Turns out I don't remember SMILES format very well

Testing out the Java2DRenderer (in the org.openscience.cdk.renderer package), I tried to make this:

Using this smile:

c1(c2ccc(c8ccccc8)cc2)
c(c3ccc(c9ccccc9)cc3)
c(c4ccc(c%10ccccc%10)cc4)
c(c5ccc(c%11ccccc%11)cc5)
c(c6ccc(c%12ccccc%12)cc6)
c1(c7ccc(c%13ccccc%13)cc7)

except that I didn't have the % signs, so it came out as:

This is because of multiple ring closures, of course. I should have used:

C1CCC(CC1)
C2CCC(CC2)
C13C(C3CCC(CC3)C4CCCCC4)
C(C5CCC(CC5)C6CCCCC6)
C(C7CCC(CC7)C8CCCCC8)
C(C9CCC(CC9)C10CCCCC10)
C13(C11CCC(CC11)C12CCCCC12)

which is much clearer. Oh yes.

Comments

Egon Willighagen said…

That's using the new Java2D-based renderer?

19 August 2008 at 09:21

gilleain said…

Er.. I thought that it was, but I was mistaken. I had confused the old renderer for the new one.

21 August 2008 at 16:21

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