Issue with adding a 3rd reactant

[jn494]

Hi,

When I add a 3rd reactant in the input file and execute ring.bat, the error message pops up and it fails to compile the code and get program.exe file.

--Example input file-- //reactant definition (note that two slashes mean that everything in that line following it is taken as a comment input reactant "CC(O)=O" input reactant "[HH]"

//Hydrogenation of acid with two H2 rule HydrogenationAcidToAlcohol{ reactant r1{ C labeled c1 O labeled o1 double bond to c1 O labeled o2 single bond to c1 H labeled h1 single bond to o2 } reactant r2{ H labeled h2 H labeled h3 single bond to h2 } reactant r3 duplicates r2 (h2=>h4, h3=>h5)

constraints{ fragment e{ C labeled c2 C labeled c3 double bond to c2 } fragment f{ C labeled c4{! connected to O with single bond} O labeled o3 double bond to c4 } ! r1 contains e ! r1 contains f } break bond (c1, o2) decrease bond order (c1, o1) break bond (h2, h3) break bond (h4, h5) form bond (h2, o1) form bond (h3, o2) form bond (h4, c1) form bond (h5, c1) }

-- Error message-- output.cpp output.cpp(35): warning C4129: 'e': unrecognized character escape sequence output.cpp(35): warning C4129: 'T': unrecognized character escape sequence output.cpp(67): error C2039: 'add_combined_constraint_3': is not a member of 'Reactiontype' D:\RING-master\cpp\reaction.h(26): note: see declaration of 'Reactiontype'

It would be appreciated if you could figure out the problem. Thanks.

[uditgupta0912]

The new version of RING allows specifying a third reactant that is not a duplicate of second reactant. This allows specifying reaction rules for biochemical reaction systems that involve 2 or more different reactants. You can specify the third reactant separately. I have also uploaded an old version of RING (RING-1.1.0) if you want to use your reaction rule specification.

Let us know if you are still having issues generating the reaction network.

[jn494]

Thanks for your reply.

Actually, there was an issue when a 3rd reactant was added in "reaction rules" part rather than in "reactant specification" part. That is, I guess the line below caused the error in the above example. ... "reactant r3 duplicates r2 (h2=>h4, h3=>h5)" ...

If I want to include 3rd reactant in the reaction rules, should I use the older version of RING (RING-1.1.0) instead of the new version?

I appreciate the help you could provide.

[uditgupta0912]

The old version of RING will accommodate reactant r3 specification as ... "reactant r3 duplicates r2 (h2=>h4, h3=>h5)" ... You can use RING-1.1.0 for the above reactant 3 specification.

The new version of RING will accommodate the following reactant specification:

reactant r2{ H labeled h2 H labeled h3 single bond to h2 } reactant r3{ H labeled h4 H labeled h5 single bond to h4 }

While adding the functionality to specify a non-duplicate reactant r3, the duplicate reactant specification got removed, the reason why you are seeing the error. I will work on the new version and add back the functionality of specifying a duplicate reactant.

For now, please use RING-1.1.0 version for network generation.

[jn494]

Thanks for your effort in resolving this issue. Unfortunately, I got the same error even after I modified the input file as you specified below.

reactant r2{ H labeled h2 H labeled h3 single bond to h2 } reactant r3{ H labeled h4 H labeled h5 single bond to h4 }

Actually, I tried a couple of more examples where non-duplicate reactant r3 was used in reaction rules but failed to compile them with the exact same error.

I would be grateful if you could figure out the problem.