Re: [Rdkit-discuss] RDKIT 2018.3 and MMPDB problem

2018-05-08 Thread Andrew Dalke 
Dear Marco,

> On May 7, 2018, at 23:59, Marco Stenta  wrote:
> I had some time to set an environment for it and test it: it works fine, as 
> far as my tests go. I will switch to this version and to the latest RDKIT now.

Thanks for the feedback. Someone else sent me a private email also saying it 
worked. I'll put together the final changes for a 2.1 release, and see about 
making it accessible from PyPI so "pip install mmpdb" will work.

> some questions:
> Is there any plan to:
> include MCS as a fragmentation method?
> extend to matched series?
> include "fuzzy" environment definitions based on pharmacophores (as BI people 
> did)?

I know of no plans for that.

As a consultant, my answer is more along the lines of "are you willing to pay 
for it?" :)

It won't be cheap.

Speaking of which, many thanks to Roche because they funded this work, just 
like that previously funded me to develop the MCS code that is now in RDKit.


> I am currently using the database file to explore the rules mainly via visual 
> inspection through spotfire by means of a series of joins to generate 
> suitable tables: would anybody be interested in this (also helping improving 
> it)?

I hope you find others and are able to get this out there.

One of the reasons for developing what eventually became mmpdb 2.0 is to make 
this sort of viewer possible.

That is, the unreleased mmpdb 1.0 didn't have canonical attachment point 
assignment, resulting in up to 6 different ways to represent a 3-cut fragment. 
This made it technically challenging to the simple sorts of analyses that mmpdb 
2.0 does now, and impossible to visualize meaningfully.

Cheers,

Andrew
da...@dalkescientific.com



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Re: [Rdkit-discuss] returning multiples matrixes in python

2018-05-08 Thread Guillaume GODIN 
Thanks Greg,

Based on the links, I will try option 3, cause my number of matrixes is a 
parameter of my function.

BR,

Guillaume



De : Greg Landrum 
Date : mardi, 8 mai 2018 à 15:30
À : Guillaume GODIN 
Cc : RDKit Discuss 
Objet : Re: [Rdkit-discuss] returning multiples matrixes in python

Hi Guillaume,

I don't think I have any specific example for this, but there's some sample 
code here on how to return a numpy array using boost::python (which is what the 
RDKit uses for the wrappers):
https://stackoverflow.com/a/3402

If you know how many elements the tuple will have when you're writing the code, 
you can use python::make_tuple:
https://github.com/rdkit/rdkit/blob/f4529c910e546af590c56eba01f96e9015c269a6/Code/Geometry/Wrap/Point.cpp#L20

or you can just create a python::list in C++ and return it as a tuple. Here's 
an example:
https://github.com/rdkit/rdkit/blob/020024ee5cb612781239e4ca152a4a51f6ff1b1d/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp#L29

-greg

On Tue, May 8, 2018 at 6:57 AM Guillaume GODIN 
mailto:guillaume.go...@firmenich.com>> wrote:
Dear All,

I’m working on a c++  reimplementation of random Coulomb matrix generator via 
RDKit. I was able to generate one matrix per conformer but how to pass  
multiples matrixes per conformer ? At the end I need a list of matrixes in 
numpy for each conformer.

Best regards,

Guillaume
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Re: [Rdkit-discuss] returning multiples matrixes in python

2018-05-08 Thread Greg Landrum 
Hi Guillaume,

I don't think I have any specific example for this, but there's some sample
code here on how to return a numpy array using boost::python (which is what
the RDKit uses for the wrappers):
https://stackoverflow.com/a/3402

If you know how many elements the tuple will have when you're writing the
code, you can use python::make_tuple:
https://github.com/rdkit/rdkit/blob/f4529c910e546af590c56eba01f96e9015c269a6/Code/Geometry/Wrap/Point.cpp#L20

or you can just create a python::list in C++ and return it as a tuple.
Here's an example:
https://github.com/rdkit/rdkit/blob/020024ee5cb612781239e4ca152a4a51f6ff1b1d/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp#L29

