Re: [Rdkit-discuss] The RDKit and GSoC 2020

[Francois Berenger]

On 20/03/2020 08:43, JW Feng wrote:

iwatobipen blog was where I found instructions for installing RDKit on
Colab.  It works but I found waiting for miniconda to install to be
too annoying. A one line apt-get command to install RDKit is easier
and faster  (~10 seconds) but it only works with Python 2.  Running
following command in a Python 3 environment results in the error
below. Getting apt-get to install RDKit correctly for Python 3 is a
good solution.

!apt-get install python-rdkit librdkit1 rdkit-data

from rdkit import Chem...

---

ModuleNotFoundError   Traceback (most recent call
last)

 [4] in ()
  1 get_ipython().system('apt-get install python-rdkit librdkit1
rdkit-data')
> 2 from rdkit import Chem

ModuleNotFoundError: No module named 'rdkit'


Try python2 instead of python3.

Your Linux distribution is probably shipping an old version of rdkit,
which only works with Python 2.

You can also push for your distribution to ship a recent version
of rdkit.

Altenatively, there is Scripts/create_deb_packages.sh
in the source tree that can create up to date packages on Ubuntu/Debian.

You need to remove your current rdkit installed packages prior to 
installing those

though.

Regards,
F.


---

Best,

JW

On Mon, Mar 16, 2020 at 4:48 AM Taka Seri  wrote:


Dear Steve, Greg and All,

Recently I moved from clab to Binder to make cloud env with python.
However I'll try to make my code more compact and share it.
Thanks for following my blog post. ;)
https://iwatobipen.wordpress.com/

Best regards,

Taka (tiwtter account / iwatobipen)

2020年3月16日(月) 16:03 Greg Landrum :

Thanks Steve,

That's really helpful. Given that we're unlikely to end up with a
decent pip-installable RDkit, I guess the snippet approach would be
the best way to go. I will try to make some time for this (or
convince iwatobipen to do it) in the reasonably near future.

Best,
-greg

On Sun, Mar 15, 2020 at 5:58 PM Steven Kearnes 
wrote:

re: rdkit+colab

In talking with folks outside of Google about rdkit+colab, I haven't
been able to establish that it's worth the trouble of making rdkit a
default dependency. It seems that a rather compact incantation [1]
does the job fairly well. This could be compressed even further, or
even turned into a colab snippet [2] for easier use.

Also, since colab doesn't play well with conda (as far as
pre-installed deps are concerned), we would at least need a
pip-installable rdkit to consider making this work.

Thanks,
Steve

On Mon, Mar 9, 2020 at 4:43 PM JW Feng  wrote:

Are you sure depictions in GSheet wouldn't be a good GSoC project?
I will ask around to find volunteers to connect with you on GSheets
and Colab.

On Fri, Mar 6, 2020 at 8:14 PM Greg Landrum 
wrote:

Hi JW,

I don't think it's a great GSoC project for a couple of reasons, but
I'd love to have RDKit integration in Google Sheets and am willing
to do some work to make that happen. I can poke around a bit to see
about how we could use the new RDKit-JS wrappers, but having access
to someone with experience writing Sheets add-ins would help. If you
know someone internally meeting that description, please put them in
touch with me.

I think making the code easily available in Colab can only be done
by someone inside google. I'm happy to help however I can with that
if you (or anyone else) can identify the right person.

Best,
-greg

On Sat, Mar 7, 2020 at 2:22 AM JW Feng  wrote:

Project suggestion:

Project 1:Implement 2D structure depiction in Google Spreadsheets.
My colleagues at Google think this is very doable.  Being able to
depict structures in Google Spreadsheets will dramatically increase
collaboration between scientists.  Imaging being able to provide
comments for a structure, design idea, or virtual screening hit in a
live Google Spreadsheet.  While there are commercial (Vortex,
Spotfire, MarvinView, Stardrop ...) and open source (Datawarrior)
packages that can read CSV files containing smiles and depict
structures, none comes close to GSheets for collaboration and ease
of use.

