Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

[Greg Landrum]

did you build boost serialize?

On Mon, Jun 19, 2017 at 12:03 PM, JP  wrote:

> Hi Greg !
>
> Unfortunately that didn't help (I delete everything in my build directory,
> then):
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
> -DBoost_NO_SYSTEM_PATHS=ON ..
>
> and make as usual.
>
> [ 62%] Linking CXX executable testReaction
> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
> `boost::archive::text_iarchive_impl text_iarchive>::load_override(boost::archive::class_name_type&)'
> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
> `boost::archive::archive_exception::archive_exception(
> boost::archive::archive_exception const&)'
> collect2: error: ld returned 1 exit status
> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
> CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/
> CMakeFiles/testReaction.dir/all' failed
> make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all]
> Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
>
> Perhaps this isn't related to the system vs user-install, boost after all?
>
>
> On 19 June 2017 at 10:38, Greg Landrum  wrote:
>
>> If you have a system boost install that you do not want to use, you
>> should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments.
>> This will (well, should) disable any usage of the system boost.
>>
>> -greg
>>
>>
>> On Mon, Jun 19, 2017 at 9:39 AM, JP  wrote:
>>
>>> HI Paul,
>>>
>>> Funny you should mention that.  I have boost 1.61 (installed manually in
>>> /opt) and system boost I installed via sudo apt-get install
>>>
>>> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep
>>> 'Version'
>>> Version: 1.58.0.1ubuntu1
>>>
>>> However I pass the BOOST path to cmake via:
>>>
>>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/  ..
>>>
>>> (I also have the $BOOST_ROOT env variable set, so I think that is
>>> redundant.  Whatever).  cmake output clearly shows it is finding/using
>>> boost 1.61
>>>
>>> Using make VERBOSE=1 I get:
>>>
>>> [ 62%] Linking CXX executable testReaction
>>> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions
>>> && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt
>>> --verbose=1
>>> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
>>> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
>>> CMakeFiles/testReaction.dir/testReaction.cpp.o  -o testReaction
>>> -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2
>>> ../../../lib/libRDKitChemTransforms.so.1.2017.03.2
>>> ../../../lib/libRDKitDescriptors.so.1.2017.03.2
>>> ../../../lib/libRDKitFingerprints.so.1.2017.03.2
>>> ../../../lib/libRDKitDepictor.so.1.2017.03.2
>>> ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization
>>> ../../../lib/libRDKitPartialCharges.so.1.2017.03.2
>>> ../../../lib/libRDKitMolTransforms.so.1.2017.03.2
>>> ../../../lib/libRDKitEigenSolvers.so.1.2017.03.2
>>> ../../../lib/libRDKitFilterCatalog.so.1.2017.03.2
>>> ../../../lib/libRDKitSubgraphs.so.1.2017.03.2
>>> ../../../lib/libRDKitSmilesParse.so.1.2017.03.2
>>> ../../../lib/libRDKitSubstructMatch.so.1.2017.03.2
>>> ../../../lib/libRDKitGraphMol.so.1.2017.03.2
