[Rdkit-discuss] RDKit training workshop: link not working

[Paul Czodrowski]

Dear RDKitters,

when trying to open this page:
https://www.eventbrite.com/e/pre-event-training-at-the-7th-rdkit-ugm

I receive a message "Whoops, the page or event you are looking for was not 
found.".

Am I simply using the wrong link, or is the event already fully booked?


Cheers,
Paul


____
Paul Czodrowski, PhD

Global Research & Development | Discovery Technologies

Merck

Merck KGaA | Frankfurter Str. 250 | Postcode: A019/001 | 64293 Darmstadt | 
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Re: [Rdkit-discuss] RDKit-MolVS intergration: Google Summer of Code Project

[Paul Czodrowski]

Susan, great news, looking forward to this project, enjoy GSoC!  Paul

Von: Susan Leung [mailto:susan.le...@st-hildas.ox.ac.uk]
Gesendet: Mittwoch, 25. April 2018 23:35
An: rdkit-discuss@lists.sourceforge.net
Betreff: [Rdkit-discuss] RDKit-MolVS intergration: Google Summer of Code Project

Hi all,

I am really excited and happy to let you know that I will be working with Greg 
on a RDKit-MolVS integration project as part of the Open Chemistry Google 
Summer of 
Code.

I have followed and used the RDKit mailing list since the start of my PhD and 
have used both RDKit and MolVS in my workflow so I'm very excited to have the 
opportunity to contribute to the code base.

In this project we aim to expand the current capabilities of MolVS and 
integrate it into RDKit so hopefully by the end of it, you will see 
improvements in the molecular standardisation tools available in RDKit.

Best wishes,

Susan



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Re: [Rdkit-discuss] [Rdkit-devel] [Announcement] 7th RDKit UGM in Cambridge UK

[Paul Czodrowski]

Great idea about the optional training on the day before.

However, I could not see any link (on the eventbrite page) regarding this 
event. There was an option for the dinner & reception, but no training..

Or is the “main UGM registration” a different place than the evenbrite page?


Paul

Von: Greg Landrum [mailto:greg.land...@gmail.com]
Gesendet: Samstag, 7. April 2018 07:14
An: RDKit Discuss ; RDKit Developers List 

Cc: Andreas Bender, PhD 
Betreff: [Rdkit-devel] [Announcement] 7th RDKit UGM in Cambridge UK

Dear all,

This year's RDKit User Group Meeting will take place from 19-21 September in 
Cambridge, UK and is being hosted by Andreas Bender at Cambridge University.

Registration for the RDKit UGM is free:
https://www.eventbrite.com/e/7th-rdkit-ugm-2018-tickets-44883066460

We will once again mostly stick to what has become a tried and true format:
Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, poster 
sessions, and talktorials. For those who haven’t attended before, talktorials 
are somewhere between a talk and a tutorial, they cover something interesting 
done with the RDKit and include the code used to do the work. During the 
presentation you'll give an overview of what you did and also show the pieces 
of the code that are central to the work. The idea is to mix the science up 
with the tutorial aspects.

Day 3 will be a hackathon: those who choose to stay will spend an intense day 
working in small groups to produce useful artifacts: new bits of code, KNIME 
nodes, KNIME workflows, tutorials, documentation, IPython notebooks, etc. We 
will once again try to structure this a bit by collecting a bunch of ideas for 
things to work on in advance. Two years ago we also did extended tutorials on 
Day 3; if there are volunteers to do tutorials and people interested in 
attending them, we'll repeat that this year as well.

As an experiment this year there will be an optional training day on Tuesday 
the 18th. Andrew Dalke (Dalke Scientific) will offer a course on Python and the 
RDKit and Daria Goldmann (KNIME) will offer a course on KNIME and the RDKit. 
Space for both of these is limited, so we'll do separate registrations for them 
(links will be included on the main UGM registration page). Many thanks to 
Andrew for coming up with the idea to do this!

There will also be, of course, social activities. This year we have the special 
opportunity to have the dinner on the 19th in the Old Library of Pembroke 
College. I can't wait for that. :-)

A more detailed announcement with additional information about place, hotels 
and logistics will follow soon.

We are looking for people who are willing to do presentations, talktorials or 
posters on the first two days. If you're interested in contributing, please 
send Greg and Andreas an email.

Lightning talks don't need to be arranged too far in advance; we will start 
collecting the list of people interested in doing those shortly before the 
event.

Best Regards,
Greg and Andreas



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Re: [Rdkit-discuss] News on 3D molecule visualization in RDKit (project: RDKit - 3Dmol.js integration)

[Paul Czodrowski]

Malitha, this is a great piece of work and I highly recommend all RDKitters to 
have a look at it..

Paul

Von: Malitha Kabir [mailto:malitha12...@gmail.com]
Gesendet: Donnerstag, 31. August 2017 01:54
An: rdkit <rdkit-discuss@lists.sourceforge.net>
Betreff: [Rdkit-discuss] News on 3D molecule visualization in RDKit (project: 
RDKit - 3Dmol.js integration)

Dear all,

I am about to share news on 3D molecule visualization in RDKit.

This summer I have worked as Google Summer Of Codes (GSoC) participant under 
supervision of  Paul Czodrowski and Greg Landrum. The codes were reviewed 
several times by Peter Gedeck and finally merged by Brian Kelley at 
rdkit:GSoC2017 branch.

I would like to request you to check whether those can come in use and drop 
your feedback for the improvement. I will keep working on it's improvement 
throughout the coming month also. Kindly feel free to visit the following link 
for work details: https://github.com/malithakabir/RDKitGSoC2017

In future, I will request information in mailing list whenever I face in 
trouble in codes rdkit code related issues. I wish, you will gladly helping me 
providing information and directions. Many thanks in advance for that.

I am extremely sorry of being unresponsive in mailing list due to the lack of 
my knowledge/ability to answer those. I am trying my best to be responsive in 
mailing list to provide community support.

On a personal note I would like to express my sincere gratitude to my mentors 
(paul and greg) and reviewer (peter) for their time and guidance throughout the 
summer 2017. And warm thanks to Brian for merging the codes.

Thank you very much for your time. Have a great day!

Sincerely,
- malitha



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Re: [Rdkit-discuss] rdkit

[Paul Czodrowski]

Dear Greg (and RDKitters),

good news is: I just re-ran “conda install -c rdkit rdkit”, and at least rdkit 
is working properly.

“import pillow” still does not work.

This is the output of “conda list”:
backports-abc 0.5   
backports.shutil-get-terminal-size 1.0.0 
bleach2.0.0 
boost 1.56.0   py27_3rdkit
bzip2 1.0.6 vc9_3  [vc9]
certifi   2017.4.17 
colorama  0.3.9 
configparser  3.5.0 
decorator 4.0.11
entrypoints   0.2.3 
enum341.1.6 
freetype  2.5.5 vc9_2  [vc9]
functools32   3.2.3.post2   
html5lib  0.9   
idisplay  0.1.2 
ipykernel 4.6.1 
ipython   5.4.1 
ipython-genutils  0.2.0 
ipywidgets6.0.0 
Jinja22.9.6 
jpeg  9bvc9_0  [vc9]
jsonschema2.6.0 
jupyter   1.0.0 
jupyter-client5.0.1 
jupyter-console   5.1.0 
jupyter-core  4.3.0 
libpng1.6.27vc9_0  [vc9]
libtiff   4.0.6 vc9_3  [vc9]
MarkupSafe1.0   
mistune   0.7.4 
mkl   2017.0.1  0
nbconvert 5.2.1 
nbformat  4.3.0 
notebook  5.0.0 
numpy 1.11.3   py27_0
olefile   0.44 py27_0
pandas0.20.1  np111py27_0
pandocfilters 1.4.1 
pathlib2  2.2.1 
pickleshare   0.7.4 
pillow4.2.0py27_0
pip   9.0.1py27_1
prompt-toolkit1.0.14
py3Dmol   0.6.3 
Pygments  2.2.0 
python2.7.131
python-dateutil   2.6.0 
python-dateutil   2.6.0py27_0
pytz  2017.2   py27_0
pyzmq 16.0.2
qtconsole 4.3.0 
scandir   1.5   
setuptools27.2.0   py27_1
setuptools36.0.1
simplegeneric 0.8.1 
singledispatch3.4.0.3   
six   1.10.0   py27_0
six   1.10.0
testpath  0.3.1 
tornado   4.5.1 
traitlets 4.3.2 
vs2008_runtime9.00.30729.5054   0
wcwidth   0.1.7 
webencodings  0.5.1 
wheel 0.29.0   py27_0
widgetsnbextension2.0.0 
win-unicode-console   0.5   
zlib  1.2.8 vc9_3  [vc9]


Best regards,
Paul



Von: Greg Landrum [mailto:greg.land...@gmail.com]
Gesendet: Mittwoch, 5. Juli 2017 06:33
An: Paul Czodrowski <paul.czodrow...@merckgroup.com>
Cc: rdkit <rdkit-discuss@lists.sourceforge.net>
Betreff: Re: [Rdkit-discuss] rdkit

The fact that "import pillow" doesn't work is very suspicious.

Can you please be sure that pillow and the rdkit are both installed in the 
active environment by executing:
"conda list"


On Wed, Jul 5, 2017 at 5:50 AM, Paul Czodrowski 
<paul.czodrow...@merckgroup.com<mailto:paul.czodrow...@merckgroup.com>> wrote:
Dear Greg (and RDKitters),

before it came to this error message, the conda installation of rdkit was 
running properly.
I then did a “conda install pillow” in this conda installation, which now 
results in this error.

BTW, “import pillow” shows:
ImportError   Traceback (most recent call last)
 in ()
> 1 import pillow

ImportError

Re: [Rdkit-discuss] rdkit

[Paul Czodrowski]

Dear Greg (and RDKitters),

before it came to this error message, the conda installation of rdkit was 
running properly.
I then did a “conda install pillow” in this conda installation, which now 
results in this error.

BTW, “import pillow” shows:
ImportError   Traceback (most recent call last)
 in ()
> 1 import pillow

ImportError: No module named pillow


“import rdkit” gives:
---
ImportError   Traceback (most recent call last)
 in ()
> 1 import rdkit

c:\users\m163729\appdata\local\continuum\anaconda2\envs\rdkit_env\lib\site-packages\rdkit\__init__.py
 in ()
  1 try:
> 2   from .rdBase import rdkitVersion as __version__
  3 except ImportError:
  4   __version__ = 'Unknown'
  5   raise

ImportError: DLL load failed: Das angegebene Modul wurde nicht gefunden.


BZW, “import PIL” works without any problems.


It does not make sense to me that a simple “conda install pillow” screws up the 
entire rdkit installion (I have never faced this before, at least when using 
several Linux boxes).

Cheers,
Paul



Von: Greg Landrum [mailto:greg.land...@gmail.com]
Gesendet: Mittwoch, 5. Juli 2017 05:44
An: Paul Czodrowski <paul.czodrow...@merckgroup.com>
Cc: rdkit <rdkit-discuss@lists.sourceforge.net>
Betreff: Re: [Rdkit-discuss] rdkit

Hi Paul,

The small bit of sample code below and the error message make no mention of 
Pillow, did you forget something in your message?

(the error that's there looks like a standard PATH problem, the kind one 
normally doesn't have while using conda)

-greg


On Tue, Jul 4, 2017 at 10:15 PM, Paul Czodrowski 
<paul.czodrow...@merckgroup.com<mailto:paul.czodrow...@merckgroup.com>> wrote:
Dear RDkitters,

I hope not to bother anyone of you with a pillow-related question, but I’m 
facing issues when running this:

from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import AllChem
==>
---
ImportError   Traceback (most recent call last)
 in ()
> 1 from rdkit import Chem
  2 from rdkit.Chem.Draw import IPythonConsole
  3 from rdkit.Chem import AllChem

c:\users\m163729\appdata\local\continuum\anaconda2\envs\rdkit_env\lib\site-packages\rdkit\__init__.py
 in ()
  1 try:
> 2   from .rdBase import rdkitVersion as __version__
  3 except ImportError:
  4   __version__ = 'Unknown'
  5   raise

ImportError: DLL load failed: Das angegebene Modul wurde nicht gefunden.


Sorry for the German message, but I hope that everyone is getting this error…

conda list pillow
Shows the following:
pillow4.2.0py27_0

Prior to the conda installation of pillow, rdkit was running properly..

Any help would be highly appreciated! (but don’t comment like: “please use 
another OS than Windows”)


Cheers,
Paul





________
Paul Czodrowski, PhD

Global Research & Development | Discovery Technologies

Merck

Merck KGaA | Frankfurter Str. 250 | Postcode: A019/001 | 64293 Darmstadt | 
Germany
Phone: +49 6151 72 3218<tel:+49%206151%20723218>
E-mail: paul.czodrow...@merckgroup.com<mailto:paul.czodrow...@merckgroup.com> | 
www.merckgroup.com<http://www.merckgroup.com/>
Mandatory information can be found at: http://www.merckgroup.com/mandatories
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[Rdkit-discuss] rdkit

[Paul Czodrowski]

Dear RDkitters,

I hope not to bother anyone of you with a pillow-related question, but I'm 
facing issues when running this:

from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import AllChem
==>
---
ImportError   Traceback (most recent call last)
 in ()
> 1 from rdkit import Chem
  2 from rdkit.Chem.Draw import IPythonConsole
  3 from rdkit.Chem import AllChem

c:\users\m163729\appdata\local\continuum\anaconda2\envs\rdkit_env\lib\site-packages\rdkit\__init__.py
 in ()
  1 try:
> 2   from .rdBase import rdkitVersion as __version__
  3 except ImportError:
  4   __version__ = 'Unknown'
  5   raise

ImportError: DLL load failed: Das angegebene Modul wurde nicht gefunden.


Sorry for the German message, but I hope that everyone is getting this error...

conda list pillow
Shows the following:
pillow4.2.0py27_0

Prior to the conda installation of pillow, rdkit was running properly..

Any help would be highly appreciated! (but don't comment like: "please use 
another OS than Windows")


Cheers,
Paul





________
Paul Czodrowski, PhD

Global Research & Development | Discovery Technologies

Merck

Merck KGaA | Frankfurter Str. 250 | Postcode: A019/001 | 64293 Darmstadt | 
Germany
Phone: +49 6151 72 3218
E-mail: paul.czodrow...@merckgroup.com<mailto:paul.czodrow...@merckgroup.com> | 
www.merckgroup.com<http://www.merckgroup.com/>
Mandatory information can be found at: http://www.merckgroup.com/mandatories
Pflichtangaben finden Sie unter: http://www.merckgroup.com/mandatories




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Re: [Rdkit-discuss] ipywidgets & py3Dmol

[Paul Czodrowski]

Dear Malitha,
Dear RDKitters,

thanks a lot for your investigations!