* Cells in columns named SMILES, or have SMILES as a substring in
the header, will be depicted in 2D using RDKit
* Cells with depicted structures move with other columns when
sorting, filtering, etc.
* Optional: depictions update when SMILES string is edited
* Bonus: calculate properties using formulas.  Ex:
Descriptors.MolWt(A1) calculates MW of SMILES in A1

Project 2:

* Make it easy to use RDKit in Google Colab [3]
* No need to install RDKit, from rdkit import Chem just works out
of the box

Best,

JW

On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum
 wrote:

Dear all,

I'm happy to share that the RDKit will once again be part of Google
Summer of Code in 2020. This is a program where Google funds
students to work on open-source projects for a couple of months over
the summer. We've 

Re: [Rdkit-discuss] The RDKit and GSoC 2020

[JW Feng]

iwatobipen blog was where I found instructions for installing RDKit on
Colab.  It works but I found waiting for miniconda to install to be too
annoying. A one line apt-get command to install RDKit is easier and faster
 (~10 seconds) but it only works with Python 2.  Running following command
in a Python 3 environment results in the error below. Getting apt-get to
install RDKit correctly for Python 3 is a good solution.

!apt-get install python-rdkit librdkit1 rdkit-data
from rdkit import Chem
...

---

ModuleNotFoundError   Traceback (most recent call last)



in ()  1 get_ipython().system('apt-get install
python-rdkit librdkit1 rdkit-data')> 2 from rdkit import Chem


ModuleNotFoundError: No module named 'rdkit'

---



Best,

JW



On Mon, Mar 16, 2020 at 4:48 AM Taka Seri  wrote:

> Dear Steve, Greg and All,
>
> Recently I moved from clab to Binder to make cloud env with python.
> However I'll try to make my code more compact and share it.
>  Thanks for following my blog post. ;) https://iwatobipen.wordpress.com/
>
> Best regards,
>
> Taka (tiwtter account / iwatobipen)
>
> 2020年3月16日(月) 16:03 Greg Landrum :
>
>> Thanks Steve,
>>
>> That's really helpful. Given that we're unlikely to end up with a decent
>> pip-installable RDkit, I guess the snippet approach would be the best way
>> to go. I will try to make some time for this (or convince iwatobipen to do
>> it) in the reasonably near future.
>>
>> Best,
>> -greg
>>
>> On Sun, Mar 15, 2020 at 5:58 PM Steven Kearnes 
>> wrote:
>>
>>> re: rdkit+colab
>>>
>>> In talking with folks outside of Google about rdkit+colab, I haven't
>>> been able to establish that it's worth the trouble of making rdkit a
>>> default dependency. It seems that a rather compact incantation
>>> 
>>> does the job fairly well. This could be compressed even further, or even
>>> turned into a colab snippet  for
>>> easier use.
>>>
>>> Also, since colab doesn't play well with conda (as far as pre-installed
>>> deps are concerned), we would at least need a pip-installable rdkit to
>>> consider making this work.
>>>
>>> Thanks,
>>> Steve
>>>
>>> On Mon, Mar 9, 2020 at 4:43 PM JW Feng  wrote:
>>>
 Are you sure depictions in GSheet wouldn't be a good GSoC project?  I
 will ask around to find volunteers to connect with you on GSheets and
 Colab.

 On Fri, Mar 6, 2020 at 8:14 PM Greg Landrum 
 wrote:

> Hi JW,
>
> I don't think it's a great GSoC project for a couple of reasons, but
> I'd love to have RDKit integration in Google Sheets and am willing to do
> some work to make that happen. I can poke around a bit to see about how we
> could use the new RDKit-JS wrappers, but having access to someone with
> experience writing Sheets add-ins would help. If you know someone
> internally meeting that description, please put them in touch with me.
>
> I think making the code easily available in Colab can only be done by
> someone inside google. I'm happy to help however I can with that if you 
> (or
> anyone else) can identify the right person.
>
> Best,
> -greg
>
> On Sat, Mar 7, 2020 at 2:22 AM JW Feng  wrote:
>
>> Project suggestion:
>>
>> Project 1:
>> Implement 2D structure depiction in Google Spreadsheets.  My
>> colleagues at Google think this is very doable.  Being able to depict
>> structures in Google Spreadsheets will dramatically increase 
>> collaboration
>> between scientists.  Imaging being able to provide comments for a
>> structure, design idea, or virtual screening hit in a live Google
>> Spreadsheet.  While there are commercial (Vortex, Spotfire, MarvinView,
>> Stardrop ...) and open source (Datawarrior) packages that can read CSV
>> files containing smiles and depict structures, none comes close to 
>> GSheets
>> for collaboration and ease of use.
>>
>>- Cells in columns named SMILES, or have SMILES as a substring in
>>the header, will be depicted in 2D using RDKit
>>- Cells with depicted structures move with other columns when
>>sorting, filtering, etc.
>>- Optional: depictions update when SMILES string is edited
>>- Bonus: calculate properties using formulas.  Ex: 
>> Descriptors.MolWt(A1)
>>calculates MW of SMILES in A1
>>
>> Project 2:
>>
>>- Make it easy to use RDKit in Google Colab
>>
>>
>>- No need to install RDKit, from 

