rect() (rkviewer.canvas.data.Compartment property) (rkviewer.canvas.data.Node property) RectanglePrim (class in rkviewer.canvas.data) RectangleSchema (class in rkviewer.iodine) RectData (class in rkviewer.canvas.data) rects_overlap() (in module rkviewer.canvas.geometry) rectSize (rkviewer.iodine.TAbstractNode attribute) (rkviewer.iodine.TAliasNode attribute) (rkviewer.iodine.TCompartment attribute) (rkviewer.iodine.TNode attribute) redo() (in module rkviewer.iodine) (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) reduce2() (rkviewer.canvas.geometry.Vec2 method) register_menu() (rkviewer.plugin_manage.PluginManager method) related_elts (rkviewer.canvas.elements.SelectBox attribute), [1] remove() (rkviewer.canvas.utils.SetSubject method) (rkviewer.events.HandlerChain method) remove_network_parameter() (rkviewer.controller.Controller method) removeParameter() (in module rkviewer.iodine)

rename_compartment() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) rename_node() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) rename_reaction() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) repeat() (rkviewer.canvas.geometry.Vec2 class method) require_kwargs_on_init() (in module rkviewer.utils) reset() (in module rkviewer.iodine) reset_runtime_vars() (in module rkviewer.config) RESIZING (rkviewer.canvas.elements.SelectBox.Mode attribute) resource_path() (in module rkviewer.utils) rgba_to_wx_colour() (in module rkviewer.utils) RIGHT (rkviewer.canvas.canvas.Alignment attribute) (rkviewer.canvas.data.TextAlignment attribute) (rkviewer.canvas.geometry.Direction attribute) rkviewer module rkviewer.canvas module rkviewer.canvas.canvas module rkviewer.canvas.data module rkviewer.canvas.elements module rkviewer.canvas.geometry module rkviewer.canvas.overlays module rkviewer.canvas.state module rkviewer.canvas.utils module rkviewer.config module rkviewer.controller module rkviewer.events module rkviewer.forms module rkviewer.iodine module rkviewer.mvc module rkviewer.plugin_manage module rkviewer.utils module RootSchema (class in rkviewer.config) rotate_unit() (in module rkviewer.canvas.geometry) rotation (rkviewer.canvas.data.Transform attribute) runtime_vars() (in module rkviewer.config) RuntimeVariables (class in rkviewer.config)

S

s_position() (rkviewer.canvas.data.Node property) s_rect() (rkviewer.canvas.data.Node property) s_size() (rkviewer.canvas.data.Node property) save_appSettings() (rkviewer.config.AppSettings method) scale (rkviewer.canvas.data.Transform attribute) (rkviewer.canvas.state.CanvasState attribute), [1] segment_intersects_line() (in module rkviewer.canvas.geometry) segment_rect_intersection() (in module rkviewer.canvas.geometry) segments_intersect() (in module rkviewer.canvas.geometry) SELECT (rkviewer.canvas.state.InputMode attribute) select_box_padding (rkviewer.config.ThemeSchema attribute) select_handle_length (rkviewer.config.ThemeSchema attribute) select_outline_padding (rkviewer.config.ThemeSchema attribute) select_outline_width (rkviewer.config.ThemeSchema attribute) SelectBox (class in rkviewer.canvas.elements) SelectBox.Mode (class in rkviewer.canvas.elements) SelectBox.SMode (class in rkviewer.canvas.elements) selected() (rkviewer.canvas.elements.ReactionElement property) selected_reaction_fill (rkviewer.config.ThemeSchema attribute) SelectionDidUpdateEvent (class in rkviewer.events) set_application_position() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_center_handle() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_compartment_border() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_compartment_border_width() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_compartment_fill() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_compartment_of_node() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_compartment_size() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_compartment_volume() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_dest_node_handle() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_dest_node_stoich() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_item() (rkviewer.canvas.utils.SetSubject method) set_layers() (rkviewer.canvas.elements.CanvasElement method) set_modifier_tip_style() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_network_parameter() (rkviewer.controller.Controller method) set_node_border_alpha() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_border_rgb() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_border_width() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_concentration() (rkviewer.controller.Controller method) set_node_fill_alpha() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_fill_rgb() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_floating_status() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_locked_status() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_name() (rkviewer.controller.Controller method) set_node_primitive_property() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_SBO() (rkviewer.controller.Controller method) set_node_shape_index() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_node_size() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_reaction_bezier_curves() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_reaction_center() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_reaction_fill_alpha() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_reaction_fill_rgb() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_reaction_line_thickness() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method)