Indeed, this issue seems somehow browser-related; please check the attachment 
which shows the output in a different browser (Firefox@openSUSE vs. IE11@Win7 
from my previous mail).

I’m now able to find a button-like widget but no structure…


This presumably looks like off-topic for this mailing list. However, if anyone 
can point into the right direction: that would be highly appreciated.


Cheers,
Paul





Paul Czodrowski, PhD

Global Research & Development | Discovery Technologies

Merck

Merck KGaA | Frankfurter Str. 250 | Postcode: A019/001 | 64293 Darmstadt | 
Germany
Phone: +49 6151 72 3218
E-mail: paul.czodrow...@merckgroup.com<mailto:paul.czodrow...@merckgroup.com> | 
www.merckgroup.com<http://www.merckgroup.com/>
Mandatory information can be found at: http://www.merckgroup.com/mandatories
Pflichtangaben finden Sie unter: http://www.merckgroup.com/mandatories

Von: Malitha Kabir [mailto:malitha12...@gmail.com]
Gesendet: Dienstag, 20. Juni 2017 10:58
An: Paul Czodrowski <paul.czodrow...@merckgroup.com>
Cc: rdkit-discuss@lists.sourceforge.net
Betreff: Re: [Rdkit-discuss] ipywidgets & py3Dmol

Dear Paul,

Kindly consider a few pieces of information provided below.

For your 2nd question:

Widgets are rendered in web browsers. So, in my sense, Python 2.7.13 instead of 
Python 3.5.3 should not cause problem with widget rendering. Python 2.7.13 
should work. My conda install uses Python 2.7.12 and it is working well with 
the notebook you attached.

For your 1st question:

The following stackoverflow discussion might help.
https://stackoverflow.com/questions/36351109/ipython-notebook-ipywidgets-does-not-show

Kindly consider the readme of ipywidgets. 
https://github.com/jupyter-widgets/ipywidgets/blob/master/README.md As per 
their suggestions, if you install ipywidgets using pip then you need to enable 
widgetsnbextension (widgets notebook extension) manually.

Running the following line from shell will do that for you.

jupyter nbextension enable --py --sys-prefix widgetsnbextension
Kindly try out the following code. It should show a slider in your notebook if 
everything is fine.

from __future__ import print_function
import ipywidgets as widgets

slider = widgets.SelectionSlider(
options=[1,2,3],
value=1
)
slider

Probably trying with different web browser may help (I am not sure though)

Best Regards,
Malitha



On Tue, Jun 20, 2017 at 1:56 PM, Paul Czodrowski 
<paul.czodrow...@merckgroup.com<mailto:paul.czodrow...@merckgroup.com>> wrote:
Dear Axel,

thanks a lot for this very helpful information!


The only difference I could figure out:
Python 2.7.13 instead of Python 3.5.3

@RDKitters:
Can this really cause such a different behavior?

Cheers,
Paul

P.S.: I’m aware of http://www.python3statement.org/ ;)


Von: Axel Pahl [mailto:axelp...@gmx.de<mailto:axelp...@gmx.de>]
Gesendet: Dienstag, 20. Juni 2017 09:35
An: 
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Betreff: Re: [Rdkit-discuss] ipywidgets & py3Dmol

Hi Paul,

I just tried the example Notebook that you provided and it runs just as in 
Greg's blog post, i.e. with the interactive slider (see attached screenshot).
This is the configuration I used (in Anaconda):

python3.5.3
rdkit 2017.03.2
notebook  5.0.0
ipywidgets6.0.0
py3Dmol   0.6.3

Kind regards,
Axel
On 20.06.2017 07:48, Paul Czodrowski wrote:
Dear RDKitters,

When trying to re-run Greg’s wonderful blog entry about the py3Dmol integration 
(https://rdkit.blogspot.de/2016/07/using-ipywidgets-and-py3dmol-to-browse.html 
), I’m getting a different behavior (check the attachment with a screenshot and 
the jupyter notebook).

Any help would be appreciated.

Cheers,
Paul




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Re: [Rdkit-discuss] ipywidgets & py3Dmol

[Paul Czodrowski]

Dear Axel,

thanks a lot for this very helpful information!


The only difference I could figure out:
Python 2.7.13 instead of Python 3.5.3

@RDKitters:
Can this really cause such a different behavior?

Cheers,
Paul

P.S.: I'm aware of http://www.python3statement.org/ ;)


Von: Axel Pahl [mailto:axelp...@gmx.de]
Gesendet: Dienstag, 20. Juni 2017 09:35
An: rdkit-discuss@lists.sourceforge.net
Betreff: Re: [Rdkit-discuss] ipywidgets & py3Dmol

Hi Paul,

I just tried the example Notebook that you provided and it runs just as in 
Greg's blog post, i.e. with the interactive slider (see attached screenshot).
This is the configuration I used (in Anaconda):

python3.5.3
rdkit 2017.03.2
notebook  5.0.0
ipywidgets6.0.0
py3Dmol   0.6.3

Kind regards,
Axel

On 20.06.2017 07:48, Paul Czodrowski wrote:
Dear RDKitters,

When trying to re-run Greg's wonderful blog entry about the py3Dmol integration 
(https://rdkit.blogspot.de/2016/07/using-ipywidgets-and-py3dmol-to-browse.html 
), I'm getting a different behavior (check the attachment with a screenshot and 
the jupyter notebook).

Any help would be appreciated.

Cheers,
Paul




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[Rdkit-discuss] ipywidgets & py3Dmol

[Paul Czodrowski]

Dear RDKitters,

When trying to re-run Greg's wonderful blog entry about the py3Dmol integration 
(https://rdkit.blogspot.de/2016/07/using-ipywidgets-and-py3dmol-to-browse.html 
), I'm getting a different behavior (check the attachment with a screenshot and 
the jupyter notebook).

Any help would be appreciated.

Cheers,
Paul




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WidgetInsidepy3Dmol.ipynb
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[Rdkit-discuss] RDKit-Py3DMol integration

[Paul Czodrowski]

Dear RDkitters,

This is to inform you exciting community Malitha Kabir who will working as a 
GoogeSummerOfCode (GSoC) student over the next couple couple of weeks on the 
RDKit-Py3DMol integration.

Let's give Malitha a warm welcome (and comprehensive replies during his GSoC 
project)!

On behalf of the mentors: Greg & Paul




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[Rdkit-discuss] OCEAN: Our Target Prediction Paper (including Source Code)

[Paul Czodrowski]

Dear RDKitters,

Our target prediction method - fully based on RDKit - has become online:
OCEAN: Optimized Cross rEActivity estimatioN
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00067

The source code can be found here:
https://github.com/rdkit/OCEAN

We will give a talk as well an hands-on workshop at the upcoming RDKit UGM end 
of October.

Cheers,
Guido & Paul



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[Rdkit-discuss] PostDoc position available

[Paul Czodrowski]

Dear RDKitters,

this is slightly off topic, but nonetheless of interest to some of you. We are 
looking for a PostDoc heavily using RDKit for our PredictiveModels machinery at 
Merck in Darmstadt. Please find below the announcement and contact me via email 
if you are interested.

Cheers,
Paul

"

Postdoctoral researcher for predictive models in drug design (m/f)



Your role: Merck is striving for leadership in the application of Digital 
Technologies across its various Businesses. In this context we are offering a 
Post Doc Position for the development and application of Machine Learning and 
Deep Learning. These techniques will be used for the prediction of 
toxicological and pharmacological endpoints. You will closely interact with 
internal experts from toxicology, medicinal chemistry, drug design, and with a 
leading academic research group in the field of Deep Learning. As outcome of 
your work, you will have a direct impact on fighting major diseases, like 
cancer.

The position is initially limited to 2 years.



As exemplary publication outlining the techniques, the interested candidate may 
have a look at our publication: http://pubs.acs.org/doi/abs/10.1021/ci400308z

You will integrate your developed tools and models into our in house tool MOCCA 
"Merck Online Computational Chemistry Analyzer".

For a brief MOCCA introduction, please have a look here: 
https://github.com/rdkit/UGM_2015/blob/master/Presentations/LightningTalk_PaulCzodrowski.pdf.



Who you are:
* PhD in Life Sciences (e.g. Chemistry, Pharmacy or Bioinformatics) or 
Computer Science
* In depth experience with Machine Learning and/or Deep Learning
* Excellent knowledge of statistics
* Solid background in the development of scientific software 
(preferred: Python/Django/RDKit/RESTful)
* You are a team player, communicative and have an out-going personality
"



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Re: [Rdkit-discuss] Pandas dataframe manipulation

[Paul Czodrowski]

Maciek, thanks for the note via private message!
To all of you: Here comes the solution to just skip entries inside a column 
that contain a combination of float and “>” :

pd.read_csv('test_mw_r2.csv', sep=';', converters={'r2': lambda x: np.NaN if x 
and x[0] == '>' else x}).dropna(axis=0)


Paul

Von: Maciek Wójcikowski [mailto:mac...@wojcikowski.pl]
Gesendet: Freitag, 11. März 2016 12:29
An: Paul Czodrowski <paul.czodrow...@merckgroup.com>
Cc: rdkit <rdkit-discuss@lists.sourceforge.net>
Betreff: Re: [Rdkit-discuss] Pandas dataframe manipulation

Hi Paul,

I would suggest:

  *   assigning dtype of dataframe/column to str/np.object
  *   cleaning up the IC50s
  *   casting to float/int as dataframe.astype()
Or alternatively you could use "converters" argument:
pd.read_csv('filename.csv', converters={'ic50_colname': lambda x: 
x.replace('>', '')})

http://pandas.pydata.org/pandas-docs/stable/generated/pandas.read_csv.html


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl<mailto:mac...@wojcikowski.pl>

2016-03-11 11:12 GMT+01:00 Paul Czodrowski 
<paul.czodrow...@merckgroup.com<mailto:paul.czodrow...@merckgroup.com>>:
Dear RDKitter & Pandas-Dataframes heavy users,

please find below a question concerning the conversion of pandas dataframes:
df = pd.DataFrame({"item": ["a", "b", "c", "d", "e"], "row1": [1,2,3,">2",5], 
"row2":[0.1,0.2,0.3,0.4,0.5],"row3":["ab","cd","ed","gh","ij"]})
df_new = df[df[["row1"]].applymap(np.isreal).all(1)]

I would like to get rid of this nasty ">2" entry in "row1" => This works 
perfect  given the snippet above.

However, when I read in a CSV file containing similar data (see the attached 
CSV) => The conversion does not work: all columns in the IC50 value are 
discarded and end up in yielding "NaN".

What is going wrong?


Thanks & Cheers,
Paul



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[Rdkit-discuss] Pandas dataframe manipulation

[Paul Czodrowski]

Dear RDKitter & Pandas-Dataframes heavy users,

please find below a question concerning the conversion of pandas dataframes:
df = pd.DataFrame({"item": ["a", "b", "c", "d", "e"], "row1": [1,2,3,">2",5], 
"row2":[0.1,0.2,0.3,0.4,0.5],"row3":["ab","cd","ed","gh","ij"]})
df_new = df[df[["row1"]].applymap(np.isreal).all(1)]

I would like to get rid of this nasty ">2" entry in "row1" => This works 
perfect  given the snippet above.

However, when I read in a CSV file containing similar data (see the attached 
CSV) => The conversion does not work: all columns in the IC50 value are 
discarded and end up in yielding "NaN".

What is going wrong?


Thanks & Cheers,
Paul



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[Rdkit-discuss] Weird iPython PandasTools notebook lookfeel

[Paul . Czodrowski]

Dear RDKitters,

on my new Windows laptop, I tried one of the PandasTools examples, which 
should give this output:

 sdfFile = os.path.join(RDConfig.RDDataDir,'NCI/first_200.props.sdf')
 frame = 
PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
 frame.info # doctest: +SKIP
bound method DataFrame.info of class 'pandas.core.frame.DataFrame'
Int64Index: 200 entries, 0 to 199
Data columns:
AMW   200  non-null values
CLOGP 200  non-null values
CP200  non-null values
CR200  non-null values
DAYLIGHT.FPG  200  non-null values
DAYLIGHT_CLOGP200  non-null values
FP200  non-null values
ID200  non-null values
ISM   200  non-null values
LIPINSKI_VIOLATIONS   200  non-null values
NUM_HACCEPTORS200  non-null values
NUM_HDONORS   200  non-null values
NUM_HETEROATOMS   200  non-null values
NUM_LIPINSKIHACCEPTORS200  non-null values
NUM_LIPINSKIHDONORS   200  non-null values
NUM_RINGS 200  non-null values
NUM_ROTATABLEBONDS200  non-null values
P130  non-null values
SMILES200  non-null values
Molecule  200  non-null values
dtypes: object(20)


However, in my case, I end up in such an output (mostly truncated):

 frame = 
PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
Patching pandas
 frame.info
bound method DataFrame.info ofAMW  CLOGPCP
  CR DAYLIGHT.FPG DAYLIGHT_CLOGP   
  FP ID  ISM 
LIPINSKI_VIOLATIONS NUM_HACCEPTORS NUM_HDONORS NUM_HETEROATOMS 
NUM_LIPINSKIHACCEPTORS NUM_LIPINSKIHDONORS NUM_RINGS NUM_ROTATABLEBONDS  
P1
[...]


Interestingly, on my Linux PC, the output for frame.info looks as 
expected.

The only difference between the two PandasTools installations:

try:
  import pandas as pd
  if 'display.width' in  pd.core.config._registered_options:
pd.set_option('display.width',20)
  if 'display.height' in  pd.core.config._registered_options:
pd.set_option('display.height',20)
  if 'display.max_colwidth' in  pd.core.config._registered_options:
pd.set_option('display.max_colwidth',20)
  #saves the default pandas rendering to allow restauration
  defPandasRendering = pd.core.frame.DataFrame.to_html
except ImportError:
  pd = None

= I changed this on my Windows laptop according to one hint from Paul 
Emsley.



Cheers  Thanks,
Paul


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Re: [Rdkit-discuss] Weird iPython PandasTools notebook lookfeel

[Paul . Czodrowski]

Dear Riccardo,

upps, that did the job!
Thanks!

