Incorrect character foundIncorrect character foundIncorrect character foundIncorrect character found
Print Page - Sandbox?
Chemical Forums
General Forums => Comments for Staff and Comments from Staff => Topic started by: curiouscat on December 01, 2012, 08:39:17 AM
Title: Sandbox?
Post by: curiouscat on December 01, 2012, 08:39:17 AM
Can I request a Sandbox thread or area? Often I can't get my LaTex code or SMILE right at first go and it'd be nice to have somewhere to test. I sweat trying to compete against the 30 minute modify limit. :)
PS. The Preview feature doesn't seem to render Tex? Or maybe it's only my stupid browser?
Wondering what others think..
Title: Re: Sandbox?
Post by: Borek on December 01, 2012, 08:55:16 AM
Tex is not rendered in the preview and unfortunately there is not much that can be done about it - preview is fetched from the server without reloading the page, and MathJax script runs on a page load. On the other hand SMILES images are created server side, so they are displayed in the preview.
We can devote some thread to testing and delete the content now and then, no problem. I can't think of a better solution at the moment. But I am open to suggestions.
It is possible to create some simple sandbox for MathJax, but it would be not integrated with the forum itself, not the idea that I like.
Title: Re: Sandbox?
Post by: curiouscat on December 01, 2012, 08:56:56 AM
Apparently SMILES don't like new lines in the SMILES code. Obvious, but I have never thought about it earlier.
Ahhhh! :P Thanks!
Title: Re: Sandbox?
Post by: Borek on December 13, 2012, 08:11:56 AM
New lines should be dealt with (almost) correctly now.
ALT text is still wrong, but this is more difficult to deal with due to the way things are organized in the forum code.
Title: Re: Sandbox?
Post by: curiouscat on December 13, 2012, 08:54:57 AM
Trying to test the limits by rendering Palytoxin. Let's see if I can break anything. :)
Title: Re: Sandbox?
Post by: sjb on December 13, 2012, 09:13:59 AM
Yeah, I looked at that the other day for the other thread, note that the wiki SMILES doesn't have stereochemical information on it.
Title: Re: Sandbox?
Post by: Borek on December 13, 2012, 09:45:13 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).
Title: Re: Sandbox?
Post by: curiouscat on December 13, 2012, 09:58:41 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. :)
Title: Re: Sandbox?
Post by: curiouscat on December 13, 2012, 12:24:39 PM
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.
Title: Re: Sandbox?
Post by: Borek on December 13, 2012, 12:36:35 PM
http://www.iupac.org/publications/pac/80/2/0277/
Title: Re: Sandbox?
Post by: curiouscat on January 02, 2013, 03:55:58 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:
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):
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
Though this might have been a better way to render it (also as per Borek's very nice IUPAC guidelines):
"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:
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?
Title: Re: Sandbox?
Post by: Borek on January 22, 2013, 06:07:40 AM
Title: Re: Sandbox?
Post by: curiouscat on January 22, 2013, 06:13:50 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.
Title: Re: Sandbox?
Post by: curiouscat on January 22, 2013, 06:29:40 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..
Title: Re: Sandbox?
Post by: Borek on January 22, 2013, 07:10:01 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).
Title: Re: Sandbox?
Post by: curiouscat on January 22, 2013, 07:11:53 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
Title: Re: Sandbox?
Post by: Borek on February 09, 2013, 08:57:39 AM
Title: Re: Sandbox?
Post by: sjb on February 19, 2013, 07:46:42 AM
In some way related to the fact you can't represent a racemic mixture, as at http://www.chemicalforums.com/index.php?topic=65809.msg236734#msg236734 ? Not sure....
Title: Re: Sandbox?
Post by: Borek on February 19, 2013, 07:51:13 AM
Hm, when chirality doesn't matter isn't it better to just show the molecule as
?
Not really, in this case there are a cis pair and a trans pair of diasteromers.
Your compound also includes and to my mind.
Title: Re: Sandbox?
