Re: [BlueObelisk-discuss] ACS meeting - dinner?

Let's see if this works... I'm arriving in LA on Saturday and will have time to help organize this. Monday night would be by far the best for me; Sunday would be OK; I'm leaving Tuesday. I have a strong visual memory of the area but am unsure if I was walking North or East when we were last

Re: [BlueObelisk-discuss] ACS meeting - dinner?

Is this taken care of? Didn't we meet at a nice restaurant a few blocks from the hotels last time? Up on Katella Ave? On Thu, Mar 24, 2011 at 8:57 PM, Robert Belford rebelf...@ualr.edu wrote: Bob, You should have gotten this. Cheers, -- Forwarded message -- From:

Re: [BlueObelisk-discuss] Mini Blue Obelisk meeting at 5th Meeting on U.S. Government Chemical Databases and Open Chemistry?

Sounds fun. Unfortunately, I'll miss BOTH of these this time around; I'll be at the CRYSTAL workshop learning all about solid state chemistry: http://www.crystal.unito.it/mssc2011/ On Thu, Aug 18, 2011 at 3:32 AM, Noel O'Boyle baoille...@gmail.com wrote: Hi all, I'll be attending the database

Re: [BlueObelisk-discuss] [BlueObelisk-SMILES] help needed -- SMILES and MMFF94 atom types

[switching to BlueObelisk-Discuss from BlueOblelisk-Smiles here] Geoff, I will look at that. What does fully validated mean exactly? I have the SMARTS business for MMFF94 charges working in Jmol now for getting the atom types -- obviously not validated! -- and I suspect it will require a bit of

Re: [BlueObelisk-discuss] [BlueObelisk-SMILES] help needed -- SMILES and MMFF94 atom types

OK, SMARTS-based MMFF94 charges are now checked in for Jmol. Obviously the settings are not perfect and will take some tweaking. I'm sure it's more complicate than I make it out to be -- probably some very odd definitions in there; certainly some I could not fathom on this first pass. I haven't

Re: [BlueObelisk-discuss] [BlueObelisk-SMILES] help needed -- SMILES and MMFF94 atom types

that... On Sat, Apr 28, 2012 at 1:03 AM, Robert Hanson hans...@stolaf.edu wrote: OK, SMARTS-based MMFF94 charges are now checked in for Jmol. Obviously the settings are not perfect and will take some tweaking. I'm sure it's more complicate than I make it out to be -- probably some very odd definitions

[BlueObelisk-discuss] OpenBabel question

OK, I'm stumped. How does one get to Rule d? Does anyone know if this code was ever tested? 03131 if (b-GetBond http://fossies.org/dox/openbabel-2.3.1/classOpenBabel_1_1OBAtom.html#a1383e1d49338b8ee6784b8b9ef889ba4(c)-IsAromatic

Re: [BlueObelisk-discuss] help needed -- SMILES and MMFF94 atom types

follow-up on this. Over the last few days I was able to extend this to fully validated MMFF94 minimization capability in Jmol with empirical rules. Here's a summary of what I just checked in. version=12.3.26_dev # code: adding empirical rules to MMFF94 calculation # #

Re: [BlueObelisk-discuss] help needed -- SMILES and MMFF94 atom types

Here's my final result. I'm satisfied; I'm pretty sure there is no way to reproduce the results of the OPTIMOL results exactly. In the cases below I'm convinced there are bugs in OPTIMOL -- mostly in not consistently recognizing 5-membered rings, but also there is something odd going on in the

Re: [BlueObelisk-discuss] OpenBabel question

, Robert Hanson hans...@stolaf.edu wrote: OK, I'm stumped. How does one get to Rule d? Does anyone know if this code was ever tested? 03131 if (b-GetBond(c)-IsAromatic()) { 03132 double Ub, Uc, pi_bc, beta; 03133 Ub = GetUParam(b); 03134 Uc = GetUParam

Re: [BlueObelisk-discuss] Java Vulnerability Note VU#636312

One point might be being missed here. All this is in relation to Java applets, not any stand-alone Java applications. It's a browser problem only. So the concern should be for the Jmol applet, not the Jmol application or JmolData (server-side Jmol). We've already started porting Jmol to

Re: [BlueObelisk-discuss] [Jmol-users] PDB - OK, who's the wise guy?

Thanks, Andrew, that history helps. And I must say, the hybrid-36 scheme really is very clever. You would probably like the base-90 scheme I cooked up for the JVXL surface file format. Unlike Peter, I have no problem with custom specifications, as long as they are clear, unambiguous, and

Re: [BlueObelisk-discuss] dinner at ACS meeting in New Orleans?