Bur I have another:
 import os
 from rdkit import RDConfig
 sdfFile = os.path.join(RDConfig.RDDataDir,'NCI/first_200.props.sdf')
 frame = 
PandasTools.LoadSDF(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
 frame[['Molecule']].head(2)
==

   
Molecule
0  img src=
data:image/png;base64,iVBORw0KGgoNSUhEUgAAASwAAAEsCAIAAAD2HxkiAAA
[...]


 frame[['SMILES']].head(2)

   SMILES
0   CC1=CC(=O)C=CC1=O
1  c1ccc2sc(SSc3nc4c4s3)nc2c1




Cheers  Thanks,
Paul




From:   Riccardo Vianello riccardo.viane...@gmail.com
To: paul.czodrow...@merckgroup.com, 
Date:   26.09.2014 09:13
Subject:Re: [Rdkit-discuss] Weird iPython PandasTools notebook 
lookfeel



Hi Paul,

I'm not a regular pandas user, so this comment could be misplaced, but 
from this output:

On Fri, Sep 26, 2014 at 9:02 AM, paul.czodrow...@merckgroup.com wrote:
 frame.info # doctest: +SKIP 
bound method DataFrame.info of class 'pandas.core.frame.DataFrame' 

it looks like you might be looking at the textual representation of the 
frame.info method, instead of calling it and look at its output with 
frame.info(). Is this intended?

Best regards,
Riccardo



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[Rdkit-discuss] PandasTools on Windows iPython notebook

[Paul . Czodrowski]

Dear RDKitter,

on my new Windows laptop, I run into this issue:

import pandas as pd
import rdkit.Chem as Chem
from rdkit.Chem import PandasTools

=

ValueErrorTraceback (most recent call 
last)
ipython-input-6-52de9e808c94 in module()
  1 import pandas as pd
  2 import rdkit.Chem as Chem
 3 from rdkit.Chem import PandasTools
  4 #import os
  5 #from rdkit import RDConfig

C:\RDKit_2013_06_1\rdkit\Chem\PandasTools.py in module()
 87   import pandas as pd
 88   if 'display.width' in  pd.core.config._registered_options:
--- 89 pd.set_option('display.width',1000)
 90   if 'display.height' in  pd.core.config._registered_options:
 91 pd.set_option('display.height',1000)

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in __call__(self, *args, **kwds)
215 
216 def __call__(self, *args, **kwds):
-- 217 return self.__func__(*args, **kwds)
218 
219 @property

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in _set_option(*args, **kwargs)
116 o = _get_registered_option(key)
117 if o and o.validator:
-- 118 o.validator(v)
119 
120 # walk the nested dict

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in inner(x)
780 def inner(x):
781 if not isinstance(x, _type):
-- 782 raise ValueError(Value must be an instance of %s % 
type_repr)
783 
784 return inner

ValueError: Value must be an instance of type 'NoneType'|type 'int' 


Is this familiar to anyone?


Cheers  Thanks,
Paul


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Re: [Rdkit-discuss] PandasTools on Windows iPython notebook

[Paul . Czodrowski]

height has been deprecated.

but, it works!

thanks, paul!!!


paul



From:   Paul Emsley pems...@mrc-lmb.cam.ac.uk
To: rdkit-discuss@lists.sourceforge.net, 
Date:   25.09.2014 19:32
Subject:Re: [Rdkit-discuss] PandasTools on Windows iPython 
notebook



On 25/09/14 18:06, paul.czodrow...@merckgroup.com wrote:
Dear RDKitter, 

on my new Windows laptop, I run into this issue: 
 
import pandas as pd 
import rdkit.Chem as Chem 
from rdkit.Chem import PandasTools 
 
= 
 
ValueErrorTraceback (most recent call 
last)
ipython-input-6-52de9e808c94 in module()
 1 import pandas as pd
 2 import rdkit.Chem as Chem
 3 from rdkit.Chem import PandasTools
 4 #import os
 5 #from rdkit import RDConfig

C:\RDKit_2013_06_1\rdkit\Chem\PandasTools.py in module()
87   import pandas as pd
88   if 'display.width' in  pd.core.config._registered_options:
--- 89 pd.set_option('display.width',1000)
90   if 'display.height' in  pd.core.config._registered_options:
91 pd.set_option('display.height',1000)

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in __call__(self, *args, **kwds)
   215 
   216 def __call__(self, *args, **kwds):
-- 217 return self.__func__(*args, **kwds)
   218 
   219 @property

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in _set_option(*args, **kwargs)
   116 o = _get_registered_option(key)
   117 if o and o.validator:
-- 118 o.validator(v)
   119 
   120 # walk the nested dict

C:\Users\m163729\AppData\Local\Continuum\Anaconda\lib\site-packages\pandas\core\config.py
 
in inner(x)
   780 def inner(x):
   781 if not isinstance(x, _type):
-- 782 raise ValueError(Value must be an instance of %s % 
type_repr)
   783 
   784 return inner

ValueError: Value must be an instance of type 'NoneType'|type 'int' 
 

Is this familiar to anyone? 

Here's a guess: 

Try changing 1000 to 20 (2 billion) in PandaTools.py 

Paul.
 



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Re: [Rdkit-discuss] question on MatchedPairs

[Paul . Czodrowski]

 
 If what you are looking for is information about what type of atom 
 [*:1] is in the original molecule, I think you can probably figure 
 it out based on the additional info that's present in the output 
 from Jameed's code.
 
 For example, here's one of the output lines from an indexing.py run 
 that I did for an RDKit blog post I'm working on (hopefully going up 
today):
 Cc1c(CCN2CCNCC2)ccc3cc(F)ccc13,Fc1ccc2cc(CCN3CCNCC3)ccc2c1,521767,
 521766,[*:1]C[*:1][H],[*:1]c1c(CCN2CCNCC2)ccc2cc(F)ccc21
 The last entry in that line is the core, which shows where the [*:
 1] is attached.
 
 Using these cores, you can get information about where points are 
 attached to them like this:
 In [2]: m = Chem.MolFromSmiles('[*:1]c1c(CCN2CCNCC2)ccc2cc(F)ccc21')
 In [3]: attaches = [x for x in m.GetAtoms() if x.GetAtomicNum()==0]
 In [7]: for at in attaches:
 if at.HasProp(molAtomMapNumber):
 nbr = at.GetNeighbors()[0]
 print at.GetProp(molAtomMapNumber),nbr.GetSymbol
 (),nbr.GetIsAromatic()
...: 
 1 C True
 
 This says that attachment point 1 is connected to a carbon which is 
aromatic.
 
 Does that help?

Absolutely, this saves my day!

Thank you very much for this snippet!


Paul


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[Rdkit-discuss] question on MatchedPairs

[Paul . Czodrowski]

Dear RDKitters,

I'm using Jameed's wonderful code for a matched pair analysis.

Given such a transformation string [*:1]C[*:1][H]
= How do I check if [*:1] is an aromatic or an aliphatic atom?


I fear that this can only be done by going back into the original 
data/output, or am I wrong ?


Cheers  Thanks,
Paul


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Re: [Rdkit-discuss] Chem.PandasTools

[Paul . Czodrowski]

Dear Grégori, 

when storing the image into a new data frame:

MMP_reaction = Chem.rdChemReactions.ReactionFromSmarts([*:1][H][*:1]C)
newnew_df = pd.DataFrame(columns=['fig'],index=[1] )
newnew_df['fig'].ix[1] = Draw.ReactionToImage(MMP_reaction)


apparently, the image can be stored in a data frame, but in the ipython 
notebook it is displayed as PIL image



Cheers  Thanks so far (in particular for the impressive speed in 
response!),
Paul

 Hi Paul,
 
 You first have to read the MMP into a reaction object 
 (Chem.ReactionFromSmarts).
 
 Greg
 
 On Friday, May 9, 2014, paul.czodrow...@merckgroup.com wrote:
 Dear Gregori  Samo,
 
 thanks for your hints.
 
 I just tried running
 
 Draw.ReactionToImage([*:1][H][*:1]C)
 
 =
 
 AttributeError: 'str' object has no attribute 'GetNumReactantTemplates'
 
 
 
 BTW, how would I finally add a picture to a Pandas data frame?
 
 
 Cheers,
 Paul


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[Rdkit-discuss] Chem.PandasTools

[Paul . Czodrowski]

Dear RDKitters,

I started to play around with the great Chem.PandasTool contribution 
provided by Nicholas and Samo.

Given such a data frame:

Transformation  npairs
1   [*:1][H][*:1]C5


how do I depict the molecular transformation in the dataframe?


I guess that I somehow have to integrate this function

def showLine_MMP(in_string):
f = in_string.split(\t)
LHS = Chem.MolFromSmiles(f[0].split()[0])
RHS = Chem.MolFromSmiles(f[0].split()[1])
mols.append(LHS)
mols.append(RHS)
return Draw.MolsToGridImage(mols,molsPerRow=2)


but I'm not sure how to accomplish this.


Cheers  Thanks,
Paul


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Re: [Rdkit-discuss] Chem.PandasTools

[Paul . Czodrowski]

Dear Gregori  Samo,

thanks for your hints.

I just tried running

Draw.ReactionToImage([*:1][H][*:1]C)

=

AttributeError: 'str' object has no attribute 'GetNumReactantTemplates'



BTW, how would I finally add a picture to a Pandas data frame?


Cheers,
Paul


 
 Hi Paul,
 
 The Draw modules also contains a ReactionToImage function;
 Your MMP can be read as a reaction.
 Hope this helps further!
 
 Grégori


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Re: [Rdkit-discuss] Possible rotatable bonds replacement

[Paul . Czodrowski]

 I could add the new descriptor as Toby provided it. People are then 
 free to pick between NumRotatableBonds() and NumStrictRotatableBonds
 (). This has the advantage of maintaining strict backwards 
 compatibility, but I could imagine it being confusing/irritating to 
 people using the code to have to choose between them (or, worse, using 
both).
 
 Another option is to just replace the current NumRotatableBonds() 
 SMARTS with the new one.
 This loses backwards compatibility, but replaces NumRotableBonds() 
 with something more correct.
 
 Finally, I could take a hybrid approach: replace the default 
 NumRotatableBonds() with the new one, but add an extra argument that
 allows the old one to be used.

 
 I'm leaning towards the second option. I'd normally go with the 
 third, but I almost view this as a bug fix for the rotatable bonds 
definition.
 
 Comments? suggestions? Other options?

I like your idea of your hybrid approach which would mean backwards 
compatibility.


paul



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[Rdkit-discuss] aggdraw freetype2

[Paul . Czodrowski]

Dear RDKitters,

on my Win7/32 bit /RDKit system, I just installed aggdraw, but apparently 
without great success:



---
IOError   Traceback (most recent call 
last)
ipython-input-7-8252074dc7a2 in module()
 1 Draw.MolsToGridImage(mols)

C:\RDKit_2013_03_1\rdkit\Chem\Draw\__init__.pyc in MolsToGridImage(mols, 
molsPerRow, subImgSize, legends, **kwargs)
252 row = i//molsPerRow
253 col = i%molsPerRow
-- 254 
res.paste(MolToImage(mol,subImgSize,legend=legends[i],**kwargs),(col*subImgSize[0],row*subImgSize[1]))
255   return res
256 

C:\RDKit_2013_03_1\rdkit\Chem\Draw\__init__.pyc in MolToImage(mol, size, 
kekulize, wedgeBonds, **kwargs)
 80 legend=''
 81 
--- 82   drawer.AddMol(mol,**kwargs)
 83 
 84   if legend:

C:\RDKit_2013_03_1\rdkit\Chem\Draw\MolDrawing.pyc in AddMol(self, mol, 
centerIt, molTrans, drawingTrans, highlightAtoms, confId, 
flagCloseContactsDist, highlightMap, ignoreHs, highlightBonds, **kwargs)
467 else:
468   color = self.elemDict.get(atom.GetAtomicNum(),(0,0,0))
-- 469 self._drawLabel(symbol, pos, font, 
color=color,orientation=orient)
470 
471 if flagCloseContactsDist0:

C:\RDKit_2013_03_1\rdkit\Chem\Draw\MolDrawing.pyc in _drawLabel(self, 
label, pos, font, color, **kwargs)
282 y1 = pos[1]
283 labelP = x1,y1
-- 284 self.canvas.addCanvasText(label,(x1,y1),font,color,**kwargs)
285 
286   def 
AddMol(self,mol,centerIt=True,molTrans=None,drawingTrans=None,

C:\RDKit_2013_03_1\rdkit\Chem\Draw\aggCanvas.pyc in addCanvasText(self, 
text, pos, font, color, **kwargs)
 81 orientation=kwargs.get('orientation','E')
 82 color = convertColor(color)
--- 83 aggFont = 
Font(color,faceMap[font.face],size=font.size*self.fontScale)
 84 
 85 blocks = list(re.finditer(r'\(.+?)\(.+?)\/\1\',text))

IOError: cannot load font (no text renderer)


freetype2 was installed via the package provided from this web site:
http://gnuwin32.sourceforge.net/packages/freetype.htm


Apparently, freetype2 is still not supported when running the aggdraw 
installtion.

For doing this, I changed aggdraw's setup.py to point to the correct 
freetype2 installation, but then the aggdraw installation gives a nasty 
error:

running install
running build
running build_ext
building 'aggdraw' extension
creating build
creating build\temp.win32-2.7
creating build\temp.win32-2.7\Release
creating build\temp.win32-2.7\Release\agg2
creating build\temp.win32-2.7\Release\agg2\src
creating build\temp.win32-2.7\Release\agg2\font_freetype
C:\Anaconda\Scripts\gcc.bat -mdll -O -Wall -DHAVE_FREETYPE2 -Iagg2/include 
-Iagg2/font_freetype -Ifreetype2.3.5.1/include 
-Ifreetype2.3.5.1/include/freetype2 -IC:\Anaconda\include -IC:\Anaconda\PC 
-c aggdraw.cxx -o build\temp.win32-2.7\Release\aggdraw.o
In file included from agg2/font_freetype/agg_font_freetype.h:28:0,
 from aggdraw.cxx:60:
agg2/include/agg_scanline_storage_bin.h: In member function 'unsigned int 
agg::scanline_storage_bin::byte_size() const':
agg2/include/agg_scanline_storage_bin.h:247:38: warning: unused variable 
'sp' [-Wunused-variable]
aggdraw.cxx: In member function 'void 
draw_adaptorPixFmt::drawtext(float*, PyObject*, FontObject*)':
aggdraw.cxx:332:45: error: there are no arguments to 'text_getchar' that 
depend
on a template parameter, so a declaration of 'text_getchar' must be 
available [-fpermissive]
aggdraw.cxx:332:45: note: (if you use '-fpermissive', G++ will accept your 
code, but allowing the use of an undeclared name is deprecated)
aggdraw.cxx: In function 'PyObject* draw_new(PyObject*, PyObject*)':
aggdraw.cxx:504:71: warning: deprecated conversion from string constant to 
'char*' [-Wwrite-strings]
aggdraw.cxx:530:67: warning: deprecated conversion from string constant to 
'char*' [-Wwrite-strings]
aggdraw.cxx:533:69: warning: deprecated conversion from string constant to 
'char*' [-Wwrite-strings]
aggdraw.cxx:536:69: warning: deprecated conversion from string constant to 
'char*' [-Wwrite-strings]
aggdraw.cxx:539:71: warning: deprecated conversion from string constant to 
'char*' [-Wwrite-strings]
aggdraw.cxx: In function 'agg::rgba8 getcolor(PyObject*, int)':
aggdraw.cxx:639:72: warning: deprecated conversion from string constant to 
'char*' [-Wwrite-strings]
aggdraw.cxx: In function 'PyObject* draw_textsize(DrawObject*, 
PyObject*)':
aggdraw.cxx:968:13: warning: unused variable 'error' [-Wunused-variable]
aggdraw.cxx: In function 'PyObject* draw_flush(DrawObject*, PyObject*)':
aggdraw.cxx:1059:72: warning: deprecated conversion from string constant 
to 'char*' [-Wwrite-strings]
aggdraw.cxx:1059:72: warning: deprecated conversion from string constant 
to 'char*' [-Wwrite-strings]
aggdraw.cxx: In function 'void draw_dealloc(DrawObject*)':
aggdraw.cxx:1114:18: warning: deleting object of abstract class type 

[Rdkit-discuss] docker.io - container for fully fledged rdkit installation on linux?

