Re: [Open Babel] MACCS key 44

2015-02-27 Thread Geoffrey Hutchison
Looks like that might have been fixed.. the parser will throw an error on the dot but actually parses and matches it okay if component grouping is specified. The component grouping isn’t actually checked but the disconnected query matches as expected. Might take a closer look this weekend.

Re: [Open Babel] MACCS key 44

2014-10-21 Thread John May
166:('?',0), # Fragments FIX: this can't be done in SMARTS Note that 166 (*).(*)” or “([!#1]).([!#1]) could also be added (based on the suffixed comment). J On Oct 20, 2014, at 3:56 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I created pull request on github

Re: [Open Babel] MACCS key 44

2014-10-21 Thread Andrew Dalke
On Oct 21, 2014, at 1:13 PM, John May wrote: Note that 166 (*).(*)” or “([!#1]).([!#1]) could also be added (based on the suffixed comment). I don't recall the history of that one. According to an old email exchange I had with T J O'Donnell in 2008: #166 is OK as (*).(*) except for SMARTS

Re: [Open Babel] MACCS key 44

2014-10-21 Thread John May
That's all I know about that key definition. Likewise - I’ve seen in a few places but not aware if it’s truly correct. Extending OB SMARTS to handle component level grouping shouldn’t be too much work. The parser just needs to label the components of the pattern. The matcher can then check

Re: [Open Babel] MACCS key 44

2014-10-21 Thread Geoffrey Hutchison
Extending OB SMARTS to handle component level grouping shouldn’t be too much work. The parser just needs to label the components of the pattern. The matcher can then check this post match (same as stereochem is implemented) by labelling the connected components. Awesome. Let me know if

Re: [Open Babel] MACCS key 44

2014-10-21 Thread Craig James
On Tue, Oct 21, 2014 at 6:12 AM, John May john.wilkinson...@gmail.com wrote: That's all I know about that key definition. Likewise - I’ve seen in a few places but not aware if it’s truly correct. Extending OB SMARTS to handle component level grouping shouldn’t be too much work. The parser

Re: [Open Babel] MACCS key 44

2014-10-21 Thread John May
Thanks Craig, Looks like that might have been fixed.. the parser will throw an error on the dot but actually parses and matches it okay if component grouping is specified. The component grouping isn’t actually checked but the disconnected query matches as expected. Might take a closer look

[Open Babel] MACCS key 44

2014-10-20 Thread Andrew Dalke
Hi all, Open Babel's MACCS definitions derive from RDKit's. As such, it doesn't define key 44 because Greg didn't know what OTHER meant. You can see that in https://github.com/openbabel/openbabel/blob/master/data/MACCS.txt with 44:('?',0), # OTHER Since that time, Accelrys has published a

Re: [Open Babel] MACCS key 44

2014-10-20 Thread Maciek Wójcikowski
Hello Andrew, I created pull request on github [ https://github.com/openbabel/openbabel/pull/96] Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-10-20 15:14 GMT+02:00 Andrew Dalke da...@dalkescientific.com: Hi all, Open Babel's MACCS definitions derive

Re: [Open Babel] MACCS key 44

2014-10-20 Thread Geoffrey Hutchison
I created pull request on github [https://github.com/openbabel/openbabel/pull/96 https://github.com/openbabel/openbabel/pull/96] And it's merged. Thanks both to Andrew and Maciek. :-) -Geoff-- Comprehensive Server