I will be there just Sat - Tuesday. Either a late dinner Sunday (8 pm) or anytime Monday would work for me. Very eager to reconnect with my favorite group! Bob On Thu, Mar 7, 2013 at 2:53 AM, John P. Overington j...@ebi.ac.uk wrote: I'll be there too. jpo -- John P. Overington, BSc

Re: [BlueObelisk-discuss] dinner at ACS meeting in New Orleans?

the development is done in Java still. See http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm - reads PyMOL session files, too! Bob On Wed, Mar 20, 2013 at 4:52 PM, Robert Hanson hans...@stolaf.edu wrote: I will be there just Sat - Tuesday. Either a late dinner Sunday (8 pm) or anytime Monday would

Re: [BlueObelisk-discuss] dinner at ACS meeting in New Orleans?

suberb idea!! On Wed, Apr 3, 2013 at 12:35 PM, Egon Willighagen egon.willigha...@gmail.com wrote: On Wed, Apr 3, 2013 at 10:35 AM, Noel O'Boyle baoille...@gmail.com wrote: Sunday after CINF reception? Yeah, that should work for me too, I think. Egon -- Dr E.L. Willighagen

Re: [BlueObelisk-discuss] Best wishes from the COD team!

Saulius, Welcome! Do you know about all the cool crystallographic capabilities of Jmol? Latest is incommensurately modulated structures. Let's talk! Bob Hanson On Mon, Feb 10, 2014 at 5:37 AM, Saulius Gražulis grazu...@ibt.lt wrote: Dear colleagues, during the two very exciting weeks of

Re: [BlueObelisk-discuss] BODR covalent radii patch (all elements)

Thank you very much for this update, Bert. I have added it to Jmol as atom.covalentRadius, and you can, for example, illustrate those in Jmol 14.1.11 using {*}.radius = {*}.covalentRadius.all On Thu, Feb 20, 2014 at 1:07 AM, Wibe de Jong wadej...@lbl.gov wrote: Hi, I have updated the

[BlueObelisk-discuss] referencing of data

Can someone explain to me the general schema for referencing data in the BODR? I'm not seeing it. For example, at https://github.com/wadejong/bodr/tree/c7917225cad829507bdd4c8c2fe7ebd3d795c021/bodr/elements I see xml and bibxml files, but I see nothing that connects those. Just randomly named

[BlueObelisk-discuss] great InChI JavaScript library

inchi.js is great fun. It is now part of JSmol. See the demo at: http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm and http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.3_2016.03.08.zip Whom do we have to thank for this? Noel? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair,

[BlueObelisk-discuss] inchi.js

This is quite cool. Does anyone know how to make it work? What its API looks like? I would like to add this to JSmol. But when I followed the instructions at https://github.com/metamolecular/inchi-js using Firefox I see in the developer console: *Successfully compiled asm.js code (loaded from

Re: [BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

On Tue, Mar 1, 2016 at 7:49 AM, Egon Willighagen wrote: > Hi all, > > Now, Noel asked about a JS translation of the CDK stack. That would be > a lot more work, and not sure if it is entirely feasible, but I'm more > than happy to discuss that with the student

Re: [BlueObelisk-discuss] owner/operator of online web service for CDK?

And, here it is! https://chemapps.stolaf.edu/olcc/examples/js/CDK_image_JS.htm Very slick! All suggestions welcome at http://olcc.ccce.divched.org/content/prog-access by the way... Bob On Tue, Aug 30, 2016 at 11:09 PM, Robert Hanson <hans...@stolaf.edu> wrote: > No, I had

Re: [BlueObelisk-discuss] owner/operator of online web service for CDK?

set of REST services described at http://rest.rguha.net - >> it hasn't been updated in many years. The JAR file should run and the code >> should compile (I think it includes the relevant CDK dependencies). >> >> But it's many version behind the latest CDK, so I woul

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

at 11:03 AM, John Mayfield <john.wilkinson...@gmail.com> wrote: > Good good, > > Fake news before fake news - a paper published in the CCG journal by the > CCG. > > John > > On 9 April 2017 at 16:51, Robert Hanson <hans...@stolaf.edu> wrote: > >> No

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

No, John. Don't worry. I just happened to look at that page prior to designing my own. On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield <john.wilkinson...@gmail.com> wrote: > Hi Bob, > > On 9 April 2017 at 13:42, Robert Hanson <hans...@stolaf.edu> wrote: > >>

Re: [BlueObelisk-discuss] Fwd: Fwd: Cahn-Ingold-Prelog rules into Jmol

Brilliant. So I see the logic. This is chemistry not computer science. Thank you, John. I will adjust the algorithm. Pretty easy fix. On Tue, Apr 11, 2017 at 7:54 AM, John Mayfield wrote: > John, what basis in the IUPAC rules leads you to this reading? > > > That

