User talk:SMILESmaster

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16:05, 29 September 2018 (UTC)

Welcome

As no one else seems to have done it yet - Welcome to Wikipedia! It’s good to see a new chemistry editor. I see you’ve set yourself the task of sorting through our SMILES strings, which is certainly something that needs doing. Might I suggest this site (doesn't work in IE) which maintains a list of errors as well as a list of pages without SMILES at all (see the ‘Browse errors’ section).

If you’re feeling social, the chemistry editing community maintains an active Wiki-project page, where we discuss problems and the like. Do feel welcome to join us (no obligation!). Finally, if you get stuck at all do feel free to drop me a message and I’ll see if I can help. --Project Osprey (talk) 09:06, 9 October 2018 (UTC)[reply]

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SMILES that I'm working on

There are a few SMILES that I've tried but failed to fix that you might be interested in helping me with. I'll link the talk page discussions.

Talk:Chromium(II)_acetate#SMILES
Talk:Gallium_arsenide#SMILES
Talk:Diamond#SMILES (arguably successful but hasn't been put in yet)

Can you look at them and see what you can do? Thank you. Care to differ or discuss with me? The N^th User 02:27, 27 November 2018 (UTC)[reply]

Thank you The_Nth_User (talk · contribs) for contacting me. I tried my best to fix the 2 SMILES's. But one needs to keep in mind that the SMILES was created to encode standard organic molecules and is not very good for organometallic structures and even worse for the inorganic ones. There is nothing like coordinate bond in the SMILES syntax. You can try to view the SMILES using the CDK depict service at https://www.simolecule.com/cdkdepict/depict.html

Actually, I realized that I forgot to put the water ligands in brackets, so the program treated the 2 after H as meaning that the hydrogen atom was in a ring. Once I put brackets in, the SMILES worked much better, but for some reason, the symbols for triple and quadruple bonds don't work, even when I use the escape codes. Care to differ or discuss with me? The N^th User 00:18, 30 November 2018 (UTC)[reply]

Also, other page with a SMILES error is dicarbon, but not even [CH0]=[CH0], which explicitly states that the molecule doesn't have any hydrogen, seems to work. Care to differ or discuss with me? The N^th User 00:23, 30 November 2018 (UTC)[reply]

The SMILES [C]=[C] is the correct SMILES for dicarbon, concerning the quadruple bond, this is not part of the standard SMILES (although some software vendors implemented it as an extension, but you cannot rely that it will work universally). Concerning the organometallic structure you are linking to, it looks that the 4 carbons have only 3 bonds, should not they have an additional hydrogen attached? SMILESmaster (talk) 09:42, 30 November 2018 (UTC)[reply]

For me, [C]=[C] renders as ethene. As for the chromium compound, the carboxylate group as a whole as a negative charge, which I put on the carbon so each oxygen could single-bond with the chromium without being hypervalent. Acetate has three hydrogen atoms, and each acetate group in the model has that number of atoms, so I do not think that it needs to be changed. However, I figured out a way to get the water to display better. Care to differ or discuss with me? The N^th User 00:43, 1 December 2018 (UTC)[reply]

I just noticed something else: For the previous SMILES, if I remove the H2 from the oxygen atom for each of the water molecules (The H2 is unnecessary because the oxygen atom in each water molecule has a formal charge of +1.), the oxygen atoms in the acetates align for the two chromium atoms. Making one of the oxygen atoms for the acetate groups lowercase (signifying resonance) reverses this, although doing this for all of the carboxylate groups does not. Care to differ or discuss with me? The N^th User 03:33, 5 December 2018 (UTC)[reply]

I started on a SMILES for lonsdaleite. So far, I have a good chunk of the crystal, but when I try to finish the second puckered hexagonal prism (I made the two atoms that I have to connect nitrogen and phosphorus in order to allow them to be found more easily.), the entire thing renders flat. Do you know why? Care to differ or discuss with me? The N^th User 06:27, 5 December 2018 (UTC)[reply]

I got that to work, but not the next step. Care to differ or discuss with me? The N^th User 03:58, 6 December 2018 (UTC)[reply]

Actually, that one would be missing a bridge if it worked. This one would be correct. Also, I think that this version would be the same thing (also correct). Care to differ or discuss with me? The N^th User 04:01, 6 December 2018 (UTC)[reply]

The best person to help with this would be Bob Hanson, the author of JSmol. This is not the problem of SMILES itself, but the way how the JSmol handles SMILES and renders it in 3D (Bob implemented a lot of tricks in JSmol to render organometallic and inorganic molecules correctly). I suppose he would be interested to help and test JSmol on these challenging cases. SMILESmaster (talk) 09:08, 6 December 2018 (UTC)[reply]

Do you know how I can contact him to ask him for help? Care to differ or discuss with me? The N^th User 23:34, 6 December 2018 (UTC)[reply]

I have a functional SMILES for diphosphorus pentoxide. Care to differ or discuss with me? The N^th User 06:13, 7 December 2018 (UTC)[reply]

It doesn't work anyone. I guess that SMILES has been updated recently, so maybe we should test the other SMILES and see which ones work now. Care to differ or discuss with me? The N^th User 19:18, 26 December 2018 (UTC)[reply]

I'm working on a SMILES for polymorph of silica that's based off of diamond (Basically, replace each carbon atom with a silicon atom then insert an oxygen atom in the middle of each silicon-silicon bond. I think that tridymite has the same relationship with lonsdaleite.) that I'm now not sure is on Wikipedia, although I thought that it was cristobalite earlier. I have a SMILES for the silica equivalent of adamantane and one for the silica equivalent of diamantane. Do you think that I should proceed with the diamond-like version or switch to another polymorph? Care to differ or discuss with me? The N^th User 00:01, 30 December 2018 (UTC)[reply]

I cannot help too much with inorganic stuff and polymorphs (this is not my area of expertise). Try to join the discussion at the JSMol page https://sourceforge.net/p/jsmol/discussion/general/ I suppose Bob Hanson (the author of JSMol) will be able to help. And BTW thank you for all your Wikipedia edits and all the best in the New Year 2019! SMILESmaster (talk) 19:32, 30 December 2018 (UTC)[reply]

I'm sorry if I bombarded you with inorganic SMILES. I figured that you we into SMILES in general, but there is a question that I have concerning the SMILES for the zwitterion of an organic molecule. Maybe you could look at that? Also, thanks for all of your feedback and advice. Care to differ or discuss with me? The N^th User 01:49, 31 December 2018 (UTC)[reply]

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Merry Christmas and a Prosperous 2019!

Hello SMILESmaster, may you be surrounded by peace, success and happiness on this seasonal occasion. Spread the WikiLove by wishing another user a Merry Christmas and a Happy New Year, whether it be someone you have had disagreements with in the past, a good friend, or just some random person. Sending you heartfelt and warm greetings for Christmas and New Year 2019.
Happy editing,

Care to differ or discuss with me? The N^th User 19:16, 26 December 2018 (UTC)[reply]

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