[Rdkit-discuss] Beta of Q1 2017 release now up

2017-03-31 Thread Greg Landrum 
[apologies for the date of this... it's not an April Fools joke]
Dear all,

I have tagged a beta of the next RDKit release here:
https://github.com/rdkit/rdkit/releases/tag/Release_2017_03_1b1

The release notes are on the release page linked above. Note that the list
of people in the acknowledgement section was mostly created automatically
from github. If you feel like I missed you, or if I got your name wrong,
please let me know so that I can update the release notes before the actual
release.

To make testing easier, I've done conda builds for 64bit linux (python 3.5
and python 2.7) and windows (just python v3.5 for the beta, there were some
problems with the python 2.7 build that will be fixed for the release).
Since this is still a beta, I've labelled them "testing", so you need to
install them like this:
conda install -c rdkit/label/testing rdkit

Unless major problems are found, I plan to do the actual release in 2-3
weeks. I'm going to be travelling for the next couple of weeks so the usual
beta period is a bit longer. Between now and then I hope to get another bug
or two fixed but this should otherwise be it for features..

Best,
-greg
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[Rdkit-discuss] NYC "RDKit Users and Learners" Meetup Monday, April 3, 7 PM at Hack Manhattan

2017-03-31 Thread Peter S. Shenkin 
For more information, see:

https://www.meetup.com/RDKit-Users-and-Learners/events/237963674/?rv=ce2&_af=event&_af_eid=237963674=on

If you have RDKit-related work that you'd like to talk about or ask about,
please let me know.

-P.
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Re: [Rdkit-discuss] generating scaffold trees

2017-03-31 Thread Axel Pahl 

Hi Markus,

to my knowledge, there is no implementation in RDKit available yet.

Kind regards,
Axel

On 31.03.2017 16:55, Markus Metz wrote:

Dear Axel and all:

I have come across an older discussion about Ansgar Schuffenhauer's 
work on scaffolds:

--

Axel Pahl 
 
Fri, 22 May 2015 04:39:33 -0700 



Dear RDKitters,

has someone used the RDKit to generate scaffold trees from molecules as
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58
I know that this is possible with ScaffoldHunter and that there is a
Pipeline Pilot component for it, but being able to do it in RDKit would
fit especially well in my workflow...

Kind regards and have a nice weekend,
Axel
--
Has there been any update regarding this matter?
Thank you very much and cheers,
Markus


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Re: [Rdkit-discuss] generating scaffold trees

2017-03-31 Thread Markus Metz 
Dear Axel and all:

I have come across an older discussion about Ansgar Schuffenhauer's work on
scaffolds:
--

Axel Pahl 

Fri, 22 May 2015 04:39:33 -0700


Dear RDKitters,

has someone used the RDKit to generate scaffold trees from molecules as
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58

I know that this is possible with ScaffoldHunter and that there is a
Pipeline Pilot component for it, but being able to do it in RDKit would
fit especially well in my workflow...

Kind regards and have a nice weekend,
Axel


--

Has there been any update regarding this matter?

Thank you very much and cheers,
Markus
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[Rdkit-discuss] San Francisco ACS

2017-03-31 Thread Greg Landrum 
Dear all,

I will be at the ACS meeting in SF next week (well, starting on Sunday).
It'd be great to meet some members of the RDKit community there, at least
to say hi. :-)

-greg
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Re: [Rdkit-discuss] DeleteSubstructs vs ReplaceSubstructs

2017-03-31 Thread Pavel Polishchuk 

Hi Maxim,

  if you change your query to SMARTS it would be possible to delete 
what you want


  m=Chem.MolFromSmiles('C1(C2=NC=CC=C2)=CC=CC(C)=C1')
  ss = Chem.MolFromSmarts('c1c1C')
  frag = AllChem.DeleteSubstructs(m, ss)
  print(Chem.MolToSmiles(frag))

Pavel.


On 03/31/2017 07:41 AM, Popov, Maxim (Ext) wrote:


Dear RDKit users,

I am trying to remove a common substructure from a number of molecules 
(with AllChem.DeleteSubstructs). My problem is best illustrated by 
this short code:


fromrdkit importChem

fromrdkit.Chem importAllChem

m=Chem.MolFromSmiles(/'C1(C2=NC=CC=C2)=CC=CC(C)=C1'/)

ss = Chem.MolFromSmiles(/'C1=CC=CC(C)=C1'/)

hyd=Chem.MolFromSmiles(/'[H]'/)

print(/"Substituting substructure with hydrogen"/)

frags = AllChem.ReplaceSubstructs(m, ss,hyd)

forfrag infrags:

print(Chem.MolToSmiles(frag))

print(/"\nDeleting substructure"/)

frag = AllChem.DeleteSubstructs(m, ss)

print(Chem.MolToSmiles(frag))

I create a toluene connected to pyridine and try to remove toluene.

When replacing toluene substructure with hydrogen 
(AllChem.ReplaceSubstructs), I receive two sets of results: pyridine 
(with explicit hydrogen) and single carbon plus single hydrogen plus 
aromatic open chain (what is left from pyridine after removing one 
ring atom).


When deleting the toluene substructure (AllChem.DeleteSubstructs), I 
receive just the open chain of ex-pyridine (corresponding to second 
set of the ReplaceSubstructs results).


Is there a way of directing DeleteSubstructs method to a specific 
variant (in this case, leaving pyridine as a ring seems to be logical).


Best regards,

Maxim



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