Re: [Rdkit-discuss] The RDKit and GSoC 2020

[Taka Seri]

Dear Steve, Greg and All,

Recently I moved from clab to Binder to make cloud env with python.
However I'll try to make my code more compact and share it.
 Thanks for following my blog post. ;) https://iwatobipen.wordpress.com/

Best regards,

Taka (tiwtter account / iwatobipen)

2020年3月16日(月) 16:03 Greg Landrum :

> Thanks Steve,
>
> That's really helpful. Given that we're unlikely to end up with a decent
> pip-installable RDkit, I guess the snippet approach would be the best way
> to go. I will try to make some time for this (or convince iwatobipen to do
> it) in the reasonably near future.
>
> Best,
> -greg
>
> On Sun, Mar 15, 2020 at 5:58 PM Steven Kearnes  wrote:
>
>> re: rdkit+colab
>>
>> In talking with folks outside of Google about rdkit+colab, I haven't been
>> able to establish that it's worth the trouble of making rdkit a default
>> dependency. It seems that a rather compact incantation
>> 
>> does the job fairly well. This could be compressed even further, or even
>> turned into a colab snippet  for
>> easier use.
>>
>> Also, since colab doesn't play well with conda (as far as pre-installed
>> deps are concerned), we would at least need a pip-installable rdkit to
>> consider making this work.
>>
>> Thanks,
>> Steve
>>
>> On Mon, Mar 9, 2020 at 4:43 PM JW Feng  wrote:
>>
>>> Are you sure depictions in GSheet wouldn't be a good GSoC project?  I
>>> will ask around to find volunteers to connect with you on GSheets and
>>> Colab.
>>>
>>> On Fri, Mar 6, 2020 at 8:14 PM Greg Landrum 
>>> wrote:
>>>
 Hi JW,

 I don't think it's a great GSoC project for a couple of reasons, but
 I'd love to have RDKit integration in Google Sheets and am willing to do
 some work to make that happen. I can poke around a bit to see about how we
 could use the new RDKit-JS wrappers, but having access to someone with
 experience writing Sheets add-ins would help. If you know someone
 internally meeting that description, please put them in touch with me.

 I think making the code easily available in Colab can only be done by
 someone inside google. I'm happy to help however I can with that if you (or
 anyone else) can identify the right person.

 Best,
 -greg

 On Sat, Mar 7, 2020 at 2:22 AM JW Feng  wrote:

