• N&PD Moderators: Skorpio | thegreenhand

  • Neuroscience & Pharmacology Discussion Welcome Guest
    Posting Rules Bluelight Rules
    Recent Journal Articles Chemistry Mega-Thread
    FREE Chemistry Databases! Self-Education Guide

⫸STICKY⫷ SMILES <-> Image <-> IUPAC

C

clubcard

Bluelighter
Joined
Apr 12, 2013
Messages
1,483
I am interested to know if this free chemistry script (Java) or other free scripts along the same lines could be added to the Bluelight site? https://opsin.ch.cam.ac.uk

I am not to keen on the use of 'Druglikeness' calculators. I think presenting the results of Lipinski's Rule of 5 alongside the data produced by the above script would be of more value. http://www.niper.gov.in/pi_dev_tools/DruLiToWeb/DruLiTo_index.html

There is even a free version of CHARMM that runs under Linux. That would be a BIG task but the results are just fantastic. https://www.charmm.org/charmm/program/versions/

Even though the site is in Chinese, https://www.drugfuture.com/chemdata/<name> returns the original patents & index papers.

The advantage I see is that people could search for similar chemicals and once a chemical has been added to the system, everyone can see it.

I am prepared to help convert the QSAR data of the ACTIVE drugs in 'Opiates' by R.Lenz et al. It's amazingly thorough but more than 90% of the drugs are inactive. Some drugs not covered by 'Opiates' is covered by 'Opioid Analgesics - Chemistry and Receptors' by Casy and Parfitt. Even then, both books end in the 1980s so there are a lot of much newer compounds.
 
I'm going to sticky this as it is a very useful resource for the aspiring molecule-doodler.
 

External Packages - CHARMM

www.charmm.org www.charmm.org


External Packages
CHARMM directly interfaces with the following packages:
These packages have to be obtained and installed separately.

Now CHARMM was written in 'modern' Fortran 96, a programming language which I know not a single thing. Has anyone had the thrill-seeking job of rewriting Fortran 96 into Java?
 
clubcard said:
Now CHARMM was written in 'modern' Fortran 96, a programming language which I know not a single thing. Has anyone had the thrill-seeking job of rewriting Fortran 96 into Java?
Click to expand...

There are some programs, findable with Google search, that translate Fortran code to C++ or Java, but I find it hard to believe that they always always produce a functioning result without you doing some corrections by hand afterwards. I think Fortran makes it a bit easier to use parallel processing in scientific computation than C++. At least that was the impression I got when listening to a Fortran parallel computing lecture some years ago.
 
atara said:
I've always used http://py-chemist.com/mol_2_chemfig
Click to expand...

Nice one.

Now, some 8 years ago I talked to a couple of programmers who had written an IMAGE<->SMILES<->IUPAC converter in Java (I think). They were prepared to let any IP to use it for about £3000 which isn't cheap BUT did have a 5 year QC on it so any problems, they fixed. I reckon they were too nice to do well but I loved their work.

If WE stored everything as IUPAC and the board brought up images and allowed people to copy as SMILES, it would end us having to hose images and I HOPE it would allow people to exchange ideas more readily.
 
In full disclosure, I spent almost 20 years as a professional games programmer BUT I only ever wrote code in assembly language so I rarely wrote entire games. Others would profile their game and I would rewrite the most time consuming part of the code in optimized assembly language. Sadly, their is little work for people who can ONLY code in such a low-level language (although many of the games I optimized were pretty famous). I mentioned that someone had written a Java IUPAC<-->SMILES<-->Image and I believe that this site uses it:


Now, it IS possible to optimize Java by following a few simple rules. For the truly hardcore, it's possible to write Java AS bytecodes. For those interested, to exit Jazelle (or indeed Java of any flavour):

R0=R1=0
bytecode $ff


But the important thing is that the Java used by this site is free to all. I would LOVE to see an image of the molecule with the IUPAC name underneath it & SMILES below that. I suspect that SMILES itself can be compressed by the simple fact that elements do not appear equally so common elements use short bitstreams while uncommon elements can use longer bitstreams.

Sorry to go on about it but if the site also had an editor, it would allow people to record & produce SMILES & IUPAC naming all within the site. It would avoid images having to be stored on other sites. BL would be a complete resource in 1 place.
 
I HOPE I am trying to do the best for chemistry. Of course, I don't discuss anything I AM doing on-line but as the patents will show, pyeyzolam (the alcohol mimic) was & is mine. In fact, pynazolam is even more euphoric but I was concerned that it WAS so euphoric. I could see people getting into deep trouble really fast. I suppose a clandestine chemist is supposed to milk a great drug for all it's worth but I always did and have concerned myself with it's safety. Want to know what my criteria is?

'Would I be happy for my own son to take this'

Thus many things were thrown away. OK, my wife ALSO tried everything and even she thought pyeyzolam was just too damned goo.
 

iChemLabs | Store

iChemLabs is a scientific software company that creates affordable and easy to use chemistry software. We create the popular brand of ChemDoodle chemical drawing software.
www.ichemlabs.com

Voila Chemdoodle - $15/month

I've even bought a 1 month contract & a friend plugged it into a simple site on his local computer.

