Wikipedia:WikiProject Chemistry/IRC discussions/24 June 2008

--- Log opened Tue Jun 24 11:52:53 EDT 2008

11:53 -!- dmacks_ [n=dmacks@pdpc/supporter/active/dmacks] has left #wikichem []

11:55 -!- ChemSpiderman [n=tony@c-68-33-211-217.hsd1.md.comcast.net] has joined #wikichem

12:00 -!- walkerma [n=chatzill@admin-151-108.potsdam.edu] has joined #wikichem

12:01 &lt;walkerma&gt; Hi there! Rifleman sent me an email; he's on his way, but he'll probably be late

12:01 &lt;+dmacks&gt; Hello all!

12:01 &lt;ChemSpiderman&gt; hi

12:02 &lt;walkerma&gt; Beetstra: Are you around?

12:03 &lt;walkerma&gt; OK, maybe we should start - did you see Wikipedia_talk:WikiProject_Chemicals ?

12:03 &lt;walkerma&gt; http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemicals#Chemical_data_in_chemboxes

12:04 &lt;+dmacks&gt; Yup. Commented there yestreday

12:04 &lt;ChemSpiderman&gt; no...looking now...been traveling

12:04 &lt;+dmacks&gt; I played with some more ideas on Sulfanilic acid/Collapsible

12:06 &lt;walkerma&gt; Wow, that looks great!

12:07 &lt;+dmacks&gt; (there are two different ways both on that same page, but they use the same trick)

12:07 &lt;+Beetstra&gt; Hi all ..

12:07 &lt;+Beetstra&gt; Yes walkerma, I am here .. but not too long

12:07 &lt;+Beetstra&gt; Just back from a trip .. so not too active

12:07 &lt;walkerma&gt; Could you take a look at http://en.wikipedia.org/wiki/Sulfanilic_acid/Collapsible

12:08 &lt;walkerma&gt; Could that work with ChemBoxNew?

12:08 &lt;+dmacks&gt; This is purely a layout trick, so it's orthogonal to having the data in a secondary page.

12:08 &lt;ChemSpiderman&gt; I like it..

12:08 &lt;ChemSpiderman&gt; good for long InChIs, names etc

12:08 &lt;walkerma&gt; Yes, but it;s the layout trick that has eluded us for many months!

12:09 &lt;ChemSpiderman&gt; much nicer than squeezing into a narrow box

12:09 &lt;walkerma&gt; If Google et al can find InChIs etc on there, this may obviate the need for having secondary pages at all?

12:09 &lt;+dmacks&gt; NB, I can't take full credit for the idea, someone else mentioned something like it somewhere (I can't remember any of the details...was about a navbox for some bio topic IIRC)

12:09 &lt;+dmacks&gt; Yes.

12:11 &lt;+dmacks&gt; chemboxbew could have that built into certain fields (it's currently stuffed into the field-value itself, so easy to move it into "what uses that value")

12:11 &lt;walkerma&gt; So we could have the data on the article page, and have a bot watching all of those pages with validated data, is that right?

12:11 &lt;ChemSpiderman&gt; same comment as usual about p,bp etc...should be one number but choose the units to display and calculate on the fly

12:11 &lt;+dmacks&gt; Yes.

12:11 &lt;walkerma&gt; Yes ChemSpiderman: PeterMR would love that!

12:12 &lt;+Beetstra&gt; That collapsible thing .. hmm .. probably

12:12 &lt;+Beetstra&gt; I don't like secondary pages .. unclear what to edit for editors

12:13 &lt;+Beetstra&gt; And as long as you know what to parse, the chemboxes are nicely parseable

12:13 &lt;+Beetstra&gt; (if you parse the raw data, not the page you see)

12:14 -!- Rifleman_82 [n=blahblah@wikipedia/Rifleman-82] has joined #wikichem

12:14 -!- mode/#wikichem [+v Rifleman_82] by ChanServ

12:14 &lt;+Rifleman_82&gt; hi all

12:14 &lt;+Rifleman_82&gt; sorry i'm late

12:14 &lt;+dmacks&gt; hiya Rifleman_82

12:14 &lt;+Rifleman_82&gt; had to shop for groceries...

12:14 &lt;+Rifleman_82&gt; hey dmacks

12:14 &lt;+Rifleman_82&gt; did i miss much?