Post by: Borek on February 19, 2013, 08:55:24 AM
OK, I see what you mean - but I have no idea what you mean ;)
I mean - I see why the "flat" representation can be too wide (mean to many things), but I have no idea how the racemic mixture SHOULD be represented?
Title: Re: Sandbox?
Post by: sjb on February 19, 2013, 09:09:16 AM
In a previous life I worked indirectly with DAYLIGHT on a few things, a sample presentation (not by me, but by someone who was in effect my boss) is at http://www.daylight.com/meetings/emug04/Lock/index.html
The cases we are discussing are ~ slide 20-23
I seem to recall that in the GSK system (as referenced above) there were "chiral" and "racemic" flags you could put on the molecule when imported from ISIS draw (as was) which helped distinguish these cases. Not sure how it worked on the back-end though :(
Title: Re: Sandbox?
Post by: Dan on February 19, 2013, 10:24:33 AM
I have no idea how the racemic mixture SHOULD be represented?
I would draw one enantiomer and indicate that it is racemic with a (±) symbol underneath it.
Title: Re: Sandbox?
Post by: Dan on February 20, 2013, 01:47:49 PM
Another incorrect "chiral" flag today -but more obviously incorrect. It seems as though specifying configuration of even non-stereogenic centres fools it into assuming the molecule is chiral:
Title: Re: Sandbox?
Post by: billnotgatez on March 03, 2013, 05:37:45 PM
I wrote the above two formulas using the formatting available in the reply box
Question 1 - which one do you like Question 2 - could I have used LATEX or SMILES
Title: Re: Sandbox?
Post by: Borek on March 03, 2013, 06:12:49 PM
Both are OK with me - it really depends on what you are trying to show. The latter is simpler, but if for some reason you want to stress out you are talking about alkyne - teh latter makes sense.
In this particular case I would not use neither SILES nor LaTeX. Call it a personal preference.
Title: Re: Sandbox?
Post by: billnotgatez on March 03, 2013, 06:20:27 PM
I am a dolt also an Adult but Do we have links to teaching SMILES and LaTex handy I think I am being common sensed challenged here, since I am not seeing any
Title: Re: Sandbox?
Post by: Borek on March 03, 2013, 06:47:37 PM
There are some basic links in the About post formatting... (http://www.chemicalforums.com/index.php?topic=59314.0) thread.
Title: Re: Sandbox?
Post by: billnotgatez on March 03, 2013, 07:55:00 PM
Did I miss any
SMILES at Daylight site http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html SMILES at wikipedia http://en.wikipedia.org/wiki/SMILES ChemSketch http://www.acdlabs.com/download/ LaTeX http://en.wikibooks.org/wiki/LaTeX/Mathematics)
Title: Re: Sandbox?
Post by: curiouscat on March 03, 2013, 10:49:43 PM
In this particular case I would not use neither SILES nor LaTeX. Call it a personal preference.
+1 SMILES only becomes relevant above a certain minimum complexity of molecule. Usually, no one needs to be reminded how, say, ethane is structured internally.
Title: Re: Sandbox?
Post by: Borek on March 04, 2013, 04:04:18 AM
SMILES at Daylight site http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html SMILES at wikipedia http://en.wikipedia.org/wiki/SMILES ChemSketch http://www.acdlabs.com/download/ LaTeX http://en.wikibooks.org/wiki/LaTeX/Mathematics)
I believe it is a good starting collection, at least for the forum. There is much more to LaTeX, but most of it is of no use for us.
Title: Re: Sandbox?
Post by: billnotgatez on March 21, 2014, 07:37:43 AM
Just smiles testing some ketones
or
Just smiles testing some acids
or
Title: Re: Sandbox?
Post by: billnotgatez on April 26, 2014, 03:30:54 AM
IUPAC rules are clear and they are defined to be used by everyone.
Yes the rules are clear but how does one mandate everyone to use them? :)
Technically you don't, but it is a matter of being clear and unambiguous. What is VO2+? IUPAC rules tell you how to write it in an unambiguous way, why not stick to them?
Title: Re: Sandbox?