-greg


On Tue, May 8, 2018 at 6:57 AM Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:

> Dear All,
>
>
>
> I’m working on a c++  reimplementation of random Coulomb matrix generator
> via RDKit. I was able to generate one matrix per conformer but how to pass
>  multiples matrixes per conformer ? At the end I need a list of matrixes in
> numpy for each conformer.
>
>
>
> Best regards,
>
>
>
> Guillaume
>
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Re: [Rdkit-discuss] another request for feedback on a new python API documentation format

2018-05-08 Thread Maciek Wójcikowski 
Hi Greg,

Speaking about the new docs - would it be possible to have documentation
for few stable releases back, like 2017.09, 2017.03, etc. Recently I was
trying to establish the changes in RDKit's API and ended up using git
blame, whereas I could be able to get that info from changing the release
on the docs.


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2018-05-02 11:17 GMT+02:00 David Cosgrove :

> Hi Greg,
> After a quick poke about, I think the new documentation looks great in
> general.  If a change is forced on you, then I suggest you just do it in a
> way that makes your life as easy as possible.  If people don't like it,
> they can always put the effort in to do something different and then I
> expect they'll quickly come round to realising that your way is perfectly
> fine.  One way of fixing the docstring formatting would be to put
> instructions and a couple of examples somewhere handy and ask people to fix
> problems when they encounter them as they read the docs.  That should be a
> small effort from each person that would hopefully fix the important ones
> quickly in a self-prioritising manner.
> Thanks for putting the time into this,
> Dave
>
>
> On Wed, May 2, 2018 at 8:40 AM, Greg Landrum 
> wrote:
>
>> Dear all,
>>
>> Just over a year ago I asked for feedback on a new documentation format
>> for the RDKit python API: https://www.mail-archive.
>> com/rdkit-discuss@lists.sourceforge.net/msg06688.html
>> Some useful feedback came in on that thread (thanks to those who replied
>> there and in private email), but I ran out of time/motivation to spend time
>> on this.
>>
>> With my motivation recharged thanks to the "fun" of using epydoc to
>> document the last release, I revisited the topic this weekend and actually
>> made some progress.[1] I'd like to gather a second round of feedback on
>> that.
>>
>> The documentation is here:
>> http://rdkit.org/docs_temp/index.html
>> The API docs (which are where the biggest changes are) are here:
>> http://rdkit.org/docs_temp/api-docs.html
>>
>> To address some of the things raised last time:
>> - This really isn't optional. It's been more than a decade since epydoc
>> was updated and it requires python 2.7.
>> - My previous attempt to auto-generate docs used pdoc (
>> https://github.com/BurntSushi/pdoc). That project also seems to have
>> died, so it's not really an option.
>> - Based upon the two factors above I decided to use the autodoc
>> functionality that's part of Sphinx. It's not perfect, but it's supported
>> (and seems likely to continue to be so since it's part of Sphinx)
>>
>> - The docs now have a search box
>>
>> - We've lost the overview (list of classes/functions/etc) that epydoc
>> provides. There likely is a way to do this with sphinx, but I haven't
>> managed to get it to work yet
>>
>> - Formatting: Some of the docstrings end up looking pretty good, others
>> are awful. Here's a module that demonstrates both sides of the coin:
>> http://rdkit.org/docs_temp/source/rdkit.Chem.AtomPairs.Pairs
>> .html#module-rdkit.Chem.AtomPairs.Pairs
>> Fixing this is "just" a matter of editing the doc strings. This is
>> reasonably mechanical, but unfortunately not automatable, work. It should
>> be done, but in the meantime the broken docstrings aren't completely
>> useless.
>>
>> There's also a github issue for this:
>> https://github.com/rdkit/rdkit/issues/1656
>> I'm doing the work on this branch:
>> https://github.com/greglandrum/rdkit/tree/dev/usinx_sphinx_autodoc
>>
>> -greg
>> [1] Remember how I said I was going to take a short break and do
>> something fun? This isn't that.
>>
>>
>> 
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> http://cozchemix.co.uk
>
>
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