[Paul . Czodrowski]

Dear RDKitters,

a few days ago, I came across one technology named docker
(http://www.docker.io/): it provides a possibility to ship a complete Linux
distribution into one container.


It attracted my interest, since I remembered one situation from the
GordonResearchConference on CADD, where I gave a workshop on using RDKit
(https://github.com/pzc/cadd-grc-2013). I was asked to run through a
hands-on installation of RDKit.

I declined to to do so due to the lack of time... Maybe some of the RDKit
pros would have done a better job!

However, what do you think of providing a docker-shipped Linux container
including a fully fledged RDKit installation?

I'm not sure if I'm skilled enough to finally pack RDKit ( Linux) into one
container, but maybe someone of the mailing list could assist me in doing
this job.


Cheers,
Paul

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Re: [Rdkit-discuss] pandas / sd-tags

[Paul . Czodrowski]

Dear Niko,

I was exactly looking for this functionality, great work!

A few follow-up questions:
* frame.set_index('_Name') did not work, but there is a name set in the SD 
file.
* Is there a way to load in only a specified list of SD tags? (I didn't 
find a names parameter for LoadSDF)
* frame.head() frame.describe() give a property ID, which is not present 
in my SD file. Where does it come from?
* frame.describe() does not show the basic statistics of the SD file.

The last three points are due to the fact that PandasTools.LoadSDF has 
fewer functionalities than PandasTools.read_table?


Cheers  big thanks again,
Paul


 
 Hi Paul,
 I am not sure if it is easily doable to get the pandas read_table 
 function to handle sd-files. However, there is some basic 
 functionality for this already built-in in the PandasTools module. 
 If you check the docktest header there is a small example. Basically, 
 
 frame = PandasTools.LoadSDF
 
(sdfFile,smilesName='SMILES',molColName='Molecule',includeFingerprints=True)
 
 loads the data from an sd-file into a dataframe, such that every 
 molecule entry corresponds to a row with the molecule in the column 
 'Molecule'. The specified smiles column is generated automatically 
 and every sd-property ends up in a column with the respective 
 property name. Additionally, if there is a property _Name set for 
 the molecule that is used as a row identifier - I assume this could 
 be made customisable in the future.
 Is this something you could use? 
 
 Kind regards,
 Niko
 
 On Jun 30, 2013, at 5:10 PM, paul.czodrow...@merckgroup.com wrote:
 
 Dear RDKitters,
 
 I was wondering if anyone has looked into the Pandas data frame with 
 respect to read in a SD file similar to this syntax:
 
 data = 
 pd.read_table(open('whatever.smi','r'),header=None,names=
 ['smiles','cas','mutagenic'])
 
 Ideally, names would be automatically set according to the SD tags.
 
 
 Cheers  Thanks,
 Paul


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[Rdkit-discuss] PyMOL-Integration

[Paul . Czodrowski]

Dear RDKitters,

when testing the PyMOL integration (given the iPython notebook from the 
tutorial):


from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import RDConfig
import os
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
cdk2mols = [x for x in Chem.SDMolSupplier('data/cdk2.sdf',removeHs=True) 
if x is not None]
from rdkit.Chem import PyMol
v = PyMol.MolViewer()
v.ShowMol(cdk2mols[0])
v.GetPNG(h=300)


I run into an error:

 2 v.GetPNG(h=300)

C:\RDKit_2013_03_1\rdkit\Chem\PyMol.py in GetPNG(self, h, w)
214   except IOError:
215 time.sleep(0.1)
-- 216 os.unlink(fd.name)
217 fd=None
218 if h is not None or w is not None:

WindowsError: [Error 32]

The actual error message is in German: there is already a temporary PNG 
written, that cannot be over-written.


Cheers  Thanks,
Paul


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[Rdkit-discuss] MMP analysis - active vs. inactive compounds

[Paul . Czodrowski]

Dear RDKitters,

has anyone applied Jameed's great code to the following scenario:
- Perform a MMP analysis with respect to a particular property (e.g. 
activity)

Given the current code, I do not see any chance to consider any property 
besides the compound ID.

It is also not possible to provide 2 files (one for the active compounds, 
one for the inactive compounds) - or am I wrong?


Cheers  Thanks,
Paul


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Re: [Rdkit-discuss] any experience boost::bad_any_cast

[Paul . Czodrowski]

Dear Greg,

thanks a lot for the build!

Unfortunately, the same error appears.

Strangely enough, the SD export works fine with our Linux installation.


Cheers  Thanks,
Paul

 https://rdkit.googlecode.com/files/RDKit_2013_03_1beta2.win32.py27.zip
 
 On Tue, Apr 23, 2013 at 10:44 AM, Greg Landrum greg.land...@gmail.com 
wrote:
  ok, I'll do a build either this evening or tomorrow a.m.
 
  On Tue, Apr 23, 2013 at 6:58 AM,  paul.czodrow...@merckgroup.com 
wrote:
  Yes, I would love to try out the windows build.
 
  Thank you so much!
 
 
  paul
 
 
  
   For the new beta, there is currently no compiled win32bit version
   available, or am I wrong?
  
 
  You're correct. I didn't do a windows binary. If you'd like to test 
it
  let me know; I can do a build and upload it.
 
  -greg


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Re: [Rdkit-discuss] any experience boost::bad_any_cast

[Paul . Czodrowski]

import sys,gzip,os
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.ML.Descriptors import MoleculeDescriptors

inF  = sys.argv[1]
if inF.endswith(.sdf.gz) or inF.endswith(.sd.gz):
cpds = [x for x in  Chem.ForwardSDMolSupplier(gzip.open(sys.argv[1])) 
if x is not None]
else:
cpds = [x for x in  Chem.SDMolSupplier(inF) if x is not None]

outF = inF+.descr.sdf
cpds_out = Chem.SDWriter(outF)
nms=[x[0] for x in Descriptors._descList]
for dedede in nms:
print dedede
#nms.remove('MolecularFormula')

calc = MoleculeDescriptors.MolecularDescriptorCalculator(nms)


for i in range(len(cpds)):
print i
descrs = calc.CalcDescriptors(cpds[i])
for x in range(len(descrs)):
cpds[i].SetProp(str(nms[x]),str(descrs[x]))
cpds_out.write(cpds[i])
cpds_out.close()
f_in = open(outF, 'rb')
file_name_gz = outF+.sdf.gz
f_out = gzip.open(file_name_gz, 'wb')
f_out.writelines(f_in)
os.remove(outF)



From:   Greg Landrum greg.land...@gmail.com
To: paul.czodrow...@merckgroup.com paul.czodrow...@merckgroup.com
Cc: rdkit-discuss@lists.sourceforge.net 
rdkit-discuss@lists.sourceforge.net
Date:   24.04.2013 17:46
Subject:Re: [Rdkit-discuss] any experience boost::bad_any_cast



Hrm, that's odd. Are you calling SetProp at any point on molecules that 
are being written to that file?

Any chance you can send a script that shows the problem? It would be 
great to get this fixed before the release later this week.


On Wednesday, April 24, 2013, wrote:
Dear Greg,

thanks a lot for the build!

Unfortunately, the same error appears.

Strangely enough, the SD export works fine with our Linux installation.


Cheers  Thanks,
Paul

 https://rdkit.googlecode.com/files/RDKit_2013_03_1beta2.win32.py27.zip

 On Tue, Apr 23, 2013 at 10:44 AM, Greg Landrum greg.land...@gmail.com
wrote:
  ok, I'll do a build either this evening or tomorrow a.m.
 
  On Tue, Apr 23, 2013 at 6:58 AM,  paul.czodrow...@merckgroup.com
wrote:
  Yes, I would love to try out the windows build.
 
  Thank you so much!
 
 
  paul
 
 
  
   For the new beta, there is currently no compiled win32bit version
   available, or am I wrong?
  
 
  You're correct. I didn't do a windows binary. If you'd like to test
it
  let me know; I can do a build and upload it.
 
  -greg


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Re: [Rdkit-discuss] any experience boost::bad_any_cast

[Paul . Czodrowski]

Dear Greg,


 
 Hi Paul,
 
 On Sun, Apr 21, 2013 at 2:01 PM,  paul.czodrow...@merckgroup.com 
wrote:
  Dear RDKitters,
 
  did anyone running into this error message when outputting a SDF:
  RuntimeError: boost::bad_any_cast: failed conversion using 
boost::any_cast
 
 One of the bug fixes in the next release (currently in beta) should
 help with this one.
 
 If it doesn't, or if you can't install either the beta or the svn
 version of the RDKit, it's probably relatively easy for me to get it
 fixed if you can provide an example script/data that shows the
 problem.
 
 -greg


For the new beta, there is currently no compiled win32bit version 
available, or am I wrong?


Paul


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[Rdkit-discuss] any experience boost::bad_any_cast

[Paul . Czodrowski]

Dear RDKitters,

did anyone running into this error message when outputting a SDF:
RuntimeError: boost::bad_any_cast: failed conversion using boost::any_cast

Cheers  Thanks,
Paul

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[Rdkit-discuss] Domain of appicability

[Paul . Czodrowski]

Dear RDKitters,

anyone worked with RDKit (data processing  descriptor calculation)  
scikit-learn (train Random Forests) and could share some experiences with 
setting up a domain of application?

Cheers  Thanks so far,
Paul


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[Rdkit-discuss] Domain of applicability

[Paul . Czodrowski]

Dear RDKitters,

anyone worked with RDKit (data processing  descriptor calculation)  
scikit-learn (train Random Forests) and could share some experiences with 
setting up/defining a domain of applicability?

Cheers  Thanks so far,
Paul


P.S.: Just resent this mail, since the last mail contained typos which 
might make future searches for keywords in the mailing list quite 
challenging... ;)


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Re: [Rdkit-discuss] windows binary installation

[Paul . Czodrowski]

Dear RDKitters,


thanks all to you for your quick help!

Sorry my typo in the setting of the environment variables - if I meet any 
of you guys in the near future, I will offer him a drink, promised!


Cheers  Thanks again!

Paul


 Subject: Re: [Rdkit-discuss] windows binary installation
 
 Morning,
 
 Find below the script I use to set those variables. (changed it to 
 plain txt due to google complaining that is a script...)
 Change it accordingly to your paths.
 
 Regards,
 Christos


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[Rdkit-discuss] RDKit Windows Installation - missing DLL - add to wiki?

[Paul . Czodrowski]

Dear RDKitters,

just to let you know - I added one % in the WindowsInstallation Wiki entry 
:)

In addition, I added two links to install missing DLLs on Win7 systems - 
based on George's findings early 2012:

http://code.google.com/p/rdkit/wiki/InstallingOnWindows



Cheers,
Paul


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[Rdkit-discuss] descriptor calculation: MOE vs. RDKit implementation

[Paul . Czodrowski]

Dear RDKitters,

how do the MOE and RDKit implementations of VSA descriptors correlate?

I was looking into the documentation and only found a fingerprint
correlation plot. Not sure if there is a correlation plot for the
descriptors as well - or maybe it was part of my dreams.

Given that particular compound:
m2 = Chem.MolFromSmiles('Clc1cc(Oc2ccc(cc2C(NC)C)C)ccc1Cl')
Exemplary, the output for
print Descriptors.PEOE_VSA2(m2)
0.0
print Descriptors.PEOE_VSA6(m2)
40.8980654091
print Descriptors.SlogP_VSA6(m2)
36.3982024108


Switching into MOE gives these values:
PEOE_VSA+2
42.35798
PEOE_VSA-2
0
PEOE_VSA+6
0
PEOE_VSA-6
2.503756
SlogP_VSA6
7.001213



First question:
A partial charge calculation is not necessary, or am I wrong?
At least, the descriptor values are not different in the above case (data
not shown).


Second question:
Am I comparing apples with peas, or is the above case just a bad example?

Let's come to some text mining of the documentation:
MOE's PEOE_VSA doc:
PEOE_VSA+2: Sum of v_i where q_i is in the range [0.10, 0.15]
RDKit's doc:
MOE Charge VSA Descriptor 2 (-0.30 = x  -0.25)
= This agrees with MOE's PEOE_VSA-5 descriptor

For the example given from above, MOE's PEOE_VSA-5 agrees with RDKit's
PEOE_VSA2: it is 0.0.
But for other compounds, the descriptor values are different to a large
extent.
Can this discrepancy also arise from the VSA calculation?

Cheers  Thanks,
Paul

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Re: [Rdkit-discuss] descriptor calculation: MOE vs. RDKit implementation

[Paul . Czodrowski]

Dear Greg,
Dear RDKitters,


 
  how do the MOE and RDKit implementations of VSA descriptors correlate?
 
 
 I've never checked, so I'm afraid I don't know. At the time we
 implemented the descriptors, we didn't have access to MOE.

I could run a comparison between MOE and RDKit and place the results in 
the wiki. However, if one considers your statements from below, then it 
may be something like a Fleissarbeit (don't get the translation to 
English - it's like hard work without much intellectual challenge), but of 
not that much value for the community.


  First question:
  A partial charge calculation is not necessary, or am I wrong?
 
 Partial charges are needed for the PEOE_VSA descriptors, but the RDKit
 will generate the charges when you call the function if you haven't
 done so already.
What a relief! After building dozens of models, I started to actually look 
into the descriptor and feared that all models are wrong, since charge 
assignment was necessary.