Post by: curiouscat on April 30, 2014, 08:27:16 AM
Technically you don't, but it is a matter of being clear and unambiguous. What is VO2+? IUPAC rules tell you how to write it in an unambiguous way, why not stick to them?
Agreed.
Title: Re: Sandbox?
Post by: billnotgatez on April 30, 2014, 08:40:58 AM
(ac) I did a quick GOOGLE and did not find this one I have yet to peruse the IUPAC rules
Title: Re: Sandbox?
Post by: Borek on April 30, 2014, 09:15:06 AM
Title: Re: Sandbox?
Post by: Xenonman on April 30, 2014, 10:01:44 AM
(ac) comes from "acuoso", aqueous in Spanish. I used it all over my Olympiad exams, without any penalization, because the entire exam was in Spanish.
Those zinc equations were for an assignment. In Spanish again.
I was taught to use (ac), as you can see. This is what every future Olympic will be taught, so I'll try to show this discrepancy, and an example of what happens when they use (ac) instead of (aq). I'll use (aq) as long as I don't forget when posting here, also.
Title: Re: Sandbox?
Post by: billnotgatez on May 03, 2014, 10:26:10 PM
Some more practice
Cobalt(II) oxide WIKI SPIDER
Cobalt(III) oxide SPIDER
Cobalt(II,III) oxide WIKI SPIDER
Cobalt(II) carbonate SPIDER
Title: Re: Sandbox?
Post by: billnotgatez on May 04, 2014, 05:26:43 AM
testing
Glycerol or Glycerin C3H8O3 WIKI SPIDER
Title: Re: Sandbox?
Post by: Borek on May 04, 2014, 06:41:14 AM
Strange. Why C(C(CO)O)O when OCC(O)CO is much simpler? Perhaps wiki has some computer generated code.
Title: Re: Sandbox?
Post by: curiouscat on May 04, 2014, 08:59:28 AM
Strange. Why C(C(CO)O)O when OCC(O)CO is much simpler? Perhaps wiki has some computer generated code.
Yes indeed. That convoluted version is almost impossible to create by hand accidentally.
Title: Re: Sandbox?
Post by: billnotgatez on May 04, 2014, 09:22:35 AM
A side note When I looked up the smiles for the Cobalt oxides WIKI was different than SPIDER But they both had the same for the Glycerin (Glycerol)
Is there a source for "standard smiles" compounds?
Title: Re: Sandbox?
Post by: Borek on May 04, 2014, 02:50:01 PM
SMILES are good for organic compounds, with well defined structure (bonds between atoms). Most inorganic compounds are more ionic and don't have easily separated molecules, so they may have well defined crystal structure (ie respective positions of atoms in the crystal) but no typical "bonds" yielding structure similar to the one in organic molecules.
IOW: SMILES are a good equivalent of stick and ball models, but not so good for infinite crystals.
Title: Re: Sandbox?
Post by: billnotgatez on May 04, 2014, 10:25:10 PM
Quote
IOW: SMILES are a good equivalent of stick and ball models, but not so good for infinite crystals.
Somewhere deep in my cranial cavity a light bulb is starting to illuminate.
Title: Re: Sandbox?
Post by: Xenonman on May 13, 2014, 05:39:34 PM
<- naphthalene attempt #1 ;D What's with that carbon charge? o-o
Title: Re: Sandbox?
Post by: curiouscat on May 13, 2014, 11:08:57 PM
I noticed I had to use the insert hyperlink function to get the required result
It seems that just a copy paste does not always work for links I think I noticed this before but probably did not remember and I do not remember why this is caused
Title: Re: Sandbox?
Post by: Borek on August 06, 2015, 05:13:51 PM
Closing parenthesis is a known source of problems in links, especially in older software. Best approach is to use url tags.
Title: Re: Sandbox?
Post by: billnotgatez on November 01, 2015, 11:25:01 PM
Oleic acid CAS Registry Number 112-80-1 Chemical formula C18H34O2 Molar mass 282.47 g·mol−1
Title: Re: Sandbox?
