This documentation describes the procedure for producing flow diagrams to represent relations between various events.

[1] To represent binary relations as diagrams.

What you have to define are objects for binary relations of events ("Step") and objects for sets of binary relations ("Pathway").

Models.wrm

?Step 	Major_Reactant 	?Molecule
 	Major_Product	?Molecule
	In_Pathway	?Pathway

?Pathway 	Components 	?Step
		PathwayDiagram 	?PathwayDiagram

?PathwayDiagram	Pathway ?Molecule
                Node  Int Float Float Int ?Molecule
                Arc   Int Int   Int   Int Int Float ?Step
                TangentArc Int Int
                Label Int Float Float Text Int

#Tags that can be renamed are "In_Pathway", "Step", and "Molecule". If you want to change the names of other tags, you also have to change w7/metab.c code and recompile xace.

Data Format

Step : "A->B"
Major_Reactant	A
Major_Product	B
In_Pathway	ABCDE

Step : "B->C"
Major_Reactant	B
Major_Product	C
In_Pathway	ABCDE

Step : "B->D"
Major_Reactant	B
Major_Product	D
In_Pathway	ABCDE

Step : "D->E"
Major_Reactant	D
Major_Product	E
In_Pathway	ABCDE

Pathway : ABCDE
Components	A->B
Components	B->C
Components	B->D
Components	D->E

Resulting diagram

[2] To include more detailed information in the diagrams

You can add information on sub-reactions ("Cofactor_Reactant" to "Cofactor_Product") and mechanisms of the process (" Enzyme") to the diagram.

Models.wrm

?Step 	Major_Reactant 	?Molecule
 	Major_Product	?Molecule
	Cofactor_Reactant	?Molecule	#added 
	Cofactor_Product	?Molecule	#added 
	Enzyme		?Process	#added  
	In_Pathway  ?Pathway

#Tags that can be renamed are "In_Pathway" and "Step". If you want to change the names of other tags, you also have to change w7/metab.c code and recompile xace.

Data Format

Step : "A->B"
Major_Reactant	A
Major_Product	B
Cofactor_Reactant	AA	#added
Cofactor_Product	BB	#added
Enzyme		phosphorylation	#added
In_Pathway	ABCDE

Resulting diagram

[3] To rearrange the diagram and save the coordinates

Since METAB can produce only a rough arrangement of nodes and arrows in the diagram, you can change positions of nodes and arrows in the diagram precisely. Rearrangement can be done interactively by clicking and dragging the objects with the middle button of the mouse. After rearrangement you have to save the coordinates from the window-menu (right button) "quit". Next time the rearranged diagram will be reproduced from the saved coordinates. If you want to see the coordinates, look in class "PathwayDiagram", which is produced automatically on saving the diagram.

Rearranged diagram

Coordinates of the diagram

PathwayDiagram : "ABCDE Diagram Info"
Pathway  "ABCDE"
Node     16 33.125000 12.375000 15 "BB"
Node     14 33.125000 8.625000 13 "AA"
Node     9 23.333334 48.000000 10 "E"
Node     7 23.333347 30.444448 8 "D"
Node     5 45.777775 30.222231 6 "C"
Node     3 35.000000 18.000000 4 "B"
Node     1 35.000000 3.000000 2 "A"
!!
!!Node   ID  x-coord    y-coord    LabelID  Metabolite
!!
Arc      20 -1 7 9 0 8.777777 "D->E" 
Arc      19 -1 3 7 0 8.528996 "B->D"
Arc      18 -1 3 5 0 8.147749 "B->C"
Arc      17 -1 14 16 -1 1.875000
Arc      12 11 1 3 0 7.500000 "A->B" 
!!
!!Arc    ID  LabelID  FromNode  ToNode  Curvature  Radius    Pathway
!!
TangentArc       12 17
!!
!! Tangent  ArcID  TangentArcID
!!
Label    15 31.125000 13.643334 "BB"
Label    13 31.025002 8.310000 "AA"
Label    11 27.500000 10.976667 "phosphorylation" 
Label    10 25.333334 47.500000 "E" 
Label    8 24.333347 28.277782 "D" 
Label    6 46.777775 28.055567 "C" 
Label    4 37.000000 17.500000 "B" 
Label    2 37.000000 2.500000 "A" 
!!
!! Label  LabelID  x-coord    y-coord    LabelText
!!