  Second question:
  Am I comparing apples with peas, or is the above case just a bad 
example?
 
 A bit of background before I answer this one:
 These descriptors each combine a VSA calculation with another
 descriptor value; mollogp, molmr, or a partial charge.
 When we implemented each of those methods we tried to follow the
 original publication as closely as we could. Most of these things
 don't have large test sets available to use to validate new
 implementations, and we didn't have access to any reference
 implementations, so I can't be sure how well we did. At this point
 others have compared the RDKit MolLogP and MolMR implementations with
 the MOE implementation and reported that it compares quite well (after
 some fixing, of course), so I have some confidence in that. The VSA
 and Gasteiger-Marsilli partial charge implementations, on the other
 hand, have never had this treatment. I'm not even sure what would
 qualify as a reference implementation of the partial charge algorithm,
 but I've never done (not has anyone else told me about doing) the
 experiment with MOE for VSA.
 
 The SLOGP_VSA, SMR_VSA, and PEOE_VSA descriptors combine a binned form
 of either MolLogP, MolMR, or the partial charge with a VSA
 contribution to get a descriptor value. The RDKit implementation
 originally used the published bin values, but at some point along the
 way (this was probably 9-10 years ago) we changed the bin definitions
 (by adding more bins) for SLOGP_VSA and SMR_VSA a bit to better
 represent the datasets we cared about at the time. You can see both
 the original bin definitions and the RDKit values here:
 
https://sourceforge.net/p/rdkit/code/2416/tree/trunk/rdkit/Chem/MolSurf.py
 at lines 109 and 142.
 
 Because of these changes I definitely would not expect 100% agreement.
 
 I would also argue that it doesn't really matter. SLOGP, SMR, partial
 charges, and possible VSA are all primary descriptors: they have a
 more-or-less direct mapping to the real world and are somewhat
 interpretable. The XXX_VSA descriptors, on the other hand, are
 intended to be used to build predictive models. As such, there's no
 need for them to be consistent across programs; the only thing that
 really matters is whether or not they are useful in building models.
 In my experience at least, the RDKit XXX_VSA descriptor
 implementations are certainly useful for that.
 
 Make sense?

Thanks for this comprehensive answer!
What I'm actually looking for are interpretable descriptors before/after 
building QSAR models. For that purpose, I started to read a little bit the 
RDKit as well as the MOE documentation and stumbled on the different 
treshold settings. Of course, my first thought was Upps, what's that 
difference?, but given your explanation, I feel much more comfortable 
now.
If I submit a paper in the near future, reviewers might give me a hard 
time, but (1) you never know, maybe Greg is reviewing and (2) why should 
be MOE more correct than RDKit?

To sum it up: By reading you email, I learnt a lot about RDKit's 
descriptor world  history, and I'm eager to share my experiences.



Once again, Greg, thanks for your elaborate post!


Cheers  Thanks,
Paul





 -greg



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Re: [Rdkit-discuss] writing sdf.gz files

[Paul . Czodrowski]

Dear Greg,


thanks a lot for your help!


Cheers,
Paul

 
 The solution from the mailing list 
 
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02127.html^

  
 file_name = sys.argv[1]+.onlylargestfrag.sdf.gz 
 test_output = gzip.open(file_name,'w+') 
 test_cpd_out = Chem.SDWriter(test_output) 
 # [...] inside a loop.. 
 test_cpd_out.write(largest_frag) 
 # outside the loop 
 test_cpd_out.flush() 
 test_output.flush() 
 test_cpd_out=None 
 test_output=None 
  
 
 gives a sdf.gz, but it seems to be corrupted when trying to gunzip 
 on the command line: 
 gzip: f.sdf.gz.onlylargestfrag.sdf.gz: unexpected end of file 
 
 
 When unzipping the file via gunzip  a.sdf.gz  blubb.sdf 
 = 
 Here comes the very last part of this file: 
  
  
 CHEMBL70380 
  RDKit  3D 
 
  30 33  0  0  0  0  0  0  0  0999 V2000 
-0.0.0. C   0  0  0  0  0  0  0  0  0  0  0  0 
 1.23200.85560. N   0  0  0  0  0  0  0  0  0  0  0  0 
 2.53790.11770. C   0  0  0  0  0  0  0  0  0  0  0  0 
 2.4393   -1.37910. O   0  0  0  0  0  0  0  0  0  0  0  0 
 3.92940.67790. C   0  0  0  0  0  0  0  0  0  0  0  0 
 5.0376   -0.33300. N   0  0  0  0  0  0  0  0  0  0  0  0 
 6.46720.12130. C   0  0  0  0  0  0  0  0  0  0  0  0 
 6.78851.58650. O   0  0  0  0  0  0  0  0  0  0  0  0 
 7.575 
  
 
 
 Apparently, the flush didn't do a good job, since the outputted file
 is not complete. 
 When moving the flush part into the loop (in which I loop over the 
 compounds_to_be_outputted) does not work as well. 
 
 
 Does anyone have a suggestion? 
 
 It seems like you have to call the .close() method, not flush().
 Here's an example.
 
 This is the equivalent of what you are doing:
 
 In [36]: gz = gzip.open('out.sdf.gz','w+')
 
 In [37]: w = Chem.SDWriter(gz)
 
 In [38]: for m in ms: w.write(m)
 
 In [39]: w.flush()
 
 In [40]: gz.flush()
 
 and it produces an error:
 
 In [41]: !gzcat out.sdf.gz | tail
 
 gzip: out.sdf.gz: unexpected end of file
   NUM_ROTATABLEBONDS  (200) 
 2
 
   P1  (200) 
 2.17
 
   SMILES  (200) 
 CC(=O)Nc1cc(C)cc(C)c1
 
 
 
 But if I use close() it seems to work:
 
 In [30]: gz = gzip.open('out.sdf.gz','w+')
 
 In [31]: w = Chem.SDWriter(gz)
 
 In [32]: for m in ms: w.write(m)
 
 In [33]: w.close()
 
 In [34]: gz.close()
 
 In [35]: !gzcat out.sdf.gz | tail
   NUM_ROTATABLEBONDS  (200) 
 2
 
   P1  (200) 
 2.17
 
   SMILES  (200) 
 CC(=O)Nc1cc(C)cc(C)c1
 
 
 
  I will take a look at the underlying C++ code and see if I can 
 figure out some way to make at least some of that unnecessary.



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[Rdkit-discuss] BRICS - discrepancies regarding the output

[Paul . Czodrowski]

Dear RDKitters,

when trying to reproduce the BRICS example from the mailing list:
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg00479.html

I end up in a different number of BRICS fragments (using 2012/9 release):

base = Chem.MolFromSmiles(n1cncnc1OCC(C1CC1)OC1CNC1)
catalog = BRICS.BRICSDecompose(base)
=
set(['[15*]C1CC1', '[3*]O[3*]', '[14*]c1ncncn1', '[15*]C1CNC1', 
'[4*]CC([4*])[8*]'])


whereas the given example on the mailing list gives:
set(['[3*]OCC(O[3*])C1CC1', '[4*]CC([4*])C1CC1', '[3*]Oc1ncncn1',
'[14*]c1ncncn1', '[3*]OCC([4*])C1CC1', '[3*]OC(C[4*])C1CC1',
'[3*]OC1CNC1', '[15*]C1CNC1'])


Does anyone have an idea if I did something wrong?


Cheers  Thanks,
Paul


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Re: [Rdkit-discuss] one flavor of MCS

[Paul . Czodrowski]

Dear Andrew,

thanks a lot for the quick hack and sorry for my late answer! I'm still
interested in that issue, but I had no access to coding facilities for
almost two days, what a shame!



 The current hooks in the MCS code don't make that possible. If you
 tweak the code a bit, I think you can get something working.

 % python hacked_fmcs.py sample_files/benzotriazole.sdf --maximize
all-matches
 [#6]:1:[#6]:[#6]:[#6]:2:[#7]:[#7]:[#7]:[#6]:2:[#6]:1 9 atoms 10
 bonds (complete search)
 == Successful matches ==
 [#7]:[#7]
 [#6]:[#6]
 [#6]:[#7]
 [#6]:[#6]:[#7]
 [#7]:[#7]:[#7]
 [#6]:[#6]:[#6]
 [#6]:[#7]:[#7]
 [#7]:[#7]:[#6]
  ...
 [#6]:1:[#6]:[#6]:[#6]:2:[#7]:[#7]:[#7]:[#6]:2:[#6]:1
 [#6]:1:[#6]:[#6]:[#6](:[#6](:[#6]:1):[#7]:[#7]):[#7]
 [#6]:1:[#6]:[#6]:[#6](:[#6](:[#6]:1):[#7]):[#7]:[#7]

 I've attached both a patch against the current version of fmcs.py
 plus the full, hacked modification. It adds a new '.matches' field
 to the MCS result. The key is the SMARTS pattern tested, the value
 is if the pattern was in enough of the molecules. (In a non-hacked
 solution I would likely return only the valid matches.)



I tried your hacked script on the example you described below as well as on
a this small data set:
CCNCc1c1
c1ccc(cc1)CN
CCNCc1c1
c1cnc[nH]


Regarding the issues you mentioned
- incomplete, untested  awkward naming
- rather slow speed
- non-canonical SMARTS
- duplicates are not filtered out
= these restrictions are OK for me!

  In addition, I would like to output the frequency of the found
  substructures

 That's much harder from fmcs. Then again, I don't know what you mean
 by frequency.

 Consider the compounds   CCOCC  CCNCC  CCPCCSCC

 The MCS is CC. The CC exists twice (uniquely) in the first
 structure, twice in the second, and three times in the third.

 Is the frequency of CC 2 or 3?

 Or do you mean the number of molecules which contain that structure,
 in which case CC exists in 3 of the structures.

That's exactly what I meant.




 In either case, I don't think the right solution is to do this in
 fmcs. You have the SMARTS patterns and the molecules, so do a SMARTS
 match yourself and get the exact statistics you want.

Following up on that topic - and also taking into account the comments by
Peter and Christos - it become clearer to me that fmcs might be not
appropriate for that kind of question.

You may be interested how such a question came by my mind:
Table 6 of this publication sparked my interest:
http://dx.doi.org/10.1002/cmdc.20124
From a conversation with Andreas Bender, it was explained to me that they
did a brute-force all-against-all MCS search in pipeline pilot. It's a
miracle for me how to code something similar in RDKit.

Following up on the example from the above section:

CCNCc1c1
c1ccc(cc1)CN
CCNCc1c1
c1cnc[nH]

= I would be more than happy to finally have this output:

newflavorOfMCS   frequency
##
c1ccc(cc1)CN 3
c1cnc[nH]1



Cheers  Thanks for all your input so far!

Paul


 Cheers,

 Andrew
 da...@dalkescientific.com

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[Rdkit-discuss] one flavor of MCS

[Paul . Czodrowski]

Dear RDKitters,

given a data set of let's say 2000 compounds, how do I extract the most
common substructures rather than the maximum common substructures?
In addition, I would like to output the frequency of the found
substructures

E.g., the output would look like that
N(CCc1c1)C, frequency: 12
Nc1c1, frequency: 10

Is such an analysis only possible via a brut-force approach?
Or can one do it smarter?



Cheers  Thanks,
Paul

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Re: [Rdkit-discuss] pilfont error message

[Paul . Czodrowski]

 
 I took a couple things out of the thread:
 1) those bad exceptions in the sping code need to be fixed.
 2) it would be helpful to have the sping canvas support the font
 'serif' as well as 'sans'.
 
 I checked in fixes for both of those this morning.

cool, thanks!


paul


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Re: [Rdkit-discuss] RDKit pgSQL cartridge on 64-bit Windows, anyone ?

[Paul . Czodrowski]

Dear Jan,

nope - but this reminds me on one UGM topic:
Could anyone provide a 64bit Win7 build?


Cheers  Thanks,
Paul


 Hi RDKitters,

 Before I embark on this journey - has anyone else attempted compiling
 and running the RDKit pgSQL cartridge on 64-bit Windows ? Gotchas,
 success stories, and fiaskos/war stories would be equally
appreciated :-).

 Cheers
 -- Jan Holst Jensen

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Re: [Rdkit-discuss] descriptor calculation - fragment counts Co.

[Paul . Czodrowski]

  I'm wondering about the total number of accessible descriptors in
RDKit:
 
  This is is my code:
  
  import sys
  from rdkit import Chem
  from rdkit.Chem import Descriptors
  from rdkit.ML.Descriptors import MoleculeDescriptors
 
  file_in  = sys.argv[1]
  file_out = file_in+.descr.sdf
  ms = [x for x in  Chem.SDMolSupplier(file_in) if x is not None]
  ms_wr = Chem.SDWriter(file_out)
 
  nms=[x[0] for x in Descriptors._descList]
  #nms.remove('MolecularFormula')
  print len(Descriptors._descList)
 
 
  calc = MoleculeDescriptors.MolecularDescriptorCalculator(nms)
 
  for i in range(len(ms)):
descrs = calc.CalcDescriptors(ms[i])
for x in range(len(descrs)):
  ms[i].SetProp(str(nms[x]),str(descrs[x]))
ms_wr.write(ms[i])
  
 
  This gives me 93 descriptors in total.
 
  A brief look and count in the Python API
  http://www.rdkit.org/docs/api/rdkit.Chem.Descriptors-module.html
  ends up in more than 170 descriptors.
 
  Another brief look (no time to grasp in more depth) reveals that
apparently
  the fr_* descriptors have not been calculated.
 
  What did I do wrong?

 I don't see anything obvious, but you are definitely getting
 incorrect results.
 Here's what I see:

 In [16]: from rdkit import Chem
 In [17]: from rdkit.ML.Descriptors import MoleculeDescriptors
 In [18]: from rdkit.Chem import Descriptors
 In [19]: len(Descriptors._descList)
 Out[19]: 177
 In [20]: calc =
 MoleculeDescriptors.MolecularDescriptorCalculator([x[0] for x in
 Descriptors._descList])
 In [21]: len(calc.GetDescriptorNames())
 Out[21]: 177
 In [22]: m = Chem.MolFromSmiles('c1c1OC')
 In [23]: ds = calc.CalcDescriptors(m)
 In [24]: len(ds)
 Out[24]: 177

 Just to eliminate some uncertainty, can you please try the above
 commands and, if you don't see 177, add this:

 In [25]: from rdkit import rdBase
 In [26]: rdBase.rdkitVersion
 Out[26]: '2012.12.1pre'

 Thanks.
 -greg

Hi Greg,

here we go:


In [4]: from rdkit import Chem
from rdkit import rdBase
from rdkit.ML.Descriptors import MoleculeDescriptors
from rdkit.Chem import Descriptors
len(Descriptors._descList)

Out[4]: 93


In [6]: calc = MoleculeDescriptors.MolecularDescriptorCalculator([x[0] for
x in Descriptors._descList])
len (calc.GetDescriptorNames())

Out[6]: 93


In [7]: m = Chem.MolFromSmiles('c1c1OC')
ds = calc.CalcDescriptors(m)
len(ds)

Out[7]: 93

In [8]: print rdBase.rdkitVersion
2012.09.1beta


Now you see that we are still using the Q3 beta :)

Only solution: Upgrading to the stable version? Or is there a workaround
available in conjunction with the Q3 beta?