> Project suggestion:
>
> Project 1:
> Implement 2D structure depiction in Google Spreadsheets.  My
> colleagues at Google think this is very doable.  Being able to depict
> structures in Google Spreadsheets will dramatically increase collaboration
> between scientists.  Imaging being able to provide comments for a
> structure, design idea, or virtual screening hit in a live Google
> Spreadsheet.  While there are commercial (Vortex, Spotfire, MarvinView,
> Stardrop ...) and open source (Datawarrior) packages that can read CSV
> files containing smiles and depict structures, none comes close to GSheets
> for collaboration and ease of use.
>
>- Cells in columns named SMILES, or have SMILES as a substring in
>the header, will be depicted in 2D using RDKit
>- Cells with depicted structures move with other columns when
>sorting, filtering, etc.
>- Optional: depictions update when SMILES string is edited
>- Bonus: calculate properties using formulas.  Ex: 
> Descriptors.MolWt(A1)
>calculates MW of SMILES in A1
>
> Project 2:
>
>- Make it easy to use RDKit in Google Colab
>
>
>- No need to install RDKit, from rdkit import Chem just works out
>of the box
>
> Best,
>
> JW
> On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum 
> wrote:
>
>> Dear all,
>>
>> I'm happy to share that the RDKit will once again be part of Google
>> Summer of Code in 2020. This is a program where Google funds students to
>> work on open-source projects for a couple of months over the summer. 
>> We've
>> participated in each of the last three years and had some cool stuff come
>> out of it.
>>
>> We're looking for a few more project ideas (along with possible
>> mentors!) as well as students.
>> Applications start in the middle of March. There's more info about
>> timelines here:
>> https://developers.google.com/open-source/gsoc/timeline
>>
>> The current set of project ideas is here and we could use a few more:
>> http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
>> I'm going to try and come up with something, but if you have
>> something to add, please let me know.
>>
>> Best,
>> -greg
>>
>>
>>
>>
>> ___
>> Rdkit-discuss mailing list

Re: [Rdkit-discuss] The RDKit and GSoC 2020

[Greg Landrum]

On Tue, Mar 10, 2020 at 12:40 AM JW Feng  wrote:

> Are you sure depictions in GSheet wouldn't be a good GSoC project?
>

Pretty sure. The major problem is that for a GSoC project to succeed you
really need a mentor available who understands the underlying technology
and who can answer questions about it. For example, last year for the
Neo4J-RDKit project we had three co-mentors: me (RDKit expertise), Stefan
Armbruster from Neo4J (Neo4J expertise), and Christian Pilger (had the
vision and understanding of why you'd actually do with RDKit integration
into Neo4J). I also don't think that it would realistically be three months
worth of full time work (more likely much shorter than that).


> I will ask around to find volunteers to connect with you on GSheets and
> Colab.
>

I'd love to have the integration there too, so if you can find someone who
can help with how the integration on the GSheets side would actually work,
I can probably do the actual coding.

Best,
-greg
___
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Re: [Rdkit-discuss] The RDKit and GSoC 2020

[Greg Landrum]

Thanks Steve,

That's really helpful. Given that we're unlikely to end up with a decent
pip-installable RDkit, I guess the snippet approach would be the best way
to go. I will try to make some time for this (or convince iwatobipen to do
it) in the reasonably near future.

Best,
-greg

On Sun, Mar 15, 2020 at 5:58 PM Steven Kearnes  wrote:

> re: rdkit+colab
>
> In talking with folks outside of Google about rdkit+colab, I haven't been
> able to establish that it's worth the trouble of making rdkit a default
> dependency. It seems that a rather compact incantation
> 
> does the job fairly well. This could be compressed even further, or even
> turned into a colab snippet  for
> easier use.
>
> Also, since colab doesn't play well with conda (as far as pre-installed
> deps are concerned), we would at least need a pip-installable rdkit to
> consider making this work.
>
> Thanks,
> Steve
>
> On Mon, Mar 9, 2020 at 4:43 PM JW Feng  wrote:
>
>> Are you sure depictions in GSheet wouldn't be a good GSoC project?  I
>> will ask around to find volunteers to connect with you on GSheets and
>> Colab.
>>
>> On Fri, Mar 6, 2020 at 8:14 PM Greg Landrum 
>> wrote:
>>
>>> Hi JW,
>>>
>>> I don't think it's a great GSoC project for a couple of reasons, but I'd
>>> love to have RDKit integration in Google Sheets and am willing to do some
>>> work to make that happen. I can poke around a bit to see about how we could
>>> use the new RDKit-JS wrappers, but having access to someone with experience
>>> writing Sheets add-ins would help. If you know someone internally meeting
>>> that description, please put them in touch with me.
>>>
>>> I think making the code easily available in Colab can only be done by
>>> someone inside google. I'm happy to help however I can with that if you (or
>>> anyone else) can identify the right person.
>>>
>>> Best,
>>> -greg
>>>
>>> On Sat, Mar 7, 2020 at 2:22 AM JW Feng  wrote:
>>>
 Project suggestion:

 Project 1:
 Implement 2D structure depiction in Google Spreadsheets.  My colleagues
 at Google think this is very doable.  Being able to depict structures in
 Google Spreadsheets will dramatically increase collaboration between
 scientists.  Imaging being able to provide comments for a structure, design
 idea, or virtual screening hit in a live Google Spreadsheet.  While there
 are commercial (Vortex, Spotfire, MarvinView, Stardrop ...) and open source
 (Datawarrior) packages that can read CSV files containing smiles and depict
 structures, none comes close to GSheets for collaboration and ease of use.

