date:20180116

Re: [Rdkit-discuss] mol file parsing, 3D or 2D

2018-01-16 Thread Greg Landrum

On Mon, Jan 15, 2018 at 11:59 PM, Jason Biggs  wrote:

> Thanks for the detailed reply
>
>
>>
>> The fact that this isn't happening for you indicates that you are reading
>> the molecules in without sanitizing them - the mol file parser calls
>> assignStereochemistry() by default if you sanitize. Are you sure that you
>> should be disabling sanitization?
>>
>>
> I did turn it off, but then afterwards I call sanitize, but with a
> user-specified option for whether to perform the
> Kekulization/setAromaticity steps.  I'm not certain what we want to set as
> the default behavior, but I want the user to have the option of having the
> molecule stay in the particular kekulized state that they input.
>

Ok, as long as you're aware that there are many parts of the code that
expect that aromaticity will be assigned. This includes the fingerprinters
and many of the descriptor calculators. Of course any SMILES that's
generated from a Kekule form is not truly canonical.

It might be worth thinking about adding an option to the aromaticity
perception code to maintain the original bond types and just set the
"isAromatic" flag on the bonds. This would allow the user-provided
resonance form to be maintained but still have aromatic markings there for
fingerprints and descriptors. That's involves touching a non-trivial amount
of code, but it could be an interesting capability to have.

I will go through the molfile parser to see what else I'm missing out on by
> doing the sanitization step afterward.
>
Would it break functionality to add a sanitizeOps optional argument to some
> of the XXXToMol functions (defaulting to SANITIZE_ALL of course)?
>

That's an interesting suggestion and shouldn't be overly hard to add; I'll
take a look at it.

Best,
-greg
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[Rdkit-discuss] Save the date: 2018 RDKit UGM

2018-01-16 Thread Greg Landrum

Dear all,

This year's RDKit UGM will take place in Cambridge England from the 19-21
September. The event will take place in the Department of Chemistry at the
University of Cambridge and our host/organizer will be Andreas Bender.

A formal announcement with more details and a registration link will come
in the next month or so, but please go ahead and mark your calendars so
that you can attend!

Best,
-greg
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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
>>
>>
>> --
>> 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-discuss Digest, Vol 123, Issue 26

2018-01-16 Thread JW Feng via Rdkit-discuss

Another +1 for MolVS.

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Denali Therapeutics Inc.
151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 | (650)
270-0628

On Tue, Jan 16, 2018 at 10:04 AM, <
rdkit-discuss-requ...@lists.sourceforge.net> wrote:

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> Today's Topics:
>
>1. Re: RDKit and Google Summer of Code 2018 (Brian Cole)
>2. Re: RDKit and Google Summer of Code 2018 (JP)
>3. Re: RDKit and Google Summer of Code 2018 (George Papadatos)
>
>
> --
>
> Message: 1
> Date: Tue, 16 Jan 2018 10:00:00 -0500
> From: Brian Cole 
> To: Francois BERENGER 
> Cc: RDKit Discuss 
> Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> +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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> Message: 2
> Date: Tue, 16 Jan 2018 18:19:46 +0100
> From: JP 
> To: Brian Cole 
> Cc: Francois BERENGER ,  RDKit Discuss
> 
> Subject: Re: [Rdkit-discuss] RDKit and Google Summer of Code 2018
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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:

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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>>> >> Rdkit-discuss@lists.sourceforge.net
>>> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>> >
>>> >
>>> >
>>> > --
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>>> > 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

2018-01-16 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
>> >>
>> >>
>> >> ___
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>> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>> >
>> >
>> >
>> > 
>> --
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>> >
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>>
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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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> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >
> >
> >
> > 
> --
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> >
> >
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>
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Re: [Rdkit-discuss] mol file parsing, 3D or 2D

[Rdkit-discuss] Save the date: 2018 RDKit UGM

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

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 123, Issue 26

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

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

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

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