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

2018-02-07 Thread Greg Landrum 
[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 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 would be
>applying a constant force to all atoms to force them into the xy plane.
>
> Frączek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical
> Structure Diagram Generation of Complex Molecules and Ligand–Protein
> Interactions." J. Chem. Inf. Model. 2016, 56, 2320-2335, DOI:
> 10.1021/acs.jcim.6b00391.
>
>
Forcing things into the xy plane is pretty simple: you just need to add a
force that tries to drive the z coordinate to zero. The embedding code
already does something analogous when you embed chiral molecules: those are
initially embedded in 4D and then refined by adding a forcefield term that
drives the fourth coordinate to zero.
Here's the bit of code that adds that term:
https://github.com/rdkit/rdkit/blob/master/Code/DistGeom/DistGeomUtils.cpp#L230


-greg


>- Another idea would be to add in point-group symmetry detection.  I'm
>using the Symmetrizer java library, described here
>https://www.ncbi.nlm.nih.gov/pubmed/22549414
>, and pretty happy with
>it overall.  One could re-implement it in C++, or include the jar in the
>External folder and write python wrappers.
>
>
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-02-07 Thread Marco Stenta 
 +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 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, 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 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:
>>> >> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>>> >>
>>> >> (Note: at the point that I'm pressing "send", that's still a copy of
>>> >> last year's project ideas).
>>> >>
>>> >> If you're willing to be a mentor (please ask me about the ~5
>>> >> hours/week required here) or have ideas, please reply to this thread.
>>> >>
>>> >> Best,
>>> >> -greg
>>> >>
>>> >>
>>> >> 
>>> --
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>>> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-02-07 Thread Greg Landrum 
A quick one on this as part of me digging out from the pile of email I
should have replied to.

Cameron's suggestion is a really good one, but unfortunately GSoC is really
about coding projects, so it doesn't work here.

But we should still talk about ways to improve the docs.

I agree that this is a really important task but it's also a bit
overwhelming and difficult to know where to start. This is too bad since
it's something you don't need to be a coder to approach; more or less any
RDKit user could contribute. Believe it or not, just having people point
out pieces of code that could be (better) documented is already useful -
I'm sure I'm not the only developer who has forgotten which bits of code
they've left un(der)documented. I often have 10-15 minute slots of time
that I could use for writing docs, but it really helps to know which pieces
should be done first.

I would love to hear suggestions for ways that we can make it easier for
people to submit improved documentation or pointers to pieces of code that
could use better documentation and then to let people know that these
options exist. It needs to be something other than "send email to the list"
though.

It's currently pretty easy to submit bug reports/feature requests using the
github interface. These could either provide suggested docs/doc changes or
point to functions/methods/classes that could be better documented. The
github guys just added the ability to specify different types of issue
templates, I could look into doing one of these for documentation requests.

-greg



On Wed, Jan 24, 2018 at 7:38 PM, Cameron Pye <cameron@gmail.com> wrote:

>  I know this isn't a particularly sexy job for a budding cheminformatician
> but...
>
> Work on the Python documentation!!!
>
> I love rdKit and occasionally think I'm pretty savvy but I can't tell you
> how often I'm scrolling through the documentation (or source) and either:
>
> a) discover something that exists but doesn't have anything documentation
> but the function signature
> or
> b) discover some some functionality that exists (and i've wanted) but
> didn't know it was there!
>
> I think this mailing list and Greg do a superb job of keeping the
> community informed and creating and maintaining the codebase but I think
> having some more "Pythonic" API documentation would be great.
>
> One shining example is the scikit-learn documentation
> <http://scikit-learn.org/stable/documentation.html> that has a quick
> start, tutorials etc.  and then in the well categorized and explanatory API
> ref has links for examples in the User Guide (akin to the "Getting Started
> with the RDKit in Python" doc) .
>
> Just my 2 cents!
>
> Thanks for all the hard work as always,
> Cam
>
>
> On Mon, Jan 15, 2018 at 12:52 PM <rdkit-discuss-request@lists.
> sourceforge.net> wrote:
>
>> Send Rdkit-discuss mailing list submissions to
>> rdkit-discuss@lists.sourceforge.net
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>> or, via email, send a message with subject or body 'help' to
>> rdkit-discuss-requ...@lists.sourceforge.net
>>
>> You can reach the person managing the list at
>> rdkit-discuss-ow...@lists.sourceforge.net
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Rdkit-discuss digest..."
>>
>>
>> Today's Topics:
>>
>>1. Re: RDKit and Google Summer of Code 2018 (Jason Biggs)
>>2. Re: RDKit and Google Summer of Code 2018 (Tim Dudgeon)
>>3. Re: 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

2018-01-24 Thread Cameron Pye 
 I know this isn't a particularly sexy job for a budding cheminformatician
but...