Post by: billnotgatez on May 10, 2016, 10:18:13 PM
Isopropyl alcohol or propan-2-ol or isopropanol C3H8O or C3H7OH or CH3CHOHCH3 or i-PrOH or (CH3)2CHOH
https://en.wikipedia.org/wiki/Isopropyl_alcohol --------------------------------------------------- acetone or propanone or propan-2-one C3H6O or (CH3)2CO
Title: Re: Sandbox?
Post by: billnotgatez on October 08, 2016, 01:42:50 PM
Image test
Title: Re: Sandbox?
Post by: sjb on November 03, 2016, 05:49:00 AM
Title: Re: Sandbox?
Post by: billnotgatez on November 24, 2016, 11:03:44 AM
Propylene glycol propane-1,2-diol C3H8O2 Molar mass 76.10 g/mol Density 1.036 g/cm3 CAS Number 57-55-6 https://en.wikipedia.org/wiki/Propylene_glycol (https://en.wikipedia.org/wiki/Propylene_glycol)
Glycerol glycerine or glycerin or 1,2,3-Propanetriol or 1,2,3-Trihydroxypropane C3H8O3 Molar mass 92.09 g/mol Density 1.261 g/cm3 CAS Number 56-81-5 https://en.wikipedia.org/wiki/Glycerol (https://en.wikipedia.org/wiki/Glycerol)
Ethanol ethyl alcohol C2H6O or CH3CH2OH or C2H5OH or EtOH Molar mass 46.068 g/mol Density 0.7893 g/cm3 (at 20 °C) CAS Number 64-17-5 https://en.wikipedia.org/wiki/Ethanol (https://en.wikipedia.org/wiki/Ethanol)
Title: Re: Sandbox?
Post by: billnotgatez on January 31, 2017, 06:18:23 PM
Lawsone https://en.wikipedia.org/wiki/Lawsone (https://en.wikipedia.org/wiki/Lawsone) IUPAC name 2-Hydroxy-1,4-naphthoquinone CAS Number 83-72-7 Chemical formula C10H6O3 Molar mass 174.15 g/mol
Citric acid https://en.wikipedia.org/wiki/Citric_acid (https://en.wikipedia.org/wiki/Citric_acid) Preferred IUPAC name 2-Hydroxypropane-1,2,3-tricarboxylic acid CAS Number 77-92-9 Chemical formula C6H8O7 Molar mass 192.12 g/mol
Title: Re: Sandbox?
Post by: billnotgatez on October 29, 2017, 09:26:44 PM
Preferred IUPAC name Benzoic acid https://en.wikipedia.org/wiki/Benzoic_acid (https://en.wikipedia.org/wiki/Benzoic_acid) Systematic IUPAC name Benzenecarboxylic acid CAS Number 65-85-0 Chemical formula C7H6O2 or C6H5COOH Molar mass 122.12 g/mol Melting point 122.41 C (252.34 F; 395.56 K)
Title: Re: Sandbox?
Post by: Borek on November 07, 2017, 02:56:17 AM
Glucose.
Title: Re: Sandbox?
Post by: billnotgatez on March 18, 2018, 03:21:24 AM
Phytic acid IUPAC name (1R,2S,3r,4R,5S,6s)-cyclohexane-1,2,3,4,5,6-hexayl hexakis[dihydrogen (phosphate)] https://en.wikipedia.org/wiki/Phytic_acid CAS Number 83-86-3 Chemical formula C6H18O24P6 Molar mass 660.03 g/mol
Title: Re: Sandbox?
Post by: Elric82 on April 04, 2018, 06:00:35 PM
CaCl 2 + Na2CO3 :rarrow: CaCO3 + 2NaCl
Just a test on my message formatting
After all, that’s what this thread is for, isn’t it? I think this thread should be a sticky, but hey, I’m too knew around here to make such suggestions. Even though I’ve lurked here for a long time. Just a thought.
Title: Re: Sandbox?
Post by: Borek on April 04, 2018, 06:12:36 PM
checking to see which multiplication symbol I like best
Title: Re: Sandbox?
