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Author Topic: Sandbox?  (Read 43744 times)

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curiouscat

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Re: Sandbox?
« Reply #15 on: December 13, 2012, 03:58:41 AM »

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.  :)
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curiouscat

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Re: Sandbox?
« Reply #16 on: December 13, 2012, 06:24:39 AM »

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.
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Borek

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Re: Sandbox?
« Reply #17 on: December 13, 2012, 06:36:35 AM »

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curiouscat

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Re: Sandbox?
« Reply #18 on: January 01, 2013, 09:55:58 PM »

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:

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?

Even the smaller Dodecahedrane  doesn't seem to work.

C12C3C4C5C1C6C7C2C8C3C9C4C1C5C6C2C7C8C9C12C31C%10C2C5C%11C6C8C(C1C9C4C7C(C2C34)C5C6C7C89)C%10%11

PS. As an aside Annulene looks pretty

C1=CC=CC=CC=CC=CC=CC=CC=CC=C1

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

« Last Edit: January 01, 2013, 10:15:14 PM by curiouscat »
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Borek

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Re: Sandbox?
« Reply #19 on: January 01, 2013, 10:42:19 PM »

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:

Quote
If desired, digits denoting ring closures can be reused.

And apparently that's what is done here.

Quote
C1=CC=CC=CC=CC=CC=CC=CC=CC=C1

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.
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curiouscat

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Re: Sandbox?
« Reply #20 on: January 01, 2013, 10:49:44 PM »

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. :)

Quote
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.
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curiouscat

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Re: Sandbox?
« Reply #21 on: January 22, 2013, 12:02:51 AM »

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.  ;D

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

[*]C1OC1[*]

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!  :P

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

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Borek

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Re: Sandbox?
« Reply #22 on: January 22, 2013, 12:07:40 AM »

[*:1]C1OC1[*:2]
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curiouscat

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Re: Sandbox?
« Reply #23 on: January 22, 2013, 12:13:50 AM »

[*:1]C1OC1[*:2]

Ah! Thanks!  :-[

[*:1]C(Cl)C(O)[*:2]>>[*:1]C1OC1[*:2]

Looks a bit ugly here... ???
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Borek

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Re: Sandbox?
« Reply #24 on: January 22, 2013, 12:26:28 AM »

[*:1]C(Cl)C(O)[*:2]>>[*:1]C1OC1[*:2]

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.
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curiouscat

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Re: Sandbox?
« Reply #25 on: January 22, 2013, 12:29:40 AM »


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..
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Borek

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Re: Sandbox?
« Reply #26 on: January 22, 2013, 01:10:01 AM »

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).
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curiouscat

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Re: Sandbox?
« Reply #27 on: January 22, 2013, 01:11:53 AM »

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".  :P
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Borek

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Re: Sandbox?
« Reply #28 on: February 09, 2013, 02:57:39 AM »

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:

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

Works now. Stupid bug.

Quote
C12C3C4C5C1C6C7C2C8C3C9C4C1C5C6C2C7C8C9C12C31C%10C2C5C%11C6C8C(C1C9C4C7C(C2C34)C5C6C7C89)C%10%11

Works, but I would not call it pretty  :o
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curiouscat

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Re: Sandbox?
« Reply #29 on: February 09, 2013, 04:26:15 AM »

Cool!
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