Re: [BlueObelisk-discuss] Fwd: Fwd: Cahn-Ingold-Prelog rules into Jmol

Thank you very much for that very clear tip, John. Thinking *chemically* was the key to understanding this logic. atomic masses are subtleties that should not radically change the picture. Jmol is applying Rules 1 and 2 correctly now based on the suite of structures Mikko gave me. (See

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

On Wed, Apr 12, 2017 at 7:54 AM, Wolf Ihlenfeldt <w...@xemistry.com> wrote: > On Wed, Apr 12, 2017 at 1:44 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > (and I wish they had thought of seqR and seqS) > > > > In case anyone is interested, here is my pseudoco

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

; St. Olaf College Chemistry > from my Windows phone > ---------- > From: Robert Hanson <hans...@stolaf.edu> > Sent: ‎4/‎11/‎2017 7:30 AM > To: BlueObelisk-Discuss <blueobelisk-discuss@lists.sourceforge.net> > Subject: Fwd: [BlueObelisk-discuss] Fwd:

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

, 2017 at 12:11 PM, Robert Hanson <hans...@stolaf.edu> wrote: > OK, so I am reading Chapter 9 now to see the gory details. I didn't know > about the root-distance check, and so now > > 1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-cyclop > ropylethyl)-pentan-3-yl]methan-1-

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

ting these rules is some type of madness. > > On 9 Apr 2017 7:05 p.m., "Robert Hanson" <hans...@stolaf.edu> wrote: > >> OK, I don't get the logic of this: >> >> >> Rule 1 (a) Higher atomic number precedes lower; >> (b) A duplicated atom, with it

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

this algorithm. The whole goal > of the Blue Obelisk is to pool our expertise to develop common > resources, to avoid exactly this situation. > > - Noel > > On 9 April 2017 at 23:53, Robert Hanson <hans...@stolaf.edu> wrote: > > "re" implementing is a great way to find

[BlueObelisk-discuss] OK, bragging -- CIP

570 lines; 40 methods. https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java Limitations: no parallel chirality paths (Mata) not processing inositols correctly no lone-pair business (S, P, imines) standard E/Z, R/S, r/s only; no allenes, no planar

[BlueObelisk-discuss] OK, I'm catching on, but...

Can someone shed some light on how this brilliant statement: Rule 3. When two ligands differ *only in that one has an atomor atom-group of higher rank in a cis-position and theother in a trans-position to the core of the stereogenicunit, *then preference is given to the former. [Mata, Lobo, et

Re: [BlueObelisk-discuss] another CIP question

ps, before John jumps on me, I had better add the intermediate l/u business: left: RSS (uu) right: RRS (lu) l > u, so right wins. Since it comes down to ordering of the RSS... list, that's what I need clarification on. We have Ranking Rule #1, which is great and helps in this case (if John

Re: [BlueObelisk-discuss] OK, I'm catching on, but...

On Fri, Apr 14, 2017 at 3:28 AM, Wolf Ihlenfeldt <w...@xemistry.com> wrote: > On Fri, Apr 14, 2017 at 1:37 AM, Robert Hanson <hans...@stolaf.edu> wrote: > > Can someone shed some light on how this brilliant statement: > > > > Rule 3. When two ligands di

[BlueObelisk-discuss] Jmol - CIP update

Jmol.___JmolVersion="14.15.2" // 4/23/17 - CIPChirality.java 633 lines all except Rule 4b (Mata) and Rule 5 for those cases. - adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral - validates on 79 known chiral compounds testing a variety of nuances - still some opportunity for

[BlueObelisk-discuss] Cohen-Ingold-Prelog rules into Jmol

Just thought I would let people know that Jmol/JSmol now can calculate R/S chirality for any carbon atom. I've been working with Jmol for 10 years and only yesterday realized it was pretty trivial to write this. Well, better late than never, right?? And only 100 lines of code. What a deal! I'm

[BlueObelisk-discuss] another CIP question

OK, on to Rule 4. I am reading Chapter 9 and its associated papers very closely now. For anyone of the opinion that "this has been done many times before" I point out that between 1966 and 1982 and 1993 and 2004 and 2013 and between all the different suggestions for revision, it's pretty hard to

Re: [BlueObelisk-discuss] Jmol - CIP update

key tests. I'm hoping to finish Rule 5 sometime tomorrow or Thursday. 743 lines. Bob On Tue, Apr 25, 2017 at 11:26 AM, Robert Hanson <hans...@stolaf.edu> wrote: > Basic Mata analysis is in. Still two structures (Examples 4 and 6, pp 1200 > and 1208) are not validating, but I know

Re: [BlueObelisk-discuss] Jmol - CIP update

Rule 5 is done. Fully validating using the first validation set that Mikko sent me (86 compounds, roughly, some 2D/3D duplicates). I'm sure there are more cases it needs testing with, though. My algorithm implementation handles Rules 4 and 5 lexicographically so that a simple Array.sort(String[])