set_reaction_modifiers() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_reaction_ratelaw() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_src_node_handle() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) set_src_node_stoich() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) setCompartmentFillColor() (in module rkviewer.iodine) setCompartmentID() (in module rkviewer.iodine) setCompartmentOfNode() (in module rkviewer.iodine) setCompartmentOutlineColor() (in module rkviewer.iodine) setCompartmentOutlineThickness() (in module rkviewer.iodine) setCompartmentPosition() (in module rkviewer.iodine) setCompartmentSize() (in module rkviewer.iodine) setCompartmentVolume() (in module rkviewer.iodine) setModifierTipStyle() (in module rkviewer.iodine) setNodeBorderColorAlpha() (in module rkviewer.iodine) setNodeBorderColorRGB() (in module rkviewer.iodine) setNodeBorderWidth() (in module rkviewer.iodine) setNodeConcentration() (in module rkviewer.iodine) setNodeCoordinate() (in module rkviewer.iodine) setNodeFillColorAlpha() (in module rkviewer.iodine) setNodeFillColorRGB() (in module rkviewer.iodine) setNodeFloatingStatus() (in module rkviewer.iodine) setNodeID() (in module rkviewer.iodine) setNodeLockedStatus() (in module rkviewer.iodine) setNodeName() (in module rkviewer.iodine) setNodePrimitiveProperty() (in module rkviewer.iodine) setNodeSBO() (in module rkviewer.iodine) setNodeShapeIndex() (in module rkviewer.iodine) setNodeSize() (in module rkviewer.iodine) setParameter() (in module rkviewer.iodine) setRateLaw() (in module rkviewer.iodine) setReactionBezierCurves() (in module rkviewer.iodine) setReactionCenterHandlePosition() (in module rkviewer.iodine) setReactionCenterPos() (in module rkviewer.iodine) setReactionDestNodeHandlePosition() (in module rkviewer.iodine) setReactionDestNodeStoich() (in module rkviewer.iodine) setReactionFillColorAlpha() (in module rkviewer.iodine) setReactionFillColorRGB() (in module rkviewer.iodine) setReactionID() (in module rkviewer.iodine) setReactionLineThickness() (in module rkviewer.iodine) setReactionModifiers() (in module rkviewer.iodine) setReactionSrcNodeHandlePosition() (in module rkviewer.iodine) setReactionSrcNodeStoich() (in module rkviewer.iodine) SetSubject (class in rkviewer.canvas.utils) shape (rkviewer.iodine.TNode attribute) shape_index (rkviewer.canvas.data.Node attribute) shapei (rkviewer.iodine.TNode attribute) sides() (rkviewer.canvas.geometry.Rect method) size (rkviewer.canvas.data.Compartment attribute) (rkviewer.canvas.data.Node attribute), [1] (rkviewer.canvas.data.RectData attribute) size() (rkviewer.canvas.overlays.CanvasOverlay property) source (rkviewer.events.DidCommitDragEvent attribute) sources (rkviewer.events.DidAddReactionEvent attribute) sources() (rkviewer.canvas.data.Reaction property) special_mode (rkviewer.canvas.elements.SelectBox attribute) SpeciesBezier (class in rkviewer.canvas.data) SpeciesNode (class in rkviewer.iodine) src_beziers (rkviewer.canvas.data.ReactionBezier attribute), [1] src_c_handle (rkviewer.canvas.data.Reaction attribute) (rkviewer.canvas.data.ReactionBezier attribute) src_handle_moved() (rkviewer.canvas.data.ReactionBezier method) srcMap (rkviewer.iodine.TNetwork attribute) STACK_EMPTY (rkviewer.iodine.ErrorCode attribute) StackEmptyError start_file() (in module rkviewer.utils) startGroup() (in module rkviewer.iodine) stoich (rkviewer.forms.StoichInfo attribute) (rkviewer.iodine.TSpeciesNode attribute) StoichError StoichInfo (class in rkviewer.forms) style (rkviewer.iodine.FontSchema attribute) Subject (class in rkviewer.canvas.utils) swapped() (rkviewer.canvas.geometry.Vec2 method) (rkviewer.config.Color method)