12:15 &lt;walkerma&gt; Take a look at http://en.wikipedia.org/wiki/Sulfanilic_acid/Collapsible

12:15 &lt;+Beetstra&gt; We could just do that with Template:Chembox_InChI

12:15 &lt;+Beetstra&gt; no problem

12:15 &lt;+Beetstra&gt; anyone can edit that template .. so

12:15 &lt;+dmacks&gt; Beetstra: if we go collapsible, the remaining advantages of seoncadry-pages are as I replied to Itub.

12:16 &lt;walkerma&gt; http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemicals#Chemical_data_in_chemboxes

12:16 &lt;+Rifleman_82&gt; inchi?

12:16 &lt;+Rifleman_82&gt; very nice

12:16 &lt;+Rifleman_82&gt; :)

12:17 &lt;+dmacks&gt; Unfortunately there's no clean way to have the whole Identifiers section be collapsible without screwing up the table-columns.

12:17 &lt;+Beetstra&gt; http://en.wikipedia.org/wiki/Template:Chembox_InChI

12:18 &lt;+Beetstra&gt; refresh, changed something

12:19 &lt;+Rifleman_82&gt; can we do that for smiles?

12:19 &lt;+Rifleman_82&gt; what did you change?

12:22 &lt;+dmacks&gt; I confess to not-understanding most of the chembox internals at all.

12:23 &lt;+Beetstra&gt; I did not change the template, see the template text ..

12:23 &lt;+dmacks&gt; (esp value2 vs value3, in the case at hand).

12:23 &lt;+dmacks&gt; Here's what is proposed: http://en.wikipedia.org/w/index.php?title=Template:Chembox_InChI/new&diff=221459502&oldid=221459410

12:24 &lt;+Beetstra&gt; Yep

12:24 &lt;+Beetstra&gt; Lets try?

12:24 &lt;+dmacks&gt; Sure.

12:24 &lt;+Beetstra&gt; .. "Our servers are currently experiencing a technical problem. This is probably temporary and should be fixed soon. Please try again in a few minutes."

12:25 &lt;+dmacks&gt; If we want to spread this game into SMILES and others, could move the collapse-formatting into a wrapper

12:25 &lt;+Beetstra&gt; seems fine

12:25 &lt;+Beetstra&gt; http://en.wikipedia.org/wiki/Benzoic_acid

12:26 &lt;+Beetstra&gt; Please check a handful of pages

12:26 &lt;+Beetstra&gt; You may have to press edit on each page to see the new InChI

12:26 &lt;+Beetstra&gt; (template updating on the server is sometimes slow)

12:26 &lt;+Rifleman_82&gt; what's that really ugly one?

12:26 &lt;+Rifleman_82&gt; the one where the InChI spans the entire 600 or so pixels across the page?

12:28 &lt;walkerma&gt; http://en.wikipedia.org/wiki/Beta-hydroxybutyryl-CoA ?

12:29 &lt;+Rifleman_82&gt; hmm this one uses inchikey

12:29 &lt;+Rifleman_82&gt; since you bring it up

12:30 &lt;+Rifleman_82&gt; should we be migrating those complex peptides (perhaps more than 10 peptide bonds) to Template:Protein?

12:30 &lt;walkerma&gt; Rifleman_82: Maybe, but that's for another discussion, I think

12:31 &lt;+Rifleman_82&gt; hmm... PhNH2, -CHO, -COCl, salicylic acid & dioxane all don't have inchis

12:31 &lt;+Beetstra&gt; I put inchi in Beta hydroxycoa

12:32 &lt;+Rifleman_82&gt; http://en.wikipedia.org/w/index.php?title=Beta-hydroxybutyryl-CoA&action=edit

12:32 &lt;+Rifleman_82&gt; nope no inchi

12:33 &lt;+Beetstra&gt; right .. my mistake ..

12:34 &lt;+Beetstra&gt; now there is

12:35 &lt;+Beetstra&gt; I think this is a wonderful solution

12:35 &lt;+dmacks&gt; exists, but I'm completely lost in the  internals to do it:(

12:36 &lt;walkerma&gt; Looks great! Beetstra: Is this now enabled for all articles with chemboxes?

