Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

[continuing to dig out from the email pile] On Mon, Jan 15, 2018 at 4:20 PM, Jason Biggs wrote: > >- I've had this on my to-do list for a few months now, implementing >the algorithm described in this paper. I think the force-field energy >minimization

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

+1 to the MolVS project as well. cheers marco 2018-01-16 18:19 GMT+01:00 JP : > Joining the fray, +1 for MolVS > > On 16 January 2018 at 16:00, Brian Cole wrote: > >> +1 to the MolVS project as well. >> >> Perhaps an easy bite-size project is to

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

(Tim Dudgeon) >> >> >> ------------------ >> >> Message: 1 >> Date: Mon, 15 Jan 2018 09:20:48 -0600 >> From: Jason Biggs <jasondbi...@gmail.com> >> To: Greg Landrum <greg.land...@gmail.com> >> Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net> >> Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018 >> Message-ID: >>

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

- > > Message: 1 > Date: Mon, 15 Jan 2018 09:20:48 -0600 > From: Jason Biggs <jasondbi...@gmail.com> > To: Greg Landrum <greg.land...@gmail.com> > Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net> > Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018 > Message-ID: >

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

+1 for Symmetrizer too, A must! De : Michal Krompiec Date : jeudi, 18 janvier 2018 à 08:18 À : Jason Biggs Cc : RDKit Discuss, Greg Landrum Objet : Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018 +1 vote for Symmetrizer. It would be very useful for preparing input for computational

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

+1 vote for Symmetrizer. It would be very useful for preparing input for computational chemistry codes. Best, Michal Krompiec Merck KGaA On Mon, 15 Jan 2018 at 15:21, Jason Biggs wrote: > >- I've had this on my to-do list for a few months now, implementing >the

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

I’d be happy to help with a MolVS-inspired standardization project. Another possible starting point is the mysterious StructChecker already within RDKit... Matt On 16 January 2018 at 18:04:24, George Papadatos (gpapada...@gmail.com) wrote: Same here. I would also add the standardisation work

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

Same here. I would also add the standardisation work done by Francis Atkinson at the EBI as an additional starting point. George. Sent from my giPhone > On 16 Jan 2018, at 17:19, JP wrote: > > Joining the fray, +1 for MolVS > >> On 16 January 2018 at 16:00,

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

Joining the fray, +1 for MolVS On 16 January 2018 at 16:00, Brian Cole wrote: > +1 to the MolVS project as well. > > Perhaps an easy bite-size project is to incorporate the open source mae > parser code into core RDKit: https://github.com/schrodinger/maeparser > > > On Mon,

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

+1 to the MolVS project as well. Perhaps an easy bite-size project is to incorporate the open source mae parser code into core RDKit: https://github.com/schrodinger/maeparser On Mon, Jan 15, 2018 at 9:08 PM, Francois BERENGER < beren...@bioreg.kyushu-u.ac.jp> wrote: > On 01/16/2018 05:51 AM,

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

On 01/16/2018 06:43 AM, Dimitri Maziuk wrote: > On 01/15/2018 02:43 PM, Tim Dudgeon wrote: > >> Could there be something in a more general project to bridge the >> compound (mol/smiles), sequence (protein/nucleotide seq + alignments) >> and structure (pdb/mmcif/mmtf) worlds? > > FWIW PDB builds

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

On 01/16/2018 05:51 AM, Tim Dudgeon wrote: > Incorporating and "industrialising" Matt's MolVS tautomer and > standardizer code? > http://molvs.readthedocs.io/en/latest/index.html If we can vote, I would vote for this one. > On 15/01/18 07:09, Greg Landrum wrote: >> Dear all, >> >> We've been

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

On 01/15/2018 02:43 PM, Tim Dudgeon wrote: > Could there be something in a more general project to bridge the > compound (mol/smiles), sequence (protein/nucleotide seq + alignments) > and structure (pdb/mmcif/mmtf) worlds? FWIW PDB builds everything up from structure because they can derive

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

Incorporating and "industrialising" Matt's MolVS tautomer and standardizer code? http://molvs.readthedocs.io/en/latest/index.html On 15/01/18 07:09, Greg Landrum wrote: Dear all, We've been invited again to participate in the OpenChemistry application for Google Summer of Code. In order

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

Agreed. Good support for reading and writing mol2 format would indeed be useful. But not convinced this alone is sexy enough for GSoC. Could there be something in a more general project to bridge the compound (mol/smiles), sequence (protein/nucleotide seq + alignments) and structure

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

- I've had this on my to-do list for a few months now, implementing the algorithm described in this paper. I think the force-field energy minimization routines already present in the RDKit can be utilized for this pretty easily. The only part that I don't think is set up already

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

On Mon, Jan 15, 2018 at 9:50 AM, Francois BERENGER < beren...@bioreg.kyushu-u.ac.jp> wrote: > Supporting mol2 files as input would be nice. > Do you mean as output? You can already (in a limited way) read them. -greg There is already some code out there, people have worked on it and > several

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

Supporting mol2 files as input would be nice. There is already some code out there, people have worked on it and several people would like to have the feature... On 01/15/2018 04:09 PM, Greg Landrum wrote: > Dear all, > > We've been invited again to participate in the OpenChemistry application

Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

Dear RDKitters, here is a project idea for GSoC 2018 (actually brought up by Greg during the Hackathon of RDKitUGM2016): Project: RDKit lite Brief explanation: Create a minimal version of the RDKit that only contains basic functionality (like MolFrom/ToSmiles and substructure search

[Rdkit-discuss] RDKit and Google Summer of Code 2018

Dear all, We've been invited again to participate in the OpenChemistry application for Google Summer of Code. In order to participate we need ideas for projects and mentors to go along with them. The current list of RDKit ideas is being maintained here: