t; web: https://hutchison.chem.pitt.edu/
>
> On Jan 12, 2021, at 4:42 PM, Craig James wrote:
>
> Dear colleagues and friends,
>
> I am officially retired from eMolecules as of December 31st.
>
> I would like to say thank you to everyone involved with the BlueObelisk
> pr
Dear colleagues and friends,
I am officially retired from eMolecules as of December 31st.
I would like to say thank you to everyone involved with the BlueObelisk
project, and particularly the OpenSMILES and IUPAC SMILES projects. It has
been a fun and rewarding collaboration. I really enjoy the
On Mon, Sep 2, 2019 at 6:01 AM Christoph Steinbeck <
christoph.steinb...@uni-jena.de> wrote:
>
> for teaching and documentation purposes, I would like to compile, with
> your help, a list of seminal papers in cheminformatics.
> It could be hosted on BlueOblisk.org and be a guidance for teaching
Expires tomorrow...
On Fri, Aug 25, 2017 at 4:15 PM, Craig James <cja...@emolecules.com> wrote:
> A while back I registered the domain name opencheminformatics.org,
> thinking it would host a broader category of open-source standards and
> documentation. I never used it, and the
A while back I registered the domain name opencheminformatics.org, thinking
it would host a broader category of open-source standards and
documentation. I never used it, and the domain is about to expire.
If anyone would like this domain, it is yours free for the asking, with the
proviso that it
I don't know if a web site qualifies as a paper...
www.opensmiles.org
Craig
On Wed, May 14, 2014 at 3:13 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
Hi all,
some weeks ago I started making an ImpactStory profile for the Blue
Obelisk. May service as back pocket material if you
On Thu, Sep 13, 2012 at 3:21 AM, Peter Murray-Rust pm...@cam.ac.uk wrote:
Has anyone compiled a set of UTF-8 codepoints (characters) that are
essential for chemistry specifically in Anglophone countries and aimed at
machine processing?
We've found via the school of hard knocks that only
Coincidentally, this was on SlashDot today:
Five leading Internet standards bodies have joined together to articulate
a set of guidelines for the creation of open standards that they
say will foster
continued innovation, competition and interoperability in the
Internet industry. ...
Andrew's explanation is exactly right and his citations are great.
The way I've heard it explained on a legal site uses the phone book,
the very case decided by the U.S. Supreme Court:
Merely collecting all phone numbers in a town, no matter how much
work, does not produce a copyrightable
On Mon, Aug 27, 2012 at 3:14 AM, Andrew Dalke da...@dalkescientific.com wrote:
I recently published the Structure Query Collection, at
https://bitbucket.org/dalke/sqc
This is a collection of different SMILES and SMARTS used as queries against a
small molecule database. I include the
Regarding a meet-up dinner in San Diego ... only four have indicated
they can make it, and now it turns out my mother is driving down from
Santa Cruz to spend the weekend and Monday with us. Would Tuesday
work out better for this event?
Craig
Hi Peter,
What to do? I really don’t know. I can think of the following:
* Go back to the IETF. Chance of success? 0.0001
Perhaps this history has been discussed before, but why is the outlook so
bleak? I would think the IETF's job is to encourage such contributions.
Craig
On 8/14/10 3:41 AM, Egon Willighagen wrote:
Hi all (and Peter's team in particular),
Converting PDF back into text is a somewhat tricky exercise, as words
can actually be characters rendered in approximately word format...
Strigi [0] does a decent but not perfect recovery of text... is there
On 7/30/10 9:48 AM, Peter Murray-Rust wrote:
I am forwarding the following open request from OpenEye through the
InChI-discuss list. Now that gthe details are clear I would be grateful
if the critical aspects could be re-reviewed.
There is an issue for me and a co-author and I'd like to know
On 7/7/10 8:20 AM, Geoffrey Hutchison wrote:
On Jul 7, 2010, at 10:48 AM, Konstantin Tokarev wrote:
LGPL requires not only availability of sources, but also possibility to
relink application with newer version of library. If static linking is used,
COMP will need to provide needed object
Something new that some of you might appreciate:
http://depict.emolecules.com/cgi-bin/mymol/depict.cgi?smiles=InChI%3D1S%2FC7H8N2%2Fc8-7%289%296-4-2-1-3-5-6%2Fh1-5H,%28H3,8,9%29width=400height=400colorscheme=cowformat=gifsubmit=image
Thanks to InChI support in OpenBabel, it was pretty simple to
Noel O'Boyle wrote:
Are some of the wedge/hash bonds in typical MOL files unrelated to
stereochemistry? That is, are some purely for depiction? If I knew
this for sure, I would not retain the wedge/hash bond designations in
the input but just work them out from the perceived stereo.
YES.
At last count, there are 38 replies to this thread.
My posting to BO and OB earnestly requesting help with the SMILES aromaticity
definition got ... zero replies on this forum, and one on OpenBabel, from Geoff.
Just pointing this out.
Open, closed, specification, standard ... it's all
Egon Willighagen wrote:
So, the arugment that was made on the Blue Obelisk Exchange is how
this is any different from MDL molfiles, Daylight SMILES, SMD (I'd
never heard about before)... has anyone ever attempted to contribute
to those standards (formally or informally), and been refused?
Christoph Steinbeck wrote:
this is great. The crowd is growing quickly. We are nine so far.
The updated list is at:
http://blueobelisk.sourceforge.net/wiki/Spring_ACS_Conference_in_San_Francisco
Add me to the list.
Craig James
Egon Willighagen wrote:
On Thu, Dec 10, 2009 at 5:01 PM, Craig James craig_ja...@emolecules.com
wrote:
If there are specific concerns about specific projects, then
I'm all for a hearty discussion. If we want to recommend
specific licenses as preferred for all OB projects, then
that's
Answering a number of comments from both BlueObelisk and OpenBabel forums,
regarding the proposal to formally define how to do comments to SMILES files.
To summarize my current opinion based on recent feedback:
1. A # character (not ';' or space) as the first character on a line
is
(Cross posted to OpenBabel-discuss and BlueObelisk-discuss)
A discussion has started in the OpenBabel list about comments in SMILES.
Currently, the SMILES spec has no provision for comments, but some
implementations allow them. For example, OpenBabel will silently ignore any
line that starts
Egon,
It was a lot of work to collect this data, and we spend a lot
of time and money keeping it very current.
Doesn't the latter not include 'creativity' ? Seriously, I have no
clue how creativity is defined legally, but looking at the music,
movies, etc, around, is mostly is just money
? OpenBabel's? Both?
3. How does the community handle membership in a group dedicated to creating
a document such as this? Is there a formal mechanism for creating some sort of
working group, or is it all ad-hoc?
Craig James
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