12:36 &lt;+Rifleman_82&gt; hmmm

12:36 &lt;+Beetstra&gt; Yep

12:36 &lt;+Rifleman_82&gt; there's a problem with coA

12:37 &lt;+Beetstra&gt; dmacks, we can just use the Collapsible list

12:37 &lt;+Beetstra&gt; we don't need a template around the template

12:37 &lt;+Rifleman_82&gt; i can't view the entire inchi

12:37 &lt;+Rifleman_82&gt; it's longer than the width of my screen

12:37 &lt;+Rifleman_82&gt; but i can't scroll horizontally using firefox

12:37 &lt;+Rifleman_82&gt; lemme try using IE

12:38 &lt;+Rifleman_82&gt; problem as in, what's the point of including it if you can't display it in a meaningful/useful way

12:38 &lt;+Beetstra&gt; Opera is fine

12:38 &lt;+dmacks&gt; Ooh, I see same thing Rifleman_82

12:38 &lt;ChemSpiderman&gt; looks fine for me in FF but I am at high resolution settings

12:38 &lt;+Rifleman_82&gt; oh? with IE it breaks automatically

12:39 &lt;+Beetstra&gt; Opera changes the size of the box, but breaks it here and there to a reasonable width

12:39 &lt;ChemSpiderman&gt; We have similar issues with FF and ChemSPider and Long InCHIs

12:39 &lt;ChemSpiderman&gt; it's been a nightmare...haven't found a solution yet

12:39 &lt;+Beetstra&gt; FF problem ..

12:39 &lt;ChemSpiderman&gt; introduces breaks

12:39 &lt;+Rifleman_82&gt; hmmm

12:39 &lt;+dmacks&gt; It's a Chembox layout issue of some sort. The box can spread wider than the screen but it's "wider than the screen" not "making the page wider", so no horizontal scrollbar in the browser.

12:39 &lt;+Rifleman_82&gt; is it easier to lobby firefox to fix it, than to fix it on our end?

12:40 &lt;+Rifleman_82&gt; haha

12:40 &lt;ChemSpiderman&gt; I'm on v3 and not seeing the issue in Wikipedia so maybe they fixed it

12:40 &lt;+Beetstra&gt; Just revert my edits to the template:chembox_inchi if needed .. we tried it now .. we know it works almost

12:40 &lt;+dmacks&gt; I'm on 2.x and do see the non-scrolliness.

12:41 &lt;walkerma&gt; The fact is, displaying the InChI that long in any format will present problems, but fortunately it must be <1% of our pages that cause this, surely?

12:41 &lt;+Rifleman_82&gt; ok let me install v3

12:41 &lt;+dmacks&gt; (lots of non-WP pages that do scary-CSS layout have the same problem though)

12:42 &lt;walkerma&gt; And if it's fixed in v3, and OK in IE, then I think we shouldn't worry. This collapsible form otherwise looks like a great step forward to me.

12:43 &lt;+Beetstra&gt; I would say .. there are a few pages which are a problem now, and this works on quite some browsers apparently

12:43 &lt;+Beetstra&gt; So if this is <1% of pages on 1 out of 10 browsers .. then it is OK

12:43 &lt;+Beetstra&gt; We need some mac-testing/linux testing

12:43 * Beetstra has to leave soon

12:44 &lt;walkerma&gt; Beetstra: Does that mean we can just have a bot patrol the "collapsible" list and watch for changes to that, in order to protect our validated data?

12:44 &lt;+Rifleman_82&gt; i can test with mac

12:44 &lt;+Rifleman_82&gt; hang on

12:44 &lt;+dmacks&gt; I'm using an x11 build of ffox on Mac, will try the "normal" Mac ffox2 and safari in a moment.

12:44 &lt;+dmacks&gt; Okay, /me leaves it to Rifleman_82

12:45 &lt;+Rifleman_82&gt; no horizontal scrollbars on ff2

12:45 &lt;+Beetstra&gt; Yes, I think we could do that

12:45 &lt;+Rifleman_82&gt; hang on for safari & IE

12:45 &lt;+dmacks&gt; So x11 vs aqua is not the determining factor.

12:45 &lt;+Rifleman_82&gt; what's that?

12:45 &lt;+Rifleman_82&gt; breaks nicely on safari

12:46 &lt;+Beetstra&gt; Someone able to run a bot on this?

12:46 &lt;+dmacks&gt; "x11" is the unixish GUI system, cross-platform to linux and friends, "aqua" is the native OS X GUI.

12:46 &lt;+Beetstra&gt; hmm .. could build it into chemobot, actually

12:46 &lt;+Rifleman_82&gt; it seems that IE mac doesn't show the inchi *at all*

12:46 &lt;+Beetstra&gt; but that would need time .. which I do not have

12:46 &lt;+Rifleman_82&gt; what do you need, a find and replace ?