Cheers  Thanks,
Paul

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Re: [Rdkit-discuss] Crippen pKa model in RDKit

[Paul . Czodrowski]

Dear James,

that's a wonderful piece of work!



 I have attached the script (in .py and .pynb formats – it really is
 nice working interactively in the iPython notebook!).  I have also
 attached the modified form of the decision tree data that was used.
 I hope these attachments come through ok, but I can’t quite remember
 the rules for this…
Attachments came through, and the iPython way is amazing!


 Not sure where to go next from here…  It would be nice to have the
 model in PMML format – but my head started to hurt when trying to
 figure this out!

Well, maybe I don't get the point, when one trains a new decision tree
(using scikit-learn), this model can be stored as pkl file.

 Does this help others out with washing functionality, etc?
Absolutely!

 Is this model too limited in just dealing with monoprotics?
I would say No.

 Where next (other than testing with a full test set)?
Any plans to move your script to the contrib/ folder?


Cheers,
Paul

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Re: [Rdkit-discuss] computing molecular descriptors for a small molecule

[Paul . Czodrowski]

this one should work:

http://code.google.com/p/rdkit/wiki/descriptor_calculation


Paul C


 Hello,

 Let's say I am in Python and have a molecule in a .sdf file,
 how do I compute all molecular descriptors for that
 molecule?

 By all molecular descriptors, I mean all that rdkit knows about.

 Do you have some example scripts around?

 Thanks a lot,
 F.

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Re: [Rdkit-discuss] neutralize charges

[Paul . Czodrowski]

Dear Hans,

you might also consider uploading a short wiki entry with the SMARTS
patterns.

Cheers  Thanks,
Paul


 Hi Andrew,

 We are doing this with a set of Smarts-based replacements. I can
 send you the Smarts but you will have to wait a couple of days as I
 cannot access them right now.

 Bye for now,
 Hans

 On 11 Oct 2012, at 08:52, Greg Landrum greg.land...@gmail.com wrote:

  Andrew,
 
  On Tue, Oct 9, 2012 at 2:21 PM, Andrew Dalke
 da...@dalkescientific.com wrote:
  Is there anything in RDKit to neutralize charges, like what
  Corina does with the 'neu' option? Quoting from the
  Corina documentation:
 
 
  • The new option -d neu neutralizes formal
  charges at acids, alcoholates, and basic nitrogens
  by adding or removing protons. Often it is useful
  to have all molecules of a database in the same
  protonation state.
 
  This feels like a set of simple structure transformations.
 
  Assuming that this really is just remove Hs from positively charged
  atoms and remove Hs from negatively charged atoms until they're
  neutral it should be relatively straightforward to do with a loop
  over atoms. There will be some book-keeping involved along the way to
  check for whether or not stereochemistry flags need to be removed or
  specified implicit Hs marked on the atoms, but that shouldn't be too
  bad.
 
  It would be a good cookbook recipe, but I'm unlikely to have the time
  to do it in the next few days.
 
  -greg

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[Rdkit-discuss] set default protonation

[Paul . Czodrowski]

Dear RDKitters,

has anyone worked so far on this topic:

http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01706.html

 Rebalance protonation states by deprotonating strong acids and/or
 protonating strong bases

This would be easy to do given a set of SMARTS patterns defining the
strong acids/bases.


E.g. these two molecules are identical:
O=C(OC)C1=CCC2[N+](C)C1CC2
C1[C@@H]2CC[C@@H](C(C(OC)=O)=C1)[N@]2C

but their charge state is not!


Cheers,
Paul


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Re: [Rdkit-discuss] ML question

[Paul . Czodrowski]

Dear Greg,


  # actual predicion
 
  prediction_dictionary = {}
  for x in cpds_w_descr:
  pred,conf=cmp.ClassifyExample(x[1:])
  NAME=x[0]
  prediction_dictionary[NAME]=pred,conf
  i+=1
  for mol in cpds:
  mol_name = mol.GetProp('_Name')
  mol.SetProp('prediction',str(prediction_dictionary[mol_name][0]))
  mol.SetProp('prediction_confidence',str(prediction_dictionary
  [mol_name][1]))
  testset_pred.write(mol)

 This is just a guess, but it looks like you're passing ClassifyExample
 a shorter vector for each point than what you passed to Grow.
 Does it work if you do: pred,conf=cmp.ClassifyExample(x)?

 -greg


wonderful, thanks for this hint!
i was too much stuck in the code...


cheers,
paul

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Re: [Rdkit-discuss] 3D SDF with hydrogens set - where have my hydrogens gone

[Paul . Czodrowski]

 Who hasn't been bitten by this?

 Try:

 SDMolSupplier(isdf, removeHs=False)


Wonderful, Jean-Paul, thank you very much!


paul

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Re: [Rdkit-discuss] PIL - molecule depiction

[Paul . Czodrowski]

Dear Greg,


 PIL is a separate python package that you need to install:
 http://www.pythonware.com/products/pil/

 I guess one important question that I forgot to ask is: Why are you
 trying to do this;
 from rdkit.sping import PIL

Forget about that! Here, I was totally on the wrong track...

When trying to depict a 2D figure from a SMILES string with that code:

mol = Chem.MolFromSmiles(smi)
AllChem.Compute2DCoords(mol)
Draw.MolToImageFile(mol, outF)


In end up in this error message:

IOError: encoder zip not available


From the wonderful source of wisdom stackoverflow.com, I found out that
pillow is recommended for usage with PIL to resolve the zlib issue.
In my case, it helped, but I'm not sure if this is a rather quick and dirty
hack.


Cheers.
Paul

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[Rdkit-discuss] PIL - molecule depiction

[Paul . Czodrowski]

Dear RDKitters,

when typing in
from rdkit.sping import PIL
I end up in this error message

Traceback (most recent call last):
  File stdin, line 1, in module
  File
/SW/python/x86_64/2.6/lib/python2.6/site-packages/rdkit/sping/PIL/__init__.py,
 line 2, in module
from pidPIL import *
  File
/SW/python/x86_64/2.6/lib/python2.6/site-packages/rdkit/sping/PIL/pidPIL.py,
 line 33, in module
import Image, ImageFont, ImageDraw
ImportError: No module named Image


My first guess would be that some path (PYTHONPATH) setting is wrong, but
I'm not sure about it...


Cheers,
Paul

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Re: [Rdkit-discuss] PIL - molecule depiction

[Paul . Czodrowski]

Dear Greg,
Dear Paul,

thanks for your prompt answers!


  Dear RDKitters,
 
  when typing in
  from rdkit.sping import PIL
  I end up in this error message
  
  Traceback (most recent call last):
   File stdin, line 1, in module
   File
  /SW/python/x86_64/2.6/lib/python2.6/site-packages/rdkit/sping/
 PIL/__init__.py,
   line 2, in module
     from pidPIL import *
   File
  /SW/python/x86_64/2.6/lib/python2.6/site-packages/rdkit/sping/
 PIL/pidPIL.py,
   line 33, in module
     import Image, ImageFont, ImageDraw
  ImportError: No module named Image
  

 Do you have PIL installed?

Good question - ctest of RDKit gives a 100 % passed percentage, which I
find fantastic! I.e. pyDepictor works, which does the 2D depiction, but
maybe I'm wrong...

BTW, the PIL directory appears rather empty:
* __init__.py
* pidPIL.py
* pilfonts/

On my windows (binary) RDKIt installation, the directory is as empty as
well, but I guess that the graphics library on Windows comes from a
different source.


Cheers  Thanks again,
Paul

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Re: [Rdkit-discuss] ctest of new build - testGrid

[Paul . Czodrowski]

Dear RDKitters,

I just wanted to mention that this issue was resolved - RDBASE was not
correctly set. A classical one, at least from mailing listing point of
view...

Thanks2Greg,
Cheers,
Paul


 
  when running ctest on a new build, I run into an issue when it comes to
  testGrid - this step takes ages and does not stop...

 Interesting. Can you please send a few pieces of additional information:
 1) the version of the RDKit you're using
 2) The operating system you're working under
 3) the output of the command ldd  Code/Geometry/testGrid, when run
 from the build directory

 Thanks,
 -greg

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[Rdkit-discuss] ctest of new build - testGrid

[Paul . Czodrowski]

Dear RDKitters,

when running ctest on a new build, I run into an issue when it comes to
testGrid - this step takes ages and does not stop...

Of course, I checked the mail archive and found out some related problems:
* --output-on-failure does not give any additional information

Simply executing testGrid from Code/Geometry gives:
***
Testing Grid
-
 testUniformGrid1

-
 testUniformGrid2

-
 testUniformGridPickling


Some other tests (prior to the testGrid part) do fail, which should be
related to an LD_LIBRARY_PATH / PYTHONPATH setting, according to:
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01332.html

http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02269.html

But I guess that it makes sense to first solve the testGrid issue, or are
the topics related to each other?


Cheers  Thanks,
Paul

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Re: [Rdkit-discuss] Gobbi_Pharm2D

[Paul . Czodrowski]

I think I found the solution by myself:

from rdkit.Chem.Pharm2D import Gobbi_Pharm2D
fds=Gobbi_Pharm2D.factory.featFactory.GetFeatureDefs()

followed by
fds['COO']   = 'C(=O)O'
COOPattern   = Chem.MolFromSmarts(fds['COO'])

and now I can search for carboxylic groups as well.

the interested reaeder might be interested why Gobbi_Pharm2D is being used
at all - because the new SMARTS is rather simple. This is due to the fact I
just wanted to give a simple example.


Cheers,
Paul


 Dear RDKitters,


 is there any way of tailoring the Gobbi_Pharm2D fingerprints?

 Or to state it that way:
 Is it possible to code his own definitions which can be used for queryin?



 Cheers  Thanks,
 Paul

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[Rdkit-discuss] Gobbi_Pharm2D

[Paul . Czodrowski]

Dear RDKitters,


is there any way of tailoring the Gobbi_Pharm2D fingerprints?

Or to state it that way:
Is it possible to code his own definitions which can be used for queryin?



Cheers  Thanks,
Paul

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Re: [Rdkit-discuss] Using Gobbi_Pharm2D - ctd

[Paul . Czodrowski]

Dear Greg,

this is VERY helpful, thanks a lot!

Nonetheless,  I might come up with a few more questions...



Cheers,
Paul


 
 Dear Paul,
 
 On Mon, Nov 7, 2011 at 12:44 PM,  paul.czodrow...@merckgroup.com 
wrote:
 
  can anyone given an example how to use the acid/base pharmacophore
  annotation using the Gobbi_Pharm2D fingerprints?
 
 
 I guess this isn't what you want, but there's an explanation of how to
 generate the Gobbi_Pharm2D fingerprints in the online documentation
 here;
 http://www.rdkit.org/new_docs/GettingStartedInPython.html#chemical-
 features-and-pharmacophores
 
 If you're just interested in using the feature types as substructure
 queries you can do something like the following:
 
 Start by getting the feature definitions:
 In [17]: from rdkit.Chem.Pharm2D import Gobbi_Pharm2D
 
 In [18]: fds=Gobbi_Pharm2D.factory.featFactory.GetFeatureDefs()
 
 In [19]: fds
 Out[19]:
 {'AG.AcidicGroup': '[$([C,S](=[O,S,P])-[O;H1])]',
  'AR.AromaticAttachment': '[$([a;D3](@*)(@*)*)]',
  'BG.BasicGroup':
 '[$([N;H2+0][$([C,a]);!$([C,a](=O))]),$([N;H1+0]([$([C,a]);!$([C,
 a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0+0]([C;!$(C(=O))])([C;!
 $(C(=O))])[C;!$(C(=O))]),$([N,n;X2;+0])]',
  'HA.Acceptor':
 '[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),
 $([Nv3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]',
  'HD.Donor': 
'[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]',
  'LH.Hydrophobic':
 '[$([C;H2,H1](!=*)[C;H2,H1][C;H2,H1][$([C;H1,H2,H3]);!$(C=*)]),
 $(C([C;H2,H3])([C;H2,H3])[C;H2,H3])]',
  'RR.AliphaticAttachment': '[$([A;D3](@*)(@*)*)]',
  'X.UnusualAtom': '[!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53]'}
 
 
 Now build SMARTS pattern matchers for the acidic and basic groups:
 
 In [20]: acidPattern = Chem.MolFromSmarts(fds['AG.AcidicGroup'])
 
 In [21]: basePattern = Chem.MolFromSmarts(fds['BG.BasicGroup'])
 
 
 Now test those out:
 
 In [22]: Chem.MolFromSmiles('CCC(=O)O').HasSubstructMatch(acidPattern)
 Out[22]: True
 
 In [24]: Chem.MolFromSmiles('CCC(=O)O').HasSubstructMatch(basePattern)
 Out[24]: False
 
 In [25]: Chem.MolFromSmiles('CCCN').HasSubstructMatch(acidPattern)
 Out[25]: False
 
 In [26]: Chem.MolFromSmiles('CCCN').HasSubstructMatch(basePattern)
 Out[26]: True
 
 
 Does this get you closer to what you want?
 
 -greg



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[Rdkit-discuss] Using Gobbi_Pharm2D - ctd

[Paul . Czodrowski]

Dear RDkitters,

can anyone given an example how to use the acid/base pharmacophore
annotation using the Gobbi_Pharm2D fingerprints?



Cheers  Thanks,
Paul

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Re: [Rdkit-discuss] Using Gobbi_Pharm2D

[Paul . Czodrowski]

Dear Greg,


if my query molecule contains any acidic functionality, I would like to get
all acids in the database - as defined by the  Gobbi pharmacophore
fingerprint.

Can this be handled by the Gobbi fingerprints?


In the GettingStartedTutorial, there is a table (on the very last page) of
the pharmacophore definition of acids:
[$([C,S](=[O,S,P])-[O;H1,-1])]

Is this of help for this request?