I don't know how much BL takes per month but I PRESUME $15/month is possible.

Yes, it's going to take someone who is an expert on building sites but from what I know, structures can be stored as SMILES strings & then displayed as images with their appropriate IUPAC name below it.

I should add that ACD/Chemsketch offer a free version so that every member can draw & manipulate chemical structures. The only thing I really miss is that it does not carry out the calculations to produce the minimum energy state in 3D. As an example, Fentanyl & BDPC do not look THAT similar in 2D but if one constructs a Dreiding Model (there goes 2-3 hours of your time) and they overlay PERFECTLY. The reason BDPC is more potent than fentanyl is because it's more rigid and it's LogP is higher.

I would be fascinated to know if the addition of beta (S) hydroxy moiety would similarly increase the potency of BDPC (or even better, MDBC whose advantages I have explained elsewhere).

Actually, I don't have any documentry evidence concerning the potency of beta hydroxy fentanyl. I know it's commonly responsible for fatal ODs in Russia (in particular) but the only report I have is from a conversation with RoboJunkie (remember him?. For those who don't, he was a close friend of Superjunkie who, as a subgraduate was making fentanyl for their own use. The usually made plain fentanyl but made 1 sample of beta hydroxy fentanyl which he reported to be about x8 more potent. Well, they got busted. Superjunky (the chemist) got 18 years and last I heard he was STILL in withdrawal after 18 months. Robojunkie was just a cheerleader/fienffriend and the police did not charge him. However, even with his family having the resources to get him the best medical treatment available, it sounds like his CNS has been permanently altered and he;s still rattling. I mean, he's getting a LOT of opioids but none of them help...
I suggest that the phenethyl group binds to an extra site and only drugs that bind with that site will be of any use. I do appreciate that it's merely an anecdote, it does make me extra cautious concerning the fentanyl/4-Phenylphenampromide/Phenoperidine/PEPAP/Anileridine and similar.... the opioids that bind to the '5th site'.
 
BTW Sometimes I can be VERY slow. I've only just begun using PubChem to search for compounds (and substructures & similar structures) which more often than not provides an appropriate reference to synthesis.

Not as good as Reaxys, but very good for nothing.
 
Bluelight.org
Psychoactive Substances - Canada
Rectify

How To Post Structural Formulae Here.​

Watch
•••
[IMG alt="Rectify"]https://bluelight.org/xf/data/avatars/m/117/117014.jpg?1632491837[/IMG]

Rectify​

Bluelighter​

It Is Important To Know How To Post Chemical Formulae aka Kekule Structures

1) Go to opsin.ch.cam.ac.uk

2) write the chemical name of the compound that you wish to post in the submit bar

3) for example, (2S)-2-ethylamino-1-phenylpropane. Play around with it until you get the desired Molecular shape to pop up. Looking up the IUPAC name on Google or Wikipedia can help.

4) Now, Select All text containing the correct, desired name in the query bar above the Submit button and Copy it

5) in the browser url box, type opsin.ch.cam.ac.uk/opsin/ and Paste the name after the last / with no space in between

6) add .png to the end of your copy and pasted name in the browser's url box and press enter. again, with no space bars in between

7) Viola. Now your Molecule has its own website! Select All and Copy its url.

8) come to bluelight and type [ I M G ] <pasted text> and finally [ / I M G ]. I had to add the spaces to make this post come out right. BUT when you are posting, you must not use any spaces there

9) Post your thread. BOOM! You're now on your way to becoming a bona fida Chemical Adept!

Remember, 1,000 Words Is Worth One Picture!

"Molecular Structure Is The Key To Understanding."--Transformer proverb.
 
Last edited:
I note that JSMOL is an open-source 3D viewer for organic chemicals. Given that it's written in Java, is it possible to add to Bluelight as viewing in 3D is of great value - especially if one is able to calculate minimum-energy conformation and overly 2 or more scaffolds.

I've also noted that https://app.syntelly.com/smiles2iupac is another online resource that converts a SMILES string into IUPAC naming.

If the 2 packages above could be included within BL it would have the potential to add a lot of new data while reducing the size of the database.
 
I discussed plug-ins with an admin and the computer says NO. The reason is security. All of the plug-ins only host the viewer on the host BBS, the rest sits on the server of the maker.

I'm STILL pretty jure their is just a JS that doesn't use ANY external access. It was used by a company that supplied a huge array of building blocks and it was just 4 files in a subdirectory. It even had the names of the two guys that wrote it and they were SO pleased to receive their first piece of 'fan mail' but it's still rather a lot of code and I suppose since our admins work for nothing, we cannot expect them to either presume the code is secure nor REALLY take the whole thing apart to learn and to ensure it doesn't leak.

I think it's a real shame since it would speed up learning so much, but as things stand, such things will not be added to BL in the foreseeable future. Nobody's fault, but we have to be certain that BLers feel secure here.
 
You must log in or register to reply here.
Top