- Cells in columns named SMILES, or have SMILES as a substring in
the header, will be depicted in 2D using RDKit
- Cells with depicted structures move with other columns when
sorting, filtering, etc.
- Optional: depictions update when SMILES string is edited
- Bonus: calculate properties using formulas.  Ex: Descriptors.MolWt(A1)
calculates MW of SMILES in A1

 Project 2:

- Make it easy to use RDKit in Google Colab


- No need to install RDKit, from rdkit import Chem just works out
of the box

 Best,

 JW
 On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum 
 wrote:

> Dear all,
>
> I'm happy to share that the RDKit will once again be part of Google
> Summer of Code in 2020. This is a program where Google funds students to
> work on open-source projects for a couple of months over the summer. We've
> participated in each of the last three years and had some cool stuff come
> out of it.
>
> We're looking for a few more project ideas (along with possible
> mentors!) as well as students.
> Applications start in the middle of March. There's more info about
> timelines here:
> https://developers.google.com/open-source/gsoc/timeline
>
> The current set of project ideas is here and we could use a few more:
> http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
> I'm going to try and come up with something, but if you have something
> to add, please let me know.
>
> Best,
> -greg
>
>
>
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
 ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
___
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Rdkit-discuss@lists.sourceforge.net

Re: [Rdkit-discuss] The RDKit and GSoC 2020

[Steven Kearnes via Rdkit-discuss]

re: rdkit+colab

In talking with folks outside of Google about rdkit+colab, I haven't been
able to establish that it's worth the trouble of making rdkit a default
dependency. It seems that a rather compact incantation

does the job fairly well. This could be compressed even further, or even
turned into a colab snippet  for
easier use.

Also, since colab doesn't play well with conda (as far as pre-installed
deps are concerned), we would at least need a pip-installable rdkit to
consider making this work.

Thanks,
Steve

On Mon, Mar 9, 2020 at 4:43 PM JW Feng  wrote:

> Are you sure depictions in GSheet wouldn't be a good GSoC project?  I will
> ask around to find volunteers to connect with you on GSheets and Colab.
>
> On Fri, Mar 6, 2020 at 8:14 PM Greg Landrum 
> wrote:
>
>> Hi JW,
>>
>> I don't think it's a great GSoC project for a couple of reasons, but I'd
>> love to have RDKit integration in Google Sheets and am willing to do some
>> work to make that happen. I can poke around a bit to see about how we could
>> use the new RDKit-JS wrappers, but having access to someone with experience
>> writing Sheets add-ins would help. If you know someone internally meeting
>> that description, please put them in touch with me.
>>
>> I think making the code easily available in Colab can only be done by
>> someone inside google. I'm happy to help however I can with that if you (or
>> anyone else) can identify the right person.
>>
>> Best,
>> -greg
>>
>> On Sat, Mar 7, 2020 at 2:22 AM JW Feng  wrote:
>>
>>> Project suggestion:
>>>
>>> Project 1:
>>> Implement 2D structure depiction in Google Spreadsheets.  My colleagues
>>> at Google think this is very doable.  Being able to depict structures in
>>> Google Spreadsheets will dramatically increase collaboration between
>>> scientists.  Imaging being able to provide comments for a structure, design
>>> idea, or virtual screening hit in a live Google Spreadsheet.  While there
>>> are commercial (Vortex, Spotfire, MarvinView, Stardrop ...) and open source
>>> (Datawarrior) packages that can read CSV files containing smiles and depict
>>> structures, none comes close to GSheets for collaboration and ease of use.
>>>
>>>- Cells in columns named SMILES, or have SMILES as a substring in
>>>the header, will be depicted in 2D using RDKit
>>>- Cells with depicted structures move with other columns when
>>>sorting, filtering, etc.
>>>- Optional: depictions update when SMILES string is edited
>>>- Bonus: calculate properties using formulas.  Ex: Descriptors.MolWt(A1)
>>>calculates MW of SMILES in A1
>>>
>>> Project 2:
>>>
>>>- Make it easy to use RDKit in Google Colab
>>>
>>>- No need to install RDKit, from rdkit import Chem just works out of
>>>the box
>>>
>>> Best,
>>>
>>> JW
>>> On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum 
>>> wrote:
>>>
 Dear all,