Cheers  Thanks,
Paul


  within a given list of SMILES codes, I would like to get matches
between
  acidic functionalies and basic functionalities as well when I do a
search
  gainst a query SMILES code.
  To be more precise: In the example given below, I would like to get all
the
  entries in the db_smiles list that bear an carboxylic acid
functionality
  (without the phenyl ring). Additionally, I would like to jump from
one
  acid to another - e.g.  jump from an carboxylic acid to an hydroxyl
group.
  Of course, this is a much weaker acid.

 I'm afraid I still don't really get it. Searching for the molecules
 that have a carboxylic acid I understand, but what do you mean about
 jumping to another acid?

 -greg

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[Rdkit-discuss] Using Gobbi_Pharm2D

[Paul . Czodrowski]

Dear RDKitters,

within a given list of SMILES codes, I would like to get matches between
acidic functionalies and basic functionalities as well when I do a search
gainst a query SMILES code.
To be more precise: In the example given below, I would like to get all the
entries in the db_smiles list that bear an carboxylic acid functionality
(without the phenyl ring). Additionally, I would like to jump from one
acid to another - e.g.  jump from an carboxylic acid to an hydroxyl group.
Of course, this is a much weaker acid.

In my understanding, 2 steps are necessary - not reflected in my snippet:
(1) Dump out the basic/acidic functionality of the query molecule
(2) Do the same task for each db_smile  find matches between the
pharmacophoric
features.


Here comes the snippet:

query_mol = Chem.MolFromSmiles('O=C(O)c1c1')
query_fp  = Generate.Gen2DFingerprint(query_mol,Gobbi_Pharm2D.factory)

for db_smile in db_smiles:
db_mol = Chem.MolFromSmiles(db_smile)
db_mol_fp = Generate.Gen2DFingerprint(query_mol,Gobbi_Pharm2D.factory)



Cheers  Thanks,
Paul

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[Rdkit-discuss] multiprocessing rdkit

[Paul . Czodrowski]

Dear RDkitters,

I'm trying to use Python's multiprocessing module in conjunction with
RDKit.

It should be applied in 2 cases:
(1) fingerprint calculation

(2) Picking Diverse Molecules



(1)

from multiprocessing import Pool
p4 = Pool(processes=4)
def fps_calc(m):
fps = [GetMorganFingerprint(x,3) for x in m]
return fps
fps =  p4.map(fps_calc,ms)

==
TypeError: 'Mol' object is not iterable

(2)

from multiprocessing import Pool
p4 = Pool(processes=4)
def distij(i,j,fps=fps):
return 1-DataStructs.DiceSimilarity(fps[i],fps[j])

def DivSelection(distij,nfps,quantity_train):
picker = MaxMinPicker()
picked_indices = picker.LazyPick(distij,nfps,quantity_train)
return picked_indices

pickIndices = p4.map(DivSelection, ???)



In the first case, I do not get the point what is going wrong. With the
following conformer generation snippet, multiprocessing works perfect:

from multiprocessing import Pool
def generateconformations(m):
  m = Chem.AddHs(m)
  ids=AllChem.EmbedMultipleConfs(m,numConfs=10)
  for id in ids:
AllChem.UFFOptimizeMolecule(m,confId=id)
  return m
p4 = Pool(processes=4)
ms = [x for x in Chem.SDMolSupplier('blockbusters.sdf')]
cms4=p4.map(generateconformations,ms)


In the second case, I'm not sure how to properly pass the variables.



Cheers  Thanks,
Paul

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Re: [Rdkit-discuss] multiprocessing rdkit

[Paul . Czodrowski]

Dear Jean-Paul,
  (1)
  
  from multiprocessing import Pool
  p4 = Pool(processes=4)

 ms = [x for x in Chem.SDMolSupplier('cpds.sdf') if x is not None]

  def fps_calc(m):
         fps = [GetMorganFingerprint(x,3) for x in m]
         return fps
  fps =  p4.map(fps_calc,ms)
  
  ==
  TypeError: 'Mol' object is not iterable
 

 The object m is a single molecule and not an iterable (array, set etc).
 I guess you snipped an important bit of code (what type is ms?)


This is really strange, since I was pretty sure that ms contains a list of
molecules (see the above statement how ms is defined).



  (2)
  
  from multiprocessing import Pool
  p4 = Pool(processes=4)
  def distij(i,j,fps=fps):
         return 1-DataStructs.DiceSimilarity(fps[i],fps[j])
 
  def DivSelection(distij,nfps,quantity_train):
         picker = MaxMinPicker()
         picked_indices = picker.LazyPick(distij,nfps,quantity_train)
         return picked_indices
  
  pickIndices = p4.map(DivSelection, ???)
 

 I imagine, even if I haven't used the multiprocessing module, that you
 would need to pass the list of parameters (tuples maybe?) to feed into
 the multiple DivSelection calls.

I tried to pass a tuple, but in my case it didn't work.



 I hope this puts you on the right track...  I am just filling in till
 Greg gives an incredible one liner which will solve all your problems.
 JP


Thanks so far,
Paul

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Re: [Rdkit-discuss] multiprocessing rdkit

[Paul . Czodrowski]

Dear Greg,
Dear Nik,


thanks for your very quick and informative answers!

I hope you two guys do not follow a battle rightaway :)


  (2)
  
  from multiprocessing import Pool
  p4 = Pool(processes=4)
  def distij(i,j,fps=fps):
         return 1-DataStructs.DiceSimilarity(fps[i],fps[j])
 
  def DivSelection(distij,nfps,quantity_train):
         picker = MaxMinPicker()
         picked_indices = picker.LazyPick(distij,nfps,quantity_train)
         return picked_indices
  
  pickIndices = p4.map(DivSelection, ???)

 The MaxMinPicker does not have any way to do the parallelization with
 multiprocessing.


Is there any setting/property of a RDKit functionality how to detect if it
is supported by multiprocessing?


Cheers,
Paul

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Re: [Rdkit-discuss] how to come to a good model

[Paul . Czodrowski]

Dear Greg,



 One suggestion would be to try doing a two class model (either combine
 two of your classes together or use only classes 0 and 2 in the
 training) and see if that helps. Another would be try using different
 descriptors. You might be able to get something useful with the
 FeatMorgan fingerprints (similar to the FCFP fingerprints).

Just to be on the sure side: is this the correct call for the feature
morgan fingerprints (radius=2)?

AllChem.GetMorganFingerprintAsBitVect(x,2,2048,useFeatures=True)



Paul


 -greg


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[Rdkit-discuss] how to come to a good model

[Paul . Czodrowski]

Dear RDKitters,

I'm in the process of training a 3-class decision tree model. I have 
roughly about 1500 compounds with an almost equal distribution of the 3 
classes.

This is the Grow command I'm using for MorganFP model:
nPossible = [0]+[2]*2048+[3]
cmp.Grow(pts,attrs=[1],nPossibleVals=[3],nTries=10,buildDriver=CrossValidate.CrossValidationDriver,treeBuilder=SigTreeBuilder,needsQuantization=False,maxDepth=3)

and these are code lines using a descriptor based model:
ndescrs = len(pts[0])-2
boundsPerVar = [0]+[1]*ndescrs+[0]
nPossible = [0]+[2]*ndescrs+[3]
attrs = range(1,ndescrs+1)
cmp.Grow(pts,attrs=attrs,nPossibleVals=nPossible,nTries=10,buildDriver=CrossValidate.CrossValidationDriver,treeBuilder=QuantTreeBoot,
 
needsQuantization=False,nQuantBounds=boundsPerVar, maxDepth=3)


Apparently, I screwed up parts of my code, because the Cycle output is 
the following:
Cycle:0
Cycle:3
Cycle:6
Cycle:9
Cycle:   12
Cycle:   15
Cycle:   18
Cycle:   21
Cycle:   24
Cycle:   27


Up to yesterday, the numbering scheme was 0,1,2 -- however, this effect 
not really worries me. Or is it somethin to take care of?

I played around with the following settings:
* random training / test set selection (training set size: 75 %)
* diverse selection of training / test set (training set size: 75 %)
* MorganFP as well as RDKit descriptors - either a random selection of the 
training set or a diverse selection
* nTries = 10 or 20 or 30


In all cases, the statistics is really bad: about 50 percent are 
misclassified, e.g.:

*** Vote Results ***
misclassified: 580/1180 (%49.15)580/1180 (%49.15)

average correct confidence:0.7837
average incorrect confidence:  0.7528


Interestingly, there is a really small difference between the average 
confidence level for the correct as well as the incorrect classifications. 
As far as I got it this tells me that the model is really bad - an 
information I already got by the vote results themselves.


Which parameters are worthhile to test?


Cheers  Thanks,
Paul


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Re: [Rdkit-discuss] cmp - store model on disk

[Paul . Czodrowski]

Dear Greg,


 Dear Paul,

 On Sat, Aug 20, 2011 at 4:35 PM, paul.czodrow...@merckgroup.com wrote:
 
  after having trained a model
  
  cmp = Composite()
  cmp.Grow
  (pts,attrs=attrs,nPossibleVals=nPossible,nTries=1,

buildDriver=CrossValidate.CrossValidationDriver,treeBuilder=QuantTreeBoot,
   needsQuantization=False,nQuantBounds=boundsPerVar, maxDepth=3)
  
 
  How can this model be stored on disk?
  pickle will not help me, because this only works for molecules, or am I
  wrong?

 You should be able to store it to disk by pickling without problems,
 something like:
 cPickle.dump(cmp,file('cmp.pkl','wb+'))

Too easy solution - I would not have dared to just try it... :)


  I would like to store this model on disk, because I would like predict
  molecules in a later stage without training evry time running the
  prediction.
  For the prediction part, I will be using cmp.ClassifyExample() - or
is
  there any other possibility?

 Pickling the models and then using ClassifyExample is correct.

 Best,
 -greg


Thanks, Greg!


Paul

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Re: [Rdkit-discuss] a documentation experiment

[Paul . Czodrowski]

Dear Greg,


very neat  nifty - I already like it a lot!


Paul


 I'd be very happy for feedback on what people think of the new format.

 -greg

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Re: [Rdkit-discuss] confusion matrix

[Paul . Czodrowski]

Dear Greg,

  I have added the code how I generate my own confusion matrix to the
Wiki.
  In my understanding, my function uses the predictions from the
out-of-bag
  prediction. But I guess that I have overlooked some nasty detail.

 You call:
   pred,conf=cmp.ClassifyExample(pts[i])
 This uses the full composite model to make each prediction, it doesn't
 do the same out-of-bag prediction done by
 ScreenComposite.ShowVoteResults

 It is possible to get both the out-of-bag confusion matrix as a python
 object (it's part of the return tuple from
 ScreenComposite.ShowVoteResults) and the breakdown of the out-of-bag
 predictions by point (not quite as straightforward, but possible).
 What exactly are you trying to do?

I'm particularly interested in understanding why the model
fingerprint-based performs rather bad. For this purpose, I would like to
analyze the chemical structures for which the predictions went wrong or did
not go wrong.



  Cheers  Thanks,
  Paul
 
 
  P.S.: When comparing the results with a PipelinePilot-based Bayesian
  catagorization model (ECFP_4  standard settings), I'm surprised to see
  that the PipelinePilot model is significantly better. I thought that
the
  MorganFingerprints are comparable to the ECFPs and would have assumed
that
  the model quality is in a similar range.

 It's probably not the fingerprints, but the model-building approach
 that makes the difference here. You can test this if you want in knime
 using the RDKit morgan fingerprints with the naive bayes fingerprint
 learner they added in version 2.4.
Just started a new thread in the knime forum :)

Cheers,
Paul

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[Rdkit-discuss] confusion matrix

[Paul . Czodrowski]

Dear RDKitters,

when training a solubility model (see
http://code.google.com/p/rdkit/wiki/TrainAThreeClassSolubilityModel

I run into the problem that three different confusion matrices are
outputted.

I wonder what is the origin of these confusion matrices. Even though x- and
y-axis might be mixed up, the diagonal entries should always be the same.
Thus, confusion matrices make me confused...


Cheers  Thanks,
Paul

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[Rdkit-discuss] more questions regarding psql

[Paul . Czodrowski]

Dear all,

I manually copied the Code directory after building rdkit into $RDBASE -
don't understand why it was not copied over...

Running make
in $RDBASE/Code/PgSQL/rdkit
gives the following:

g++ -fomit-frame-pointer -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2
-fstack-protector -funwind-tables -fasynchronous-unwind-tables -g  -Wall
-Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
-Wendif-labels -fno-strict-aliasing -fwrapv -fpic -shared  rdkit_io.o
mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o
-L/SW/python/lib/python2.6/site-packages/rdkit//lib -L/usr/lib
-lFileParsers_static -lSmilesParse_static -lFingerprints_static
-lSubgraphs_static -lSubstructMatch_static -lDescriptors_static
-lPartialCharges_static -lGraphMol_static -lDataStructs_static
-lRDGeometryLib_static -lRDGeneral_static -o rdkit.so
/usr/lib/gcc/i586-suse-linux/4.5/../../../../i586-suse-linux/bin/ld: cannot
find -lFileParsers_static
collect2: ld returned 1 exit status
make: *** [rdkit.so] Error 1



Cheers,
Paul

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[Rdkit-discuss] questions regarding psql

[Paul . Czodrowski]

dear rdkitters,

i'm following greg's great emolecules tutorial.
psql was installed by our sysadmin on my linux pc. therefore, i'm not 100%
familiar with all installation settings.

createdb works.
but i wonder where to find rdkit.sql?
according to the wikie (
http://code.google.com/p/rdkit/wiki/DatabaseCreation2), it is placed
in /usr/local/pgsql/share/contrib/rdkit.sql.
this does not hold true on my pc - i would have been actually surprised...

browsing through the svn repository on the , the only sql file i found is
rddata.sql:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Data/

any help would be highly appreciated.


cheers  thanks,
paul

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Re: [Rdkit-discuss] questions regarding psql

[Paul . Czodrowski]

Dear Greg,
Dear Adrian,



thanks for your hints!

I just rebuilt rdkit (the beta Q2 release), but I cannot find
$RDBASE/Code/PgSQL/rdkit


Is there any flag/setting I overlooked?

I did the following:
make -D
PYTHON_NUMPY_INCLUDE_PATH=/SW/python/lib/python2.6/site-packages/numpy/core/include/
 -DRDK_INSTALL_INTREE=0 -DCMAKE_INSTALL_PREFIX=/SW/python/ ..

no other specific changes...


Cheers,
paul



 Did you look at /usr/share/postgresql/$PGVERSION/contrib/rdkit.sql?
 This is where it would be on a Debian-based system.