Post by: Arkcon on January 13, 2021, 07:59:53 AM
[smiles](T)C(D)(H)(OH)/smiles]
Humph. Seems not to work for me. Chiral methanol? Anyone? That's where two of the hydrogens are replaced with a tritium and a deuterium.
Title: Re: Sandbox?
Post by: AWK on January 13, 2021, 08:26:07 AM
Title: Re: Sandbox?
Post by: billnotgatez on January 17, 2021, 09:03:32 PM
IUPAC name 4-Nitrobenzoic acid Other names p-Nitrobenzoic acid Chemical formula C7H5NO4 https://en.wikipedia.org/wiki/4-Nitrobenzoic_acid (https://en.wikipedia.org/wiki/4-Nitrobenzoic_acid)
IUPAC name 3-Nitrobenzoic acid Other names m-Nitrobenzoic acid Chemical formula C7H5NO4 https://en.wikipedia.org/wiki/3-Nitrobenzoic_acid (https://en.wikipedia.org/wiki/3-Nitrobenzoic_acid)
IUPAC name 2-Nitrobenzoic acid Other names o-Nitrobenzoic acid Chemical formula C7H5NO4 https://en.wikipedia.org/wiki/2-Nitrobenzoic_acid (https://en.wikipedia.org/wiki/2-Nitrobenzoic_acid)
Title: Re: Sandbox?
Post by: billnotgatez on June 22, 2021, 09:30:20 AM
Title: Re: Sandbox?
Post by: billnotgatez on July 24, 2021, 09:13:23 AM
Dichloromethane
Chemical formula CH2Cl2 Molar mass 84.93 g·mol−1 Density 1.3266 g/cm3 (20 °C) Melting point −96.7 °C (−142.1 °F; 176.5 K) Boiling point 39.6 °C (103.3 °F; 312.8 K)
https://en.wikipedia.org/wiki/Dichloromethane
Bromine, 35Br Standard atomic weight Ar, std(Br) [79.901, 79.907] conventional: 79.904 Atomic number (Z)35 Phase at STP liquid Melting point(Br2) 265.8 K (−7.2 °C, 19 °F) Boiling point(Br2) 332.0 K (58.8 °C, 137.8 °F) Density (near r.t.)Br2, liquid: 3.1028 g/cm3
https://en.wikipedia.org/wiki/Bromine
Title: Re: Sandbox?
Post by: billnotgatez on August 18, 2021, 10:11:10 AM
UPAC name Citric acid Preferred IUPAC name 2-Hydroxypropane-1,2,3-tricarboxylic acid Chemical formula C6H8O7 Molar mass 192.123 g/mol (anhydrous), 210.14 g/mol (monohydrate)
Title: Re: Sandbox?
Post by: billnotgatez on May 05, 2022, 12:51:05 PM
Methyl orange https://en.wikipedia.org/wiki/Methyl_orange Preferred IUPAC name Sodium 4-{[4-(dimethylamino)phenyl]diazenyl}benzene-1-sulfonate Other names Sodium 4-[(4-dimethylamino)phenylazo]benzenesulfonate CAS Number 547-58-0 Chemical formula C14H14N3NaO3S Molar mass 327.33 g·mol−1
Dimethyl-4-phenylenediamine https://en.wikipedia.org/wiki/Dimethyl-4-phenylenediamine (https://en.wikipedia.org/wiki/Dimethyl-4-phenylenediamine) Preferred IUPAC name N1,N1-Dimethylbenzene-1,4-diamine Other names p-Aminodimethylaniline; N,N-Dimethyl-p-phenylenediamine; 4-(Dimethylamino)aniline; p-Amino-N,N-dimethylaniline; p-(Dimethylamino)aniline; DMPPDA; Dimethyl-p-phenylenediamine; 4-Amino-N,N-dimethylaniline; p-Dimethylaminophenylamine; DMPD CAS Number 99-98-9 Chemical formula C8H12N2 Molar mass 136.198 g·mol−1
Title: Re: Sandbox?
Post by: billnotgatez on May 23, 2022, 10:10:38 AM