[BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-02 Thread Noel O'Boyle
(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. There are three places where stereochemical information can be stored in these files: the coordinates, the atom parity

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 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. There are three p

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

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

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-02 Thread Greg Landrum
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 wrote: > On 2 March 2010 09:40, Peter Murray-Rust wrote: >> Thanks, >> This is a useful initiative >> >> On Tue, Mar 2, 2010 at 9:14 AM, Noel O'Boyle wrote: >>> >>> (Reposted from

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-02 Thread Noel O'Boyle
On 2 March 2010 11:23, Greg Landrum 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 wrote: >> On 2 March 2010 09:40, Peter Murray-Rust wrote: >>> Thanks, >>> This is a useful initiative >>> >>> On Tue, Mar 2,

Re: [BlueObelisk-discuss] Stereochemistry in MDL files

2010-03-02 Thread Geoffrey Hutchison
On Mar 2, 2010, at 6:46 AM, Noel O'Boyle wrote: >> nasty stuff... better to avoid stereochem in 0D files. > > That's great Greg - you've obviously a lot of experience with this. > Will do as you suggest across the board. At least we will have two > toolkits behaving the same. I'll write up the s