Re: [Rdkit-discuss] Coot heading to Fedora

On 18/11/2016 18:35, Gianluca Sforna wrote: > I just wanted to mention that coot (crystallographic macromolecular > building toolkit)[1] is the first package (at least, that I know of) > requiring rdkit as a dependency under review [2] to enter Fedora > repositories. I've been cheering you on

Re: [Rdkit-discuss] Coot heading to Fedora

Hopefully you know that there is already a Cairo-based renderer in C++ and are modifying/improving that? Or does what is there "have so much room for improvement" that it's better to start over? -greg On Fri, Nov 18, 2016 at 3:05 PM +0100, "Paul Emsley" wrote:

Re: [Rdkit-discuss] Coot heading to Fedora

On 18/11/2016 23:47, Greg Landrum wrote: > Hopefully you know that there is already a Cairo-based renderer in C++ and are > modifying/improving that? Oh. Either I didn't know about that or I'd forgotten about it. My code was well under-way before I heard about David's contribution and I

Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

That's a really nice presentation. -P. On Fri, Nov 18, 2016 at 3:16 AM, Greg Landrum wrote: > This is a very big topic, and one where I would very much like to improve > the RDKit. John Mayfield gave a great talk on the issues (and some ideas > about fixing them based

Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

Le 18/11/2016 à 09:16, Greg Landrum a écrit : > Fixing the larger problems is a *lot* of work and not something that > is likely to happen quickly, but there is some low-hanging fruit (like > cutting crossed bonds) that I ought to be able to do something about.[1] > > -greg > [1] the trick is to

Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

This is a very big topic, and one where I would very much like to improve the RDKit. John Mayfield gave a great talk on the issues (and some ideas about fixing them based on his work with the CDK) at the UGM that some of you may find interesting 

Re: [Rdkit-discuss] GenerateDepictionMatching[23]DStructure (a bit off-topic)

As Greg says, this is a large area and somewhat of a diversion from my original intention. All I was asking for was a set of test cases so I can ensure that my port of the original Python code in AllChem.py to C++ behaves correctly. That seems like a sensible first step before embarking on

[Rdkit-discuss] Coot heading to Fedora

I just wanted to mention that coot (crystallographic macromolecular building toolkit)[1] is the first package (at least, that I know of) requiring rdkit as a dependency under review [2] to enter Fedora repositories. Regards G. [1] https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ [2]

Re: [Rdkit-discuss] uff atomic partial charge

Dear Rafal, the RDKit UFF implementation does not include an electrostatic term. Best regards, Paolo On 11/18/16 08:58, Rafal Roszak wrote: > Hi all, > > How can I get atomic partial charged used by UFF? In original paper is > stated that "Partial charges are obtained using the recently

[Rdkit-discuss] uff atomic partial charge

Hi all, How can I get atomic partial charged used by UFF? In original paper is stated that "Partial charges are obtained using the recently published QEq charge equilibration scheme" as described in http://pubs.acs.org/doi/pdf/10.1021/j100161a070. Is RDKit follow this scheme? Regards, Rafał