 I'm happy to share that the RDKit will once again be part of Google
 Summer of Code in 2020. This is a program where Google funds students to
 work on open-source projects for a couple of months over the summer. We've
 participated in each of the last three years and had some cool stuff come
 out of it.

 We're looking for a few more project ideas (along with possible
 mentors!) as well as students.
 Applications start in the middle of March. There's more info about
 timelines here:
 https://developers.google.com/open-source/gsoc/timeline

 The current set of project ideas is here and we could use a few more:
 http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
 I'm going to try and come up with something, but if you have something
 to add, please let me know.

 Best,
 -greg




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

>>> ___
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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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Re: [Rdkit-discuss] The RDKit and GSoC 2020

[JW Feng]

Are you sure depictions in GSheet wouldn't be a good GSoC project?  I will
ask around to find volunteers to connect with you on GSheets and Colab.

On Fri, Mar 6, 2020 at 8:14 PM Greg Landrum  wrote:

> Hi JW,
>
> I don't think it's a great GSoC project for a couple of reasons, but I'd
> love to have RDKit integration in Google Sheets and am willing to do some
> work to make that happen. I can poke around a bit to see about how we could
> use the new RDKit-JS wrappers, but having access to someone with experience
> writing Sheets add-ins would help. If you know someone internally meeting
> that description, please put them in touch with me.
>
> I think making the code easily available in Colab can only be done by
> someone inside google. I'm happy to help however I can with that if you (or
> anyone else) can identify the right person.
>
> Best,
> -greg
>
> On Sat, Mar 7, 2020 at 2:22 AM JW Feng  wrote:
>
>> Project suggestion:
>>
>> Project 1:
>> Implement 2D structure depiction in Google Spreadsheets.  My colleagues
>> at Google think this is very doable.  Being able to depict structures in
>> Google Spreadsheets will dramatically increase collaboration between
>> scientists.  Imaging being able to provide comments for a structure, design
>> idea, or virtual screening hit in a live Google Spreadsheet.  While there
>> are commercial (Vortex, Spotfire, MarvinView, Stardrop ...) and open source
>> (Datawarrior) packages that can read CSV files containing smiles and depict
>> structures, none comes close to GSheets for collaboration and ease of use.
>>
>>- Cells in columns named SMILES, or have SMILES as a substring in the
>>header, will be depicted in 2D using RDKit
>>- Cells with depicted structures move with other columns when
>>sorting, filtering, etc.
>>- Optional: depictions update when SMILES string is edited
>>- Bonus: calculate properties using formulas.  Ex: Descriptors.MolWt(A1)
>>calculates MW of SMILES in A1
>>
>> Project 2:
>>
>>- Make it easy to use RDKit in Google Colab
>>
>>- No need to install RDKit, from rdkit import Chem just works out of
>>the box
>>
>> Best,
>>
>> JW
>> On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum 
>> wrote:
>>
>>> Dear all,
>>>
>>> I'm happy to share that the RDKit will once again be part of Google
>>> Summer of Code in 2020. This is a program where Google funds students to
>>> work on open-source projects for a couple of months over the summer. We've
>>> participated in each of the last three years and had some cool stuff come
>>> out of it.
>>>
>>> We're looking for a few more project ideas (along with possible
>>> mentors!) as well as students.
>>> Applications start in the middle of March. There's more info about
>>> timelines here:
>>> https://developers.google.com/open-source/gsoc/timeline
>>>
>>> The current set of project ideas is here and we could use a few more:
>>> http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
>>> I'm going to try and come up with something, but if you have something
>>> to add, please let me know.
>>>
>>> Best,
>>> -greg
>>>
>>>
>>>
>>>
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
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Re: [Rdkit-discuss] The RDKit and GSoC 2020

[Greg Landrum]

Hi JW,

I don't think it's a great GSoC project for a couple of reasons, but I'd
love to have RDKit integration in Google Sheets and am willing to do some
work to make that happen. I can poke around a bit to see about how we could
use the new RDKit-JS wrappers, but having access to someone with experience
writing Sheets add-ins would help. If you know someone internally meeting
that description, please put them in touch with me.

