[curiouscat]

Not always good for forum formatting, but apparently the engine survived.

Although rendered image is not following IUPAC suggestions - it should be more compact. There are things that can be improved in the indigo, so far one of my suggestions made its way into the code (but I have no idea when it is will be released).

Still impressive.  I was expecting an error message when I put that in. 

[curiouscat]

Although rendered image is not following IUPAC suggestions - it should be more compact.

What are IUPAC conventions on image rendering? I am curious. Do you have a link? I couldn't google anything up.

[Borek]

http://www.iupac.org/publications/pac/80/2/0277/

[curiouscat]

Was trying to throw Fullerenes at SMILES for fun but can't seem to make it work.  Any ideas?

Buckministerfullerene

Stealing the SMILES string off ChemSpider / Wikipedia:



Incidently shouldn't the molecule have 60 C entities since it's a C₆₀?  Was surprised that the Wikipedia / Chemspider strings only went up to C11. What gives?

Even the smaller Dodecahedrane  doesn't seem to work.



PS. As an aside Annulene looks pretty



Though this might have been a better way to render it (also as per Borek's very nice IUPAC guidelines):

[Borek]

All I can do is to forward these problems to the Indigo team (and be sure I will, although I know they are having a time off right now).

c12c3c4c5c1c6c7c8c2c9c1c3c2c3c4c4c%10c5c5c6c6c7c7c%11c8c9c8c9c1c2c1c2c3c4c3c4c%10c5c5c6c6c7c7c%11c8c8c9c1c1c2c3c2c4c5c6c3c7c8c1c23

Incidently shouldn't the molecule have 60 C entities since it's a C₆₀?  Was surprised that the Wikipedia / Chemspider strings only went up to C11. What gives?

To quote Daylight SMILES description:

If desired, digits denoting ring closures can be reused.

And apparently that's what is done here.

Though this might have been a better way to render it (also as per Borek's very nice IUPAC guidelines):

Forwarding to indigo team as well.

[curiouscat]

All I can do is to forward these problems to the Indigo team (and be sure I will, although I know they are having a time off right now).

Sure. Thanks!

Just doing our lil' bit to make the Open Source Ecosystem a wee bit better, one bug report at a time.

If desired, digits denoting ring closures can be reused.

And apparently that's what is done here.

Of course. Makes sense. Thanks! Somehow I was expecting to see a C60 index; dumb in hindsight. Lost sight of what these indexes meant.

[curiouscat]

You can PM yourself Tex to test it.

"You have exceeded the limit of 10 personal messages per hour."

Not a big deal at all, but just was funny how one can keep hitting the law of unintended consequences. 

Who'd have thought of Dan's idea and then all because it took stupid me 10 attempts to get this SMILES right:



Was even funnier coz' Reply or Quote is the only way to get the SMILES in the past message sandbox attempts and SMF won't let me try that now. (Ha! If someone gets what I write! ).

Guess I'll be in the doghouse for an hour! 

PS. Is there a way to get R1 and R2 rendered in SMILES?

[Borek]

[curiouscat]

Ah! Thanks! 



Looks a bit ugly here...

[Borek]

Looks a bit ugly here...

Another thing to report, once I am sure it is something to report 

Turned out problems with C60 are somewhere on our side - I was unlucky enough to hit two separate bugs on the forum and on my own computer, I assumed if it doesn't work here nor there it must be a problem with the SMILES renderer - but that's not the case.

[curiouscat]

Another thing to report, once I am sure it is something to report 

Turned out problems with C60 are somewhere on our side - I was unlucky enough to hit two separate bugs on the forum and on my own computer, I assumed if it doesn't work here nor there it must be a problem with the SMILES renderer - but that's not the case.

Did you have to do a lot of coding to integrate SMILES on "our side"? Wondering what "our side" bugs are like..

[Borek]

Did you have to do a lot of coding to integrate SMILES on "our side"? Wondering what "our side" bugs are like..

Something like several hours to modify forum sources - including time needed to find out how the BBC tags are analyzed and where. But it took several days to compile the renderer, as we discussed in the past.

And I have no idea what the bug is - yet. Most likely % sign is treated incorrectly. Trick is, I don't pass it - I have modified the program so that what is passed is just a hexadecimal representation of the original SMILES (so 434F is passed instead of CO), this way I don't have to care about the data sanitization (assuming the renderer just ignores incorrect input; I bet it does).

[curiouscat]

Did you have to do a lot of coding to integrate SMILES on "our side"? Wondering what "our side" bugs are like..

Something like several hours to modify forum sources - including time needed to find out how the BBC tags are analyzed and where. But it took several days to compile the renderer, as we discussed in the past.

And I have no idea what the bug is - yet. Most likely % sign is treated incorrectly. Trick is, I don't pass it - I have modified the program so that what is passed is just a hexadecimal representation of the original SMILES (so 434F is passed instead of CO), this way I don't have to care about the data sanitization (assuming the renderer just ignores incorrect input; I bet it does).

Wow, sounds crazy difficult. Somehow I was thinking it's a "plugin". 

[Borek]

Was trying to throw Fullerenes at SMILES for fun but can't seem to make it work.  Any ideas?

Buckministerfullerene

Stealing the SMILES string off ChemSpider / Wikipedia:

Works now. Stupid bug.

Works, but I would not call it pretty 

[curiouscat]

Cool!