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Automatic Arrange of Biochemical Pathway fails because of complexity - how to solve this problem?

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my Name is Susanne, I'm a german student and I'm going to write my dissertation about a special biochemical pathway. Therefore I have drawn a biochemical Pathway using yEd. I have to use SBGN as Notation to integrate all the needed information into that diagram.

So there are a lot of edges and nodes and crossovers in that drawing and the automatic layouts don't work correctly with that different kinds of nodes I have to use.

I just try to explain it in an example reaction:

There is always a substrate, let me call it "A" in a ellipse as node, linked with a smaller node as "Process Node = PN". The PN is then linked to an enzyme-node, for example "E" but also linked to an AND-Operator which then lead to the products of that reaction, "B" and "C".

"B" and "C" are then substrates for another reaction and so on ...

So when I try to use the automatic arrangements, it just pulls the enzyme-node far away of the PN- and substrate-nodes. My question in that case is, how to make a fixed link between the enzyme- and PN-nodes?  In best case there is a possibility to make clear defined spacings between the nodes. After that they should not be changed when I use the layouts to design the complete pathway.

I hope you understand my english and you have some ideas to help me out.

If you need a drawing for better understanding, please contact me so I will make an example drawing to put it online. I can also send you an example file from yEd.

Thank you very much for your help in advance.

Kind Regards,

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