I think making the code easily available in Colab can only be done by
someone inside google. I'm happy to help however I can with that if you (or
anyone else) can identify the right person.

Best,
-greg

On Sat, Mar 7, 2020 at 2:22 AM JW Feng  wrote:

> Project suggestion:
>
> Project 1:
> Implement 2D structure depiction in Google Spreadsheets.  My colleagues at
> Google think this is very doable.  Being able to depict structures in
> Google Spreadsheets will dramatically increase collaboration between
> scientists.  Imaging being able to provide comments for a structure, design
> idea, or virtual screening hit in a live Google Spreadsheet.  While there
> are commercial (Vortex, Spotfire, MarvinView, Stardrop ...) and open source
> (Datawarrior) packages that can read CSV files containing smiles and depict
> structures, none comes close to GSheets for collaboration and ease of use.
>
>- Cells in columns named SMILES, or have SMILES as a substring in the
>header, will be depicted in 2D using RDKit
>- Cells with depicted structures move with other columns when sorting,
>filtering, etc.
>- Optional: depictions update when SMILES string is edited
>- Bonus: calculate properties using formulas.  Ex: Descriptors.MolWt(A1)
>calculates MW of SMILES in A1
>
> Project 2:
>
>- Make it easy to use RDKit in Google Colab
>
>- No need to install RDKit, from rdkit import Chem just works out of
>the box
>
> Best,
>
> JW
> On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum 
> wrote:
>
>> Dear all,
>>
>> I'm happy to share that the RDKit will once again be part of Google
>> Summer of Code in 2020. This is a program where Google funds students to
>> work on open-source projects for a couple of months over the summer. We've
>> participated in each of the last three years and had some cool stuff come
>> out of it.
>>
>> We're looking for a few more project ideas (along with possible mentors!)
>> as well as students.
>> Applications start in the middle of March. There's more info about
>> timelines here:
>> https://developers.google.com/open-source/gsoc/timeline
>>
>> The current set of project ideas is here and we could use a few more:
>> http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
>> I'm going to try and come up with something, but if you have something to
>> add, please let me know.
>>
>> Best,
>> -greg
>>
>>
>>
>>
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>>
>
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Re: [Rdkit-discuss] The RDKit and GSoC 2020

[Peter S. Shenkin]

"Cells in columns named SMILES, or have SMILES as a substring in the
header, will be depicted in 2D using RDKit"

Sounds like a great project, but I think the above can be improved upon as
a specification. In many or even most situations, users will want to be
able to view the SMILES as a string and simultaneously visualize the
structures. Also, tying behavior of a column exclusively to the column
title is not (as far as I know) a standard Gsheets paradigm. Or at least I
hope not. 

I don't know know whether Gsheets provides a facility for addition of new
formulas, but if this is allowed, it might be reasonable to remove the
title dependence by introducing a formula with a name like "RDDEPICT". So
if a SMILES appears as text in cell A1, filling A2 with the depiction would
be accomplished by setting A2 to "=RDDEPICT(A1)". This would presumably
also automatically update if A1 changes using Gsheets' built-in handling of
dependencies.

If addition of formulas is not possible, it is probably possible to
accomplish the the same thing using the Gsheets Javascript API.

Either way, I think something like this would be better than tying the
behavior to the column title, even if the latter should be possible.

-P.