 On Tue, Jul 5, 2011 at 14:03, Greg Landrum greg.land...@gmail.com
wrote:
  Dear Paul,
 
  On Tue, Jul 5, 2011 at 2:55 PM,  paul.czodrow...@merckgroup.com
wrote:
 
  dear rdkitters,
 
  i'm following greg's great emolecules tutorial.
  psql was installed by our sysadmin on my linux pc. therefore, i'm not
100%
  familiar with all installation settings.
 
  createdb works.
  but i wonder where to find rdkit.sql?
  according to the wikie (
  http://code.google.com/p/rdkit/wiki/DatabaseCreation2), it is placed
  in /usr/local/pgsql/share/contrib/rdkit.sql.
  this does not hold true on my pc - i would have been actually
surprised...
 
  Do you know if your sysadmins followed the instructions for building
  and installing the cartridge
  (http://code.google.com/p/rdkit/wiki/BuildingTheCartridge)? That
  process creates the rdkit.sql file.
 
  -greg
 
 

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[Rdkit-discuss] apply model - use Composite

[Paul . Czodrowski]

Dear all,

I'm trying to apply a Composite model on a test set.
However, no output is generated. At least, no error/warning, but I cannot
jugde if the model gives any predictions.

This is the model


  
 nms=[x[0] for x in Descriptors._descList]  
  
 nms.remove('MolecularFormula') 
  
 calc = MoleculeDescriptors.MolecularDescriptorCalculator(nms)  
  
 descrs = [calc.CalcDescriptors(x) for x in ms] 
  
 ndescrs = len(calc.GetDescriptorNames())   
  

  
 pts=[] 
  

  
 for i,m in enumerate(ms):  
  
     if m.GetProp('SOL_classification')=='(A) low': 
  
         act=2  
  
     elif m.GetProp('SOL_classification')=='(B) medium':
  
         act=1  
  
     else:  
  
         act = 0
  
     pts.append([m.GetProp('NAME')]+list(descrs[i])+[act])  
  

  
 cPickle.dump(pts,file('descrs.pkl','wb+')) 
  

  
 from rdkit.ML import ScreenComposite   
  
 pts = cPickle.load(file('descrs.pkl','rb'))
  
 ndescrs = len(pts[0])-2
  
 boundsPerVar = [0]+[1]*ndescrs+[0] 
  
 nPossible = [0]+[2]*ndescrs+[3]
  
 attrs = range(1,ndescrs+1) 
  
 cmp = Composite()  
  
 
cmp.Grow(pts,attrs=attrs,nPossibleVals=nPossible,nTries=10,buildDriver=CrossValidate.CrossValidationDriver,
  
 treeBuilder=QuantTreeBoot, needsQuantization=False,nQuantBounds=boundsPerVar, 
maxDepth=3)
 res = ScreenComposite.ShowVoteResults(range(len(pts)), pts, cmp, 3, 
0,errorEstimate=True)

  




Now I would like to use the model to do predictions for the test set:


   
 test1 = [x for x in Chem.SDMolSupplier('test1.sdf') if x is not None]  
   
 nms_test1=[x[0] for x in Descriptors._descList]
   
 nms_test1.remove('MolecularFormula')   
   
 calc_test1 = MoleculeDescriptors.MolecularDescriptorCalculator(nms_test1)  
   
 descrs_test1 = [calc_test1.CalcDescriptors(x) for x in test1]  
   
 pts_test1 = [] 
   
 for i,m in enumerate(test1):   
   
     if m.GetProp('SOL_classification')=='(A) low': 
   
         act=2  
   
     elif m.GetProp('SOL_classification')=='(B) medium':
   
         act=1 

Re: [Rdkit-discuss] ML, rdkit, 3class model

[Paul . Czodrowski]

Dear all,

 Dear Paul,

 On Tue, Jun 7, 2011 at 4:54 PM,  paul.czodrow...@merck.de wrote:
 
  Dear folks,
 
  finally, I updated the Wiki entry for the 3class model:
  http://code.google.com/p/rdkit/wiki/TrainAThreeClassSolubilityModel
 
 
  Do you have any explanation for the bad statistics? [see at the end
The
  output]
 
  Of course, this is not a simple question. But maybe I did stupid
mistake..
 

 Aside from what looks like a mis-labeling of the data points (it looks
 like you've labeled the high solubility points low and vice versa), I
 don't see anything obviously wrong. I don't think that I would expect
 a fingerprint-based model to be able to do a particularly good job of
 being able to model solubility, so I'm not particularly surprised that
 you're getting bad stats.

Regarding the classification, this should be correct. The solubility data
is given in the molar range. Therefore, very low logS numbers ( -3)
correspond to very insoluble compounds.
Or am I wrong?



 I tried your dataset using a descriptor-based model based on the
 example in this wiki page:
 http://code.google.com/p/rdkit/wiki/BuildingModelsUsingDescriptors1
 The descriptor calculation stays the same, but I had to tell the
 model-building code to use three classes, which involved changing the
 line:
 nPossible = [0]+[2]*ndescrs+[2]
 to:
 nPossible = [0]+[2]*ndescrs+[3]
 and the call to ShowVoteResults from:
 res = ScreenComposite.ShowVoteResults(range(len(pts)), pts, cmp, 2, 0,
 errorEstimate=True)
 to:
 res = ScreenComposite.ShowVoteResults(range(len(pts)), pts, cmp, 3, 0,
 errorEstimate=True)

 Doing that I get the following results:

*** Vote Results ***
 misclassified: 232/1025 (%22.63)   232/1025 (%22.63)

 average correct confidence:0.9485
 average incorrect confidence:  0.8434

Results Table:

  132  40   0  |  63.77
   73 313  69  |  77.67
1  49 348  |  83.25
  --- --- ---
64.08   77.86   83.45


The statistics looks indeed better.


Thanks so far,

Paul



 Which shows that something something reasonable is happening. It's not
 (IMO) a bad start for a solubility model, certainly from here one
 could start doing parameter tuning to try and improve the model.

 -greg

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[Rdkit-discuss] mysql,frowns -- rdkit

[Paul . Czodrowski]

Dear folks,

I have some old code which I would like to convert smoothly to rdkit.
I have set-up a MySQL database of molecules given MOL2 and SMILES. The
substructure search happens via frowns:

db_smiles = db.do('SELECT ligand_id, smiles FROM ligands;')

ligand_ids = []
for db_smile in db_smiles:
try:
db_can_smiles = Smiles.smilin(db_smile[1]).cansmiles()
match = pattern.match(Smiles.smilin(db_can_smiles))
if match != None:
ligand_ids.append(db_smile[0])
except:
pass #print Warning: failed for to recognize \%s\
SMILES stringbr\n %db_smile[1]


return ligand_ids


Do I necessarily need to convert MySQL to PostgreSQL? A quick google search
shows me that this should be feasible, but I have never done it so far.

Or can I just replace the frowns SMILES search by the RDkit SMILES search?


Cheers  Thanks,
Paul

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[Rdkit-discuss] Antwort: Re: Antwort: Re: Antwort: Re: random forest in RDKit - ctd.

[Paul . Czodrowski]

Dear Jean-Paul  Greg,

the solution is too easy...

Thanks!

Cheers,
Paul

 try:
 from rdkit import ML

 (MY FIRST HELPFUL POST!!)

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 Early Stage Researcher

 InhibOx Ltd
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 (+44 / 0) 1865 262 034



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[Rdkit-discuss] Antwort: Ways people can help

[Paul . Czodrowski]

Dear Greg,


 - Write todos, tutorials, or sample scripts

I would jump here, even though I'm quite new to RDKit.
Since I'm especially interested in the ML capabilities, I would be willing
to expand the ML tutorial you started.
e.g. I could provide a literature data set for solubility  - huah, not very
exciting, but I would see this as a test case.

Then, one could add the prediction to a test set and extract the most
similar compounds.


Cheers,
Paul



 - Add/Expand/Improve the documentation.
 - Add test cases for existing code
 - Contribute a new descriptor (in python, java, or C++)
 - Contribute a new fingerprint (in python, java, or C++)
 - Contribute a new algorithm (in python, java, or C++)
 - Contribute a reader/writer for a new molecular file format (probably
 needs to be in C++)
 - Fix a bug

 Any other ideas or feedback?

 Anything I can do to make some of these easier?

 -greg


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[Rdkit-discuss] Antwort: Re: random forest in RDKit - ctd.

[Paul . Czodrowski]

Dear Greg,


 
  However, I wonder how to build a 3-class model:
 
  
  for i,m in enumerate(ms):
   if m.GetProp('ACTIVITY_CLASS')=='active':
   act=1
   else:
   act=0
   pts.append([m.GetProp('CompoundName')]+list(descrs[i])+[act])
  
 
  Naively, I just tried act 0,1 or 2 - but this did not work.

 You do need to add 0,1,2, but you also need to change the last value
 in nPossible (the number of values each descriptor + the activity can
 take) to 3. Something like this (not tested):
 nPossible = [0]+[2]*ndescrs+[3]

 Then it should work.


Where does ndescrs come from?

Using the MorganFingerprint example from the Wiki:
# build fingerprints:
fps = [AllChem.GetMorganFingerprintAsBitVect(x,2,2048) for x in ms]
nPossible = [0]+[2]*fps+[3]


This did not work.
Does your example code only go with descriptors rather than fingerprints?

Cheers  Thanks,
Paul

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[Rdkit-discuss] PDB processing

[Paul . Czodrowski]

Dear folks,

is there a way to add occupancy  B-factors (e.g. 1.00 50.0) to a PDB file?


Thanks  Cheers,
Paul

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[Rdkit-discuss] random forest in RDKit - ctd.

[Paul . Czodrowski]

Dear Greg,

the Wiki is a great place to start right from scratch with the RDKit ML
capabilities!

However, I wonder how to build a 3-class model:


for i,m in enumerate(ms):
 if m.GetProp('ACTIVITY_CLASS')=='active':
  act=1
 else:
  act=0
 pts.append([m.GetProp('CompoundName')]+list(descrs[i])+[act])


Naively, I just tried act 0,1 or 2 - but this did not work.


Cheers  Thanks,
Paul


P.S.: Although I'm rather to RDKit, I'm willing to continue the Wiki-Entry
regarding the ML capabilities. But someone should cross-check, if I don't
add any errors..

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[Rdkit-discuss] rdBase.so

[Paul . Czodrowski]

Dear folks,

what could be the reason causing the following error:


[GCC 4.3.2 20080917 (Red Hat 4.3.2-4)] on linux2
Type help, copyright, credits or license for more information.
 from rdkit import Chem
Traceback (most recent call last):
  File stdin, line 1, in module
  File /usr/local/rdkit/rdkit/Chem/__init__.py, line 18, in module
from rdkit import rdBase
ImportError: /usr/local/rdkit/rdkit/rdBase.so: undefined symbol:
_ZN5boost6python9converter8registry6insertEPFPvP7_objectEPFvS5_PNS1_30rvalue_from_python_stage1_dataEENS0_9type_infoEPFPK11_typeobjectvE



Thanks,
Paul

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[Rdkit-discuss] PubChem search

[Paul . Czodrowski]

Dear RDKit users,

has anyone used RDKit for local searches of PubChem?
Can be approximate numbers of the performance be given how long a
substructure search takes for, let's say, 50 million compounds?

Best regards,
Paul

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[Rdkit-discuss] Antwort: Installation fails for KNIME nodes

[Paul . Czodrowski]

Dear all,

I extracted the archive and copied the files to the plugins/ and features/
directories - now it works!

Thanks to George Papadatos for his help!

Cheers,
Paul



 Dear all,

 I tried to install the RDKit KNIME nodes, but it fails on my machine.

 The starup window of the installation states:
 The software items you selected may not be valid with your current
 installation. Do you want to open the wizard anyway to review the
 selections?

 I'm running KNIME 2.2.2 on a Linux 33 bit PC. For the installation, I
 downloaded the ZIP archive to my machine.

 When the sources are enabled, the following error occurs:
 
 Cannot complete the request.  See the details.
 Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
 0.9.0.0027626] requiredCapability:
 org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.win32.x86/[0.9.0.
 0027592,0.9.0.0027592]
 Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
 0.9.0.0027626] requiredCapability:
 org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.linux.x86_64/[1.0.0.
 0027615,1.0.0.0027615]
 Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
 0.9.0.0027626] requiredCapability:
 org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.macosx.x86_64/[0.9.0.
 0027589,0.9.0.0027589]
 

 When I disable the sources, this error appears:
 
 An error occurred while collecting items to be installed
   No repository found containing:
 org.rdkit.knime.bin.linux.x86/osgi.bundle/0.9.0.0027561
   No repository found containing:
 org.rdkit.knime.binaries.feature/org.eclipse.update.feature/0.9.0.0027615
   No repository found containing:
 org.rdkit.knime.feature/org.eclipse.update.feature/0.9.0.0027626
   No repository found containing:
 org.rdkit.knime.nodes/osgi.bundle/0.9.0.0027626
   No repository found containing:
 org.rdkit.knime.types/osgi.bundle/0.9.0.0027618
 

 Any ideas?

 Thank you very much in advance!


 Cheers,
 Paul


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[Rdkit-discuss] Installation fails for KNIME nodes

[Paul . Czodrowski]

Dear all,

I tried to install the RDKit MOE nodes, but it fails on my machine.

The starup window of the installation states:
The software items you selected may not be valid with your current
installation. Do you want to open the wizard anyway to review the
selections?

I'm running KNIME 2.2.2 on a Linux 33 bit PC. For the installation, I
downloaded the ZIP archive to my machine.

When the sources are enabled, the following error occurs:

Cannot complete the request.  See the details.
Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
0.9.0.0027626] requiredCapability:
org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.win32.x86/[0.9.0.0027592,0.9.0.0027592]
Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
0.9.0.0027626] requiredCapability:
org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.linux.x86_64/[1.0.0.0027615,1.0.0.0027615]
Unsatisfied dependency: [org.rdkit.knime.source.feature.feature.group
0.9.0.0027626] requiredCapability:
org.eclipse.equinox.p2.iu/org.rdkit.knime.bin.macosx.x86_64/[0.9.0.0027589,0.9.0.0027589]


When I disable the sources, this error appears:

An error occurred while collecting items to be installed
  No repository found containing:
org.rdkit.knime.bin.linux.x86/osgi.bundle/0.9.0.0027561
  No repository found containing:
org.rdkit.knime.binaries.feature/org.eclipse.update.feature/0.9.0.0027615
  No repository found containing:
org.rdkit.knime.feature/org.eclipse.update.feature/0.9.0.0027626
  No repository found containing:
org.rdkit.knime.nodes/osgi.bundle/0.9.0.0027626
  No repository found containing:
org.rdkit.knime.types/osgi.bundle/0.9.0.0027618


Any ideas?

Thank you very much in advance!


Cheers,
Paul

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