T

TAbstractNode (class in rkviewer.iodine) tail (rkviewer.events.HandlerChain attribute) TAliasNode (class in rkviewer.iodine) targets (rkviewer.events.DidAddReactionEvent attribute) targets() (rkviewer.canvas.data.Reaction property) tcolor_to_wx() (rkviewer.controller.Controller method) TCompartment (class in rkviewer.iodine) TEE (rkviewer.canvas.data.ModifierTipStyle attribute) text (rkviewer.canvas.data.ChoiceItem attribute) text_field_bg (rkviewer.config.ThemeSchema attribute) text_field_border (rkviewer.config.ThemeSchema attribute) text_field_fg (rkviewer.config.ThemeSchema attribute) text_item (rkviewer.canvas.data.CompositeShape attribute) TextAlignment (class in rkviewer.canvas.data) TextPosition (class in rkviewer.canvas.data) TextPrim (class in rkviewer.canvas.data) TextSchema (class in rkviewer.iodine) theme (rkviewer.config.RootSchema attribute) ThemeSchema (class in rkviewer.config) thickness (rkviewer.canvas.data.SpeciesBezier attribute) (rkviewer.iodine.TReaction attribute)

thickness() (rkviewer.canvas.data.Reaction property) tip (rkviewer.canvas.data.HandleData attribute), [1] tipStyle (rkviewer.iodine.TReaction attribute) TNetwork (class in rkviewer.iodine) TNetworkDict (class in rkviewer.iodine) TNode (class in rkviewer.iodine) to_tuple() (rkviewer.events.CanvasEvent method) to_wx_point() (rkviewer.canvas.geometry.Vec2 method) to_wx_rect() (rkviewer.canvas.geometry.Rect method) to_wxcolour() (rkviewer.config.Color method) toolbar_bg (rkviewer.config.ThemeSchema attribute) TOP (rkviewer.canvas.canvas.Alignment attribute) (rkviewer.canvas.geometry.Direction attribute) Transform (class in rkviewer.canvas.data) TransformSchema (class in rkviewer.iodine) translation (rkviewer.canvas.data.Transform attribute) TReaction (class in rkviewer.iodine) TrianglePrim (class in rkviewer.canvas.data) TriangleSchema (class in rkviewer.iodine) TSpeciesNode (class in rkviewer.iodine) TStack (class in rkviewer.iodine) twin (rkviewer.canvas.elements.BezierHandle attribute), [1]

U

unbind_handler() (in module rkviewer.events) undo() (in module rkviewer.iodine) (rkviewer.controller.Controller method) (rkviewer.mvc.IController method) union() (rkviewer.canvas.geometry.Rect method) (rkviewer.canvas.utils.SetSubject method)

update() (rkviewer.canvas.elements.SelectBox method) update_all() (rkviewer.mvc.IView method) update_curve() (rkviewer.canvas.data.SpeciesBezier method) update_view() (rkviewer.controller.Controller method) (rkviewer.mvc.IController method)

V

validate_schema() (in module rkviewer.config) validateNodes() (in module rkviewer.iodine) validateState() (in module rkviewer.iodine) value (rkviewer.canvas.data.ChoiceItem attribute) Vec2 (class in rkviewer.canvas.geometry)

VERTICAL (rkviewer.canvas.canvas.Alignment attribute) vgap (rkviewer.config.ThemeSchema attribute) view (rkviewer.controller.Controller attribute) volume (rkviewer.canvas.data.Compartment attribute) (rkviewer.iodine.TCompartment attribute)

W

weight (rkviewer.iodine.FontSchema attribute) window_pos (rkviewer.canvas.overlays.Minimap attribute), [1]

window_size (rkviewer.canvas.overlays.Minimap attribute), [1] wx_to_tcolor() (rkviewer.controller.Controller method)

X

x() (rkviewer.canvas.geometry.Vec2 property)

Y

y() (rkviewer.canvas.geometry.Vec2 property)

Z

ZOOM (rkviewer.canvas.state.InputMode attribute)

zoom_slider_bg (rkviewer.config.ThemeSchema attribute)