On Fri, Mar 6, 2020 at 8:24 PM JW Feng  wrote:

> Project suggestion:
>
> Project 1:
> Implement 2D structure depiction in Google Spreadsheets.  My colleagues at
> Google think this is very doable.  Being able to depict structures in
> Google Spreadsheets will dramatically increase collaboration between
> scientists.  Imaging being able to provide comments for a structure, design
> idea, or virtual screening hit in a live Google Spreadsheet.  While there
> are commercial (Vortex, Spotfire, MarvinView, Stardrop ...) and open source
> (Datawarrior) packages that can read CSV files containing smiles and depict
> structures, none comes close to GSheets for collaboration and ease of use.
>
>- Cells in columns named SMILES, or have SMILES as a substring in the
>header, will be depicted in 2D using RDKit
>- Cells with depicted structures move with other columns when sorting,
>filtering, etc.
>- Optional: depictions update when SMILES string is edited
>- Bonus: calculate properties using formulas.  Ex: Descriptors.MolWt(A1)
>calculates MW of SMILES in A1
>
> Project 2:
>
>- Make it easy to use RDKit in Google Colab
>
>- No need to install RDKit, from rdkit import Chem just works out of
>the box
>
> Best,
>
> JW
> On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum 
> wrote:
>
>> Dear all,
>>
>> I'm happy to share that the RDKit will once again be part of Google
>> Summer of Code in 2020. This is a program where Google funds students to
>> work on open-source projects for a couple of months over the summer. We've
>> participated in each of the last three years and had some cool stuff come
>> out of it.
>>
>> We're looking for a few more project ideas (along with possible mentors!)
>> as well as students.
>> Applications start in the middle of March. There's more info about
>> timelines here:
>> https://developers.google.com/open-source/gsoc/timeline
>>
>> The current set of project ideas is here and we could use a few more:
>> http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
>> I'm going to try and come up with something, but if you have something to
>> add, please let me know.
>>
>> Best,
>> -greg
>>
>>
>>
>>
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>>
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Re: [Rdkit-discuss] The RDKit and GSoC 2020

[JW Feng]

Project suggestion:

Project 1:
Implement 2D structure depiction in Google Spreadsheets.  My colleagues at
Google think this is very doable.  Being able to depict structures in
Google Spreadsheets will dramatically increase collaboration between
scientists.  Imaging being able to provide comments for a structure, design
idea, or virtual screening hit in a live Google Spreadsheet.  While there
are commercial (Vortex, Spotfire, MarvinView, Stardrop ...) and open source
(Datawarrior) packages that can read CSV files containing smiles and depict
structures, none comes close to GSheets for collaboration and ease of use.

   - Cells in columns named SMILES, or have SMILES as a substring in the
   header, will be depicted in 2D using RDKit
   - Cells with depicted structures move with other columns when sorting,
   filtering, etc.
   - Optional: depictions update when SMILES string is edited
   - Bonus: calculate properties using formulas.  Ex:
Descriptors.MolWt(A1) calculates
   MW of SMILES in A1

Project 2:

   - Make it easy to use RDKit in Google Colab
   
   - No need to install RDKit, from rdkit import Chem just works out of the
   box

Best,

JW
On Sun, Feb 23, 2020 at 11:48 PM Greg Landrum 
wrote:

> Dear all,
>
> I'm happy to share that the RDKit will once again be part of Google Summer
> of Code in 2020. This is a program where Google funds students to work on
> open-source projects for a couple of months over the summer. We've
> participated in each of the last three years and had some cool stuff come
> out of it.
>
> We're looking for a few more project ideas (along with possible mentors!)
> as well as students.
> Applications start in the middle of March. There's more info about
> timelines here:
> https://developers.google.com/open-source/gsoc/timeline
>
> The current set of project ideas is here and we could use a few more:
> http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
> I'm going to try and come up with something, but if you have something to
> add, please let me know.
>
> Best,
> -greg
>
>
>
>
> ___
> Rdkit-discuss mailing list
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>
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[Rdkit-discuss] The RDKit and GSoC 2020

[Greg Landrum]

Dear all,

I'm happy to share that the RDKit will once again be part of Google Summer
of Code in 2020. This is a program where Google funds students to work on
open-source projects for a couple of months over the summer. We've
participated in each of the last three years and had some cool stuff come
out of it.

We're looking for a few more project ideas (along with possible mentors!)
as well as students.
Applications start in the middle of March. There's more info about
timelines here:
https://developers.google.com/open-source/gsoc/timeline

The current set of project ideas is here and we could use a few more:
http://wiki.openchemistry.org/GSoC_Ideas_2020#RDKit_Project_Ideas
I'm going to try and come up with something, but if you have something to
add, please let me know.

Best,
-greg
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