Work on the Python documentation!!!

I love rdKit and occasionally think I'm pretty savvy but I can't tell you
how often I'm scrolling through the documentation (or source) and either:

a) discover something that exists but doesn't have anything documentation
but the function signature
or
b) discover some some functionality that exists (and i've wanted) but
didn't know it was there!

I think this mailing list and Greg do a superb job of keeping the community
informed and creating and maintaining the codebase but I think having some
more "Pythonic" API documentation would be great.

One shining example is the scikit-learn documentation
<http://scikit-learn.org/stable/documentation.html> that has a quick start,
tutorials etc.  and then in the well categorized and explanatory API ref
has links for examples in the User Guide (akin to the "Getting Started with
the RDKit in Python" doc) .

Just my 2 cents!

Thanks for all the hard work as always,
Cam


On Mon, Jan 15, 2018 at 12:52 PM <
rdkit-discuss-requ...@lists.sourceforge.net> wrote:

> Send Rdkit-discuss mailing list submissions to
> rdkit-discuss@lists.sourceforge.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> or, via email, send a message with subject or body 'help' to
> rdkit-discuss-requ...@lists.sourceforge.net
>
> You can reach the person managing the list at
> rdkit-discuss-ow...@lists.sourceforge.net
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Rdkit-discuss digest..."
>
>
> Today's Topics:
>
>1. Re: RDKit and Google Summer of Code 2018 (Jason Biggs)
>2. Re: RDKit and Google Summer of Code 2018 (Tim Dudgeon)
>3. Re: 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

2018-01-17 Thread Guillaume GODIN 
+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 chemistry codes.
Best,
Michal Krompiec
Merck KGaA

On Mon, 15 Jan 2018 at 15:21, Jason Biggs 
<jasondbi...@gmail.com<mailto:jasondbi...@gmail.com>> 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 
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 would be applying a constant 
force to all atoms to force them into the xy plane.

Frączek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical Structure 
Diagram Generation of Complex Molecules and Ligand–Protein Interactions." J. 
Chem. Inf. Model. 2016, 56, 2320-2335, DOI: 10.1021/acs.jcim.6b00391.


  *   Another idea would be to add in point-group symmetry detection.  I'm 
using the Symmetrizer java library, described here 
https://www.ncbi.nlm.nih.gov/pubmed/22549414, and pretty happy with it overall. 
 One could re-implement it in C++, or include the jar in the External folder 
and write python wrappers.

Jason Biggs


On Mon, Jan 15, 2018 at 1:09 AM, Greg Landrum 
<greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote:
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:
http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas

(Note: at the point that I'm pressing "send", that's still a copy of last 
year's project ideas).

If you're willing to be a mentor (please ask me about the ~5 hours/week 
required here) or have ideas, please reply to this thread.