12:46 &lt;+Beetstra&gt; No, monitoring changes to chemical pages

12:47 &lt;+Rifleman_82&gt; like your irc based bot?

12:47 &lt;+Beetstra&gt; Like CheMoBot does now for some on it's 'watchlist'

12:47 &lt;+Beetstra&gt; Yes

12:47 &lt;+Rifleman_82&gt; ok

12:47 &lt;+Rifleman_82&gt; oh, it IS your IRC bot

12:47 &lt;+Beetstra&gt; Reporting here ..

12:47 &lt;+Beetstra&gt; Heh

12:47 &lt;+Beetstra&gt; When someone changes something inside a chembox new

12:47 &lt;+Rifleman_82&gt; hmm...

12:47 &lt;+Beetstra&gt; Is not too difficult

12:48 &lt;+Beetstra&gt; well .. doable .. :-)

12:48 &lt;+Rifleman_82&gt; so ... are we sticking with chembox within the article?

12:48 &lt;+Beetstra&gt; It does not have to exclude the other option

12:48 &lt;+dmacks&gt; Rifleman_82: a list of those that have would be useful, but need manual checking. Some have the full non-breaking string also in there.

12:48 &lt;+Rifleman_82&gt; if someone can code for awb, i can run it and do manual checking

12:48 &lt;+Rifleman_82&gt; single purpose this time though

12:49 &lt;+dmacks&gt; (Well, it's commented-out, but it should still be removed)

12:49 * dmacks knows zilch AWB.

12:49 * Beetstra hides

12:49 &lt;+Rifleman_82&gt; haha

12:49 &lt;+Rifleman_82&gt; dirk was the expert for the last project

12:49 &lt;+Rifleman_82&gt; fixing chembox --> chembox new

12:49 &lt;+Rifleman_82&gt; but if you're busy, we all understand

12:50 &lt;+dmacks&gt; Shame this "dirk" fellow isn't here and we only have "Beetstra" :)

12:50 &lt;walkerma&gt; We just need to find a grant to PAY him to do it!

12:50 &lt;+Beetstra&gt; hehe

12:50 &lt;+Rifleman_82&gt; heh

12:50 &lt;+Rifleman_82&gt; maybe some of that IUPAC money

12:50 &lt;+Rifleman_82&gt; actually

12:51 &lt;+Beetstra&gt; Do we want the same for SMILES?

12:51 &lt;+Rifleman_82&gt; if only IUPAC had a registry of physical properties...

12:52 &lt;+Rifleman_82&gt; i used to tell my students that MSDS's are NOT authoritative sources

12:52 &lt;+Rifleman_82&gt; for physical data, etc

12:53 &lt;walkerma&gt; Beetstra: Good question> I'd say yes. Simple ones don't cause a problem, but even alpha-pinene has it broken

12:53 &lt;walkerma&gt; http://en.wikipedia.org/wiki/Alpha-Pinene

12:53 &lt;+Rifleman_82&gt; haha

12:53 &lt;+Rifleman_82&gt; side issue

12:53 &lt;+Rifleman_82&gt; articles like this

12:53 &lt;+Rifleman_82&gt; i can understand we don't like having greek letters in the article title

12:53 &lt;+Rifleman_82&gt; do we prefer alpha-Pinene? or &alpha;-Pinene?

12:54 &lt;+Rifleman_82&gt; but it's really a small issue at thisp oint

12:54 &lt;+Rifleman_82&gt; what's not working?

12:55 &lt;walkerma&gt; Look at the SMILES - it is on two lines in my browser (Firefox 2.x)

12:55 &lt;+dmacks&gt; (I'd go with the greek-letter for the real article)

12:55 &lt;+Rifleman_82&gt; i removed teh line break

12:55 &lt;walkerma&gt; That makes it unfindable in a Google search

12:55 &lt;+Rifleman_82&gt; just

12:56 &lt;+Rifleman_82&gt; the line breaks?

12:57 &lt;walkerma&gt; Yes, I think line breaks do that. My point is: alpha-Pinene is not a complex molecule, yet even there an unbroken SMILES causes the chembox to widen a bit.

12:57 &lt;+Beetstra&gt; I think that I did the SMILES as well

12:58 * Beetstra goes

12:59 &lt;+Rifleman_82&gt; see ya dirk

12:59 &lt;+Rifleman_82&gt; thanks :)

12:59 &lt;+dmacks&gt; Is there a #length or similar function that tells the size (either in chars or pixels) of a string?

12:59 &lt;+Rifleman_82&gt; i'm using FF3 and the inchi doesn't look right

12:59 &lt;+Rifleman_82&gt; it breaks now, but it still fills the page width

13:00 -!- Beetstra [n=djbeetst@Wikimedia/Beetstra] has quit ["Bye Bye"]

13:00 &lt;walkerma&gt; Thanks DIrk!

13:00 &lt;walkerma&gt; A bigger one is at http://en.wikipedia.org/wiki/24-Ethyl_coprostanol

13:00 &lt;walkerma&gt; This looks much better with the hide feature

13:01 &lt;+Rifleman_82&gt; how many characters does it break ?

13:02 &lt;+Rifleman_82&gt; aesthetically it's not quite there yet :(

13:02 &lt;+Rifleman_82&gt; can we use a fixed width font?

13:02 &lt;+Rifleman_82&gt; or embed a &lt;tt&gt;?

13:02 &lt;walkerma&gt; dmacks: A #length parameter would make it very elegant, as long as it doesn't get horribly complicated!

13:03 &lt;walkerma&gt; Rifleman_82: What is &lt;tt&gt; ?

13:03 &lt;+Rifleman_82&gt; if you have variable width font...

13:03 &lt;+Rifleman_82&gt; typewriter font

13:03 &lt;+dmacks&gt; Right. /me was thinking "if longer than SOMETHING, use the hide trick, else just display it", for InChI, SMILES, etc.

13:03 &lt;+Rifleman_82&gt; it's an html tag

13:03 &lt;walkerma&gt; dmacks: Yes, that would be great if straightforward

13:03 &lt;+Rifleman_82&gt; http://www.htmlcodetutorial.com/_TT.html

13:06 &lt;+dmacks&gt; Looks like &lt;code&gt;...&lt;/code&gt; is a WP-standard tag.

13:10 &lt;walkerma&gt; dmacks: Would you be able to explore that further? If it's a problem, perhaps the fixed width font could help?

13:10 &lt;+dmacks&gt; Sure

13:10 &lt;+Rifleman_82&gt; let me try the TT

13:11 &lt;walkerma&gt; Since time is ticking on, I'm guessing we'll have to break up soon. While Rifleman_82 tests the TT, I wanted to try and conclude some things.

13:12 &lt;+dmacks&gt; #len exists in MediaWiki but is not installed on Wikimedia public projects:(

13:12 &lt;walkerma&gt; It seems that we HAVE a solution (finally!) to the display problem. Thanks dmacks! We still have some things up in the air regarding how we STORE validated data, but perhaps we can discuss that further on-wiki etc?

13:13 &lt;+dmacks&gt; Concurred

13:13 &lt;+Rifleman_82&gt; my tweak to smiles doesn't seem to have damaged anything http://en.wikipedia.org/wiki/Benzoic_acid?action=purge

13:13 &lt;+Rifleman_82&gt; when you're free

13:14 &lt;+Rifleman_82&gt; you guys can take a look at something else... if it's broken please revert

13:15 &lt;walkerma&gt; Looks OK to me, as long as Google can still find it OK

13:15 &lt;+dmacks&gt; looks fine to me too.

13:16 &lt;+dmacks&gt; (google doesn't care about fonts:)

13:16 &lt;walkerma&gt; Rifleman_82: Should we close now? ChemSpiderman?

13:16 &lt;+Rifleman_82&gt; yup

13:16 &lt;ChemSpiderman&gt; nothing from me really...I was hoping we would discuss the comilation of the DB some..

13:16 &lt;ChemSpiderman&gt; but are out of time

13:16 &lt;+Rifleman_82&gt; perhaps we can put that on the agenda for the next mtg

13:16 &lt;ChemSpiderman&gt; ajmaline is waiting for all on this list to respond to...old email discussion

13:17 &lt;walkerma&gt; Sure

13:17 &lt;walkerma&gt; Thanks all!

13:17 &lt;ChemSpiderman&gt; bye

13:18 -!- ChemSpiderman [n=tony@c-68-33-211-217.hsd1.md.comcast.net] has quit []

13:18 * dmacks closes log

--- Log closed Tue Jun 24 13:18:51 EDT 2008