Re: [BlueObelisk-discuss] Structure database that can be queried by SPARQL?

ase to look at? Neo4j can export in RDF format. > Do you have a paper or tech report? > On 12/3/2020 8:35 AM, Greg Landrum wrote: > > Not quite what you're asking for, but: if you're willing to use neo4j to > store the graph (which rules out SPARQL I guess) you can use the RDKit >

Re: [BlueObelisk-discuss] Structure database that can be queried by SPARQL?

Not quite what you're asking for, but: if you're willing to use neo4j to store the graph (which rules out SPARQL I guess) you can use the RDKit neo4j plugin: https://github.com/rdkit/neo4j-rdkit That gets you efficient substructure search and similarity search. -greg On Tue, Dec 1, 2020 at 4:04

Re: [BlueObelisk-discuss] Software for ligands

On Fri, Aug 19, 2016 at 9:36 AM, Peter Murray-Rust wrote: > > On Thu, Aug 18, 2016 at 7:51 PM, Geoffrey Hutchison > wrote: > >> > I have suggested that there are Open tools that they may not yet have >> discovered. They have needs for (at least): >> > * 2-D

Re: [BlueObelisk-discuss] Software for ligands

Orca does indeed look interesting. For those who care about such things, however, orca is unfortunately not open-source. It falls into the category that Pirhadi et al. refer to as "source-available" licenses: https://orcaforum.cec.mpg.de/license.html -greg On Thu, Aug 18, 2016 at 2:38 PM, jay

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

I can probably help with that Egon, at least as far as the RDKit bit is concerned. On Tuesday, 1 March 2016, Egon Willighagen wrote: > Geoff, > > thanks for the suggestions. I need to look at the HTML code that uses > $foo.js and create an SVG image... emscripting

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

On Thu, Aug 18, 2011 at 10:32 AM, Noel O'Boyle baoille...@gmail.com wrote: Hi all, I'll be attending the database meeting organising by the NCI on Aug 25-26, and arriving on the afternoon of the 24th. Anyone interested in meeting up for dinner? My flight gets in at 6pm on the 24th, so I

[BlueObelisk-discuss] question: rules for absolute stereochemistry labels of chiral phosphates

Hi, I've spent a while beating my head against this without much success, so I figured I'd ask around. The attached mol file contains a chiral phosphorus center; I'm trying to figure out whether the label for that center should be R or S. My usual approach to this is to draw the thing in Marvin

Re: [BlueObelisk-discuss] question: rules for absolute stereochemistry labels of chiral phosphates

Dear Wolf, On Sat, Jul 23, 2011 at 10:50 PM, Wolf Ihlenfeldt w...@xemistry.com wrote: Ghost atoms for stereo resolution are only added starting after the first expanded shell, when a multi-bond to a new ligand is traversed, i.e. the first time in the 2nd sphere. Adding ghost atoms directly 

Re: [BlueObelisk-discuss] Open Quantum Mechanics codes?

On Wed, Mar 31, 2010 at 9:42 AM, Peter Murray-Rust pm...@cam.ac.uk wrote: I do not agree that understanding compilers is necessary for understanding compchem :-) This is certainly true. However, I don't think it's unreasonable to expect users of open-source software to either understand

Re: [BlueObelisk-discuss] Where to meet for the Blue Obelisk Dinner in SF?

On Mon, Mar 8, 2010 at 7:16 PM, Moses Hohman mo...@collaborativedrug.com wrote: Ha! : ) If we're looking for Italian around Moscone, the locals (from Collaborative Drug Discovery, Inc.) recommend La Briciola at 3rd and Bryant. Apparently they're very nice and the food's great. We've done group

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

On Wed, Mar 3, 2010 at 4:00 PM, Noel O'Boyle baoille...@gmail.com wrote: On 3 March 2010 14:48, Craig James craig_ja...@emolecules.com wrote: 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

Re: [BlueObelisk-discuss] Dinner at upcoming ACS SF meeting

I will also be in SF for the ACS and would really enjoy meeting everyone face to face. Monday night sounds great. Best regards, -greg -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online

Re: [Blueobelisk-discuss] SourceForge problems

On Mon, Aug 17, 2009 at 1:31 PM, Noel O'Boylebaoille...@gmail.com wrote: Hello all, When I access http://sf.net without logging in (in Firefox 3.0 or IE on WinXP), it's fine. However, if I log into SourceForge, I get Error 500. This is new for me. Can anyone check whether they have the same

Re: [Blueobelisk-discuss] BO dinner places

Hi Rajarshi, I think I missed the post where the date of the dinner was announced. Can you please re-post? Thanks, -greg On Mon, Aug 3, 2009 at 2:17 AM, Rajarshi Guharajarshi.g...@gmail.com wrote: Hi, for those planning to attend the BO dinner in DC, here are four possible places around the

Re: [Blueobelisk-discuss] BO dinner in DC?

On Tue, Jul 21, 2009 at 2:25 PM, Rajarshi Guharajarshi.g...@gmail.com wrote: Hi, looks like the time for another BO dinner is coming up. Does anybody have any recommendations/suggestions for a meeting spot? And who'll be there? I will be there. -greg