Best,
-greg

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

2018-01-17 Thread Michal Krompiec 
+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 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 would be
>applying a constant force to all atoms to force them into the xy plane.
>
> Frączek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical
> Structure Diagram Generation of Complex Molecules and Ligand–Protein
> Interactions." J. Chem. Inf. Model. 2016, 56, 2320-2335, DOI:
> 10.1021/acs.jcim.6b00391.
>
>
>
>- Another idea would be to add in point-group symmetry detection.  I'm
>using the Symmetrizer java library, described here
>https://www.ncbi.nlm.nih.gov/pubmed/22549414, and pretty happy with it
>overall.  One could re-implement it in C++, or include the jar in the
>External folder and write python wrappers.
>
>
> Jason Biggs
>
>
> On Mon, Jan 15, 2018 at 1:09 AM, Greg Landrum 
> wrote:
>
>> 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:
>> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>>
>> (Note: at the point that I'm pressing "send", that's still a copy of last
>> year's project ideas).
>>
>> If you're willing to be a mentor (please ask me about the ~5 hours/week
>> required here) or have ideas, please reply to this thread.
>>
>> Best,
>> -greg
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-16 Thread Matthew Swain 
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 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, 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, Jan 15, 2018 at 9:08 PM, Francois BERENGER 
 wrote:
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 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:
>> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>>
>> (Note: at the point that I'm pressing "send", that's still a copy of
>> last year's project ideas).
>>
>> If you're willing to be a mentor (please ask me about the ~5
>> hours/week required here) or have ideas, please reply to this thread.
>>
>> Best,
>> -greg
>>
>>
>> --
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>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-16 Thread George Papadatos 
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, 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, Jan 15, 2018 at 9:08 PM, Francois BERENGER 
>>>  wrote:
>>> 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 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:
>>> >> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>>> >>
>>> >> (Note: at the point that I'm pressing "send", that's still a copy of
>>> >> last year's project ideas).
>>> >>
>>> >> If you're willing to be a mentor (please ask me about the ~5
>>> >> hours/week required here) or have ideas, please reply to this thread.
>>> >>
>>> >> Best,
>>> >> -greg
>>> >>
>>> >>
>>> >> --
>>> >> Check out the vibrant tech community on one of the world's most
>>> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> >>
>>> >>
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-16 Thread 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 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, 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 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:
>> >> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>> >>
>> >> (Note: at the point that I'm pressing "send", that's still a copy of
>> >> last year's project ideas).
>> >>
>> >> If you're willing to be a mentor (please ask me about the ~5
>> >> hours/week required here) or have ideas, please reply to this thread.
>> >>
>> >> Best,
>> >> -greg
>> >>
>> >>
>> >> 
>> --
>> >> Check out the vibrant tech community on one of the world's most
>> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> >>
>> >>
>> >> ___
>> >> Rdkit-discuss mailing list
>> >> Rdkit-discuss@lists.sourceforge.net
>> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>> >
>> >
>> >
>> > 
>> --
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>> >
>> >
>> >
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>> > Rdkit-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>> >
>>
>> 
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>
>
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-16 Thread Brian Cole 
+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, 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 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:
> >> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
> >>
> >> (Note: at the point that I'm pressing "send", that's still a copy of
> >> last year's project ideas).
> >>
> >> If you're willing to be a mentor (please ask me about the ~5
> >> hours/week required here) or have ideas, please reply to this thread.
> >>
> >> Best,
> >> -greg
> >>
> >>
> >> 
> --
> >> Check out the vibrant tech community on one of the world's most
> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >>
> >>
> >> ___
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> >> Rdkit-discuss@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >
> >
> >
> > 
> --
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> >
> >
> >
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> >
>
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-15 Thread Francois BERENGER 
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 everything up from structure because they can derive
> bonds from the coordinates and that's the only way you can do it in the
> code. Without bonds, trying to link compounds in a sequence doesn't
> really work even if you have two cysteins in a bog standard protein
> sequence, with generic compounds it gets too hard fast.
> 
> PDB has in the mmCIF chem. comp. model "leaving atom flag" that marks
> *a* bonding site but it doesn't tell you what kind of bond can form
> there, nor what to do if there's more than one. You need a whole lot of
> other code to figure out how to link two compounds into a sequence.

Chimera can do the PDB to MOL2 conversion (so there might be some
code to look at since UCSF Chimera is open source).

If you want their algorithm, I think it is in there:

@article {JCC:JCC540120716,
author = {Meng, Elaine C. and Lewis, Richard A.},
title = {Determination of molecular topology and atomic hybridization
states from heavy atom coordinates},
journal = {Journal of Computational Chemistry},
volume = {12},
number = {7},
publisher = {John Wiley & Sons, Inc.},
issn = {1096-987X},
url = {http://dx.doi.org/10.1002/jcc.540120716},
doi = {10.1002/jcc.540120716},
pages = {891--898},
year = {1991},
}

> And then there's structure calculation that I don't know if there's
> anything that works on not proteins, or can predict disordered regions
> well etc.
> 
> If anyone's counting votes, pretty 2D depictions get mine.
> 
> 
> 
> --
> Check out the vibrant tech community on one of the world's most
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> 
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-15 Thread Francois BERENGER 
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 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:
>> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>>
>> (Note: at the point that I'm pressing "send", that's still a copy of
>> last year's project ideas).
>>
>> If you're willing to be a mentor (please ask me about the ~5
>> hours/week required here) or have ideas, please reply to this thread.
>>
>> Best,
>> -greg
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>> ___
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>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> 
> 
> 
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> 
> 
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-15 Thread Dimitri Maziuk 
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
bonds from the coordinates and that's the only way you can do it in the
code. Without bonds, trying to link compounds in a sequence doesn't
really work even if you have two cysteins in a bog standard protein
sequence, with generic compounds it gets too hard fast.

