Re: [BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-03 Thread Noel O'Boyle
On 2 March 2010 11:23, Greg Landrum greg.land...@gmail.com wrote: Dear Noel, Thanks for the repost; this helps. My 2 cents are below. On Tue, Mar 2, 2010 at 11:34 AM, Noel O'Boyle baoille...@gmail.com wrote: On 2 March 2010 09:40, Peter Murray-Rust pm...@cam.ac.uk wrote: Thanks, This is

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-03 Thread Craig James
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.

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-03 Thread Greg Landrum
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] Stereochemistry in MDL files

2010-03-02 Thread Peter Murray-Rust
Thanks, This is a useful initiative On Tue, Mar 2, 2010 at 9:14 AM, Noel O'Boyle baoille...@gmail.com wrote: (Reposted from my blog following Greg's suggestion ) Hello all, Right now, I'm adding stereo (i.e. double bond stereochemistry, and chirality) to the MDL Mol format in OpenBabel.

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-02 Thread Noel O'Boyle
On 2 March 2010 09:40, Peter Murray-Rust pm...@cam.ac.uk wrote: Thanks, This is a useful initiative On Tue, Mar 2, 2010 at 9:14 AM, Noel O'Boyle baoille...@gmail.com wrote: (Reposted from my blog following Greg's suggestion ) Hello all, Right now, I'm adding stereo (i.e. double bond

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-02 Thread Noel O'Boyle
On 2 March 2010 11:23, Greg Landrum greg.land...@gmail.com wrote: Dear Noel, Thanks for the repost; this helps. My 2 cents are below. On Tue, Mar 2, 2010 at 11:34 AM, Noel O'Boyle baoille...@gmail.com wrote: On 2 March 2010 09:40, Peter Murray-Rust pm...@cam.ac.uk wrote: Thanks, This is