Re: [BlueObelisk-discuss] Jmol - CIP update

Basic Mata analysis is in. Still two structures (Examples 4 and 6, pp 1200 and 1208) are not validating, but I know why. Haven't implemented multi-reference like/unlike checking or a final check for complex pseudochirality involving Mata analysis. Both should be simple enough. We'll see! All

Re: [BlueObelisk-discuss] Jmol - CIP update

t; wrote: > > On 29 April 2017 at 20:54, Robert Hanson <hans...@stolaf.edu> wrote: > >> The algorithm will fail for some more complex nested aspects of Rule 4b. >> I decided to be satisfied for now with only those examples in IUPAC Blue >> Book 2013 Chapter 9. My und

Re: [BlueObelisk-discuss] Jmol - CIP update

that is mistaken, not Jmol. Thanks again. John for the great test cases. Do keep sending me any tough cases you might have. 1018 lines completes Rule 4b (for now!) Bob On Tue, May 9, 2017 at 10:04 PM, Robert Hanson <hans...@stolaf.edu> wrote: > yeah! I'll pass on that one -- after all,

Re: [BlueObelisk-discuss] Jmol - CIP update

Book 2013. These are being checked by IUPAC. There's actually quite a large errata page for that book already. With regards to an "Open" CIP -- I strongly suggest not going there. If you are seriously interested in this, join/form an IUPAC project. Bob On Sat, Apr 29, 2017 at 2:54 PM,

Re: [BlueObelisk-discuss] Jmol - CIP update

Thanks, again, John. That fix is checked in. I had forgotten to check for r and s at other than the root atom. That reminds me to say that the BB validation suite is missing a lot of good tests such as this one. So one really great contribution would be to create an open validation set that

Re: [BlueObelisk-discuss] Jmol - CIP update

* 5/17/16 Jmol 14.15.5. adds helicene M/P chirality; 959 lines * validated using CCDC * structures HEXHEL02 HEXHEL03 HEXHEL04 ODAGOS ODAHAF * http://pubs.rsc.org/en/content/articlehtml/2017/CP/C6CP07552E On Sat, May 13, 2017 at 11:43 PM, Robert Hanson <hans...@stolaf.edu> wrote: >

Re: [BlueObelisk-discuss] Proposed amendment to CIP Rule 1b

On Wed, May 17, 2017 at 2:20 PM, John Mayfield <john.wilkinson...@gmail.com> wrote: > > On 17 May 2017 at 18:01, Robert Hanson <hans...@stolaf.edu> wrote: > >> Oh, that is very cool. So you think this is a failure of Rule 4b in the >> IUPAC rules? Very impressive.

Re: [BlueObelisk-discuss] Jmol - CIP update

OK, final (?) report. Always a good sign when code simplifies. I've tightened up the algorithm, which passes all pertinent Chapter 9 tests, plus several more. After removing unnecessary code, Jmol's CIP implementation is now back to 970 lines, even with added (minimal) Kekule considerations and

[BlueObelisk-discuss] Proposed amendment to CIP Rule 1b

I'm interested in two things. First, feedback on a proposed amendment to CIP Rule 1b. Second, suggestions for how to officially propose this. Current Rule 1: *(1a) higher atomic number precedes lower;* *(1b) a duplicate atom node whose corresponding nonduplicated atom node is the root or

Re: [BlueObelisk-discuss] Jmol - CIP update

e at https://sourceforge.net/projects/jmol/files/Jmol/ A great challenge for April! Bob On Thu, Apr 27, 2017 at 12:21 AM, Robert Hanson <hans...@stolaf.edu> wrote: > Rule 5 is done. Fully validating using the first validation set that Mikko > sent me (86 compounds, roughly, some 2D/3D

Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

Great idea! ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss

[BlueObelisk-discuss] Fwd: case #CAS-843334-G6D6X8: PubChem Question - https://pubchem.ncbi.nlm.nih.g... TRACKING:000412000010244

: PubChem Question - https://pubchem.ncbi.nlm.nih.g... TRACKING:00041210244 To: Robert Hanson Hi, A follow up: This is an issue with the OEChem toolkit adopted by PubChem workflow to process chemical structures and to generate 3D coordinates. It has problems with allenic structures. The team

Re: [BlueObelisk-discuss] First BlueObelisk article now OpenAccess

yeah -- well, Happy New Year 2022! Seems I picked up and replied to a message from 2015!!! NO idea how that happened. On Mon, Jan 17, 2022 at 11:58 PM Egon Willighagen < egon.willigha...@gmail.com> wrote: > > > On Tue, 18 Jan 2022 at 06:53, Robert Hanson via Blueobelisk-discuss