PDB has in the mmCIF chem. comp. model "leaving atom flag" that marks
*a* bonding site but it doesn't tell you what kind of bond can form
there, nor what to do if there's more than one. You need a whole lot of
other code to figure out how to link two compounds into a sequence.

And then there's structure calculation that I don't know if there's
anything that works on not proteins, or can predict disordered regions
well etc.

If anyone's counting votes, pretty 2D depictions get mine.
-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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

2018-01-15 Thread Tim Dudgeon 
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 to participate we need ideas for projects and mentors to go 
along with them.


The current list of RDKit ideas is being maintained here:
http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas

(Note: at the point that I'm pressing "send", that's still a copy of 
last year's project ideas).


If you're willing to be a mentor (please ask me about the ~5 
hours/week required here) or have ideas, please reply to this thread.


Best,
-greg


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

2018-01-15 Thread Tim Dudgeon 
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 (pdb/mmcif/mmtf) worlds?
OK, so that's far too much to ask for, but is there something that could 
be plucked out from there that is useful and achievable?


Tim


On 15/01/18 09:19, Greg Landrum wrote:



On Mon, Jan 15, 2018 at 9:50 AM, Francois BERENGER 
> 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 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
> 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:
>
http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas

>
> (Note: at the point that I'm pressing "send", that's still a copy of
> last year's project ideas).
>
> If you're willing to be a mentor (please ask me about the ~5
hours/week
> required here) or have ideas, please reply to this thread.
>
> Best,
> -greg
>
>
>

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

2018-01-15 Thread Jason Biggs 
   - 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 would be
   applying a constant force to all atoms to force them into the xy plane.

Frączek, T., "Simulation-Based Algorithm for Two-Dimensional Chemical
Structure Diagram Generation of Complex Molecules and Ligand–Protein
Interactions." J. Chem. Inf. Model. 2016, 56, 2320-2335, DOI:
10.1021/acs.jcim.6b00391.



   - Another idea would be to add in point-group symmetry detection.  I'm
   using the Symmetrizer java library, described here
   https://www.ncbi.nlm.nih.gov/pubmed/22549414, and pretty happy with it
   overall.  One could re-implement it in C++, or include the jar in the
   External folder and write python wrappers.


Jason Biggs


On Mon, Jan 15, 2018 at 1:09 AM, Greg Landrum 
wrote:

> 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:
> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
>
> (Note: at the point that I'm pressing "send", that's still a copy of last
> year's project ideas).
>
> If you're willing to be a mentor (please ask me about the ~5 hours/week
> required here) or have ideas, please reply to this thread.
>
> Best,
> -greg
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-15 Thread Greg Landrum 
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 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
> > 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:
> > http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
> >
> > (Note: at the point that I'm pressing "send", that's still a copy of
> > last year's project ideas).
> >
> > If you're willing to be a mentor (please ask me about the ~5 hours/week
> > required here) or have ideas, please reply to this thread.
> >
> > Best,
> > -greg
> >
> >
> > 
> --
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >
> >
> >
> > ___
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> >
>
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-15 Thread Francois BERENGER 
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
> 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:
> http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas
> 
> (Note: at the point that I'm pressing "send", that's still a copy of
> last year's project ideas).
> 
> If you're willing to be a mentor (please ask me about the ~5 hours/week
> required here) or have ideas, please reply to this thread.
> 
> Best,
> -greg
> 
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> 
> 
> 
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Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018

2018-01-15 Thread Axel Pahl 

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 
capabilities, (...)) in order to make it easier to create bindings to 
the RDKit from other languages or to port the RDKit to other languages.


Expected results:
A minimal version of the RDKit that could be bound to from other 
languages like Go, Rust or Nim, would immensely enhance its reach by 
introducing cheminformatics capabilities to languages where this 
functionality is currently still missing or lacking.


Prerequisites: C, C++

Mentor: t.b.d.

Kind regards,
Axel

On 15.01.2018 08:09, Greg Landrum wrote:

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:
http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas

(Note: at the point that I'm pressing "send", that's still a copy of 
last year's project ideas).


If you're willing to be a mentor (please ask me about the ~5 
hours/week required here) or have ideas, please reply to this thread.


Best,
-greg


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

2018-01-14 Thread Greg Landrum 
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:
http://wiki.openchemistry.org/GSoC_Ideas_2018#RDKit_Project_Ideas

(Note: at the point that I'm pressing "send", that's still a copy of last
year's project ideas).

If you're willing to be a mentor (please ask me about the ~5 hours/week
required here) or have ideas, please reply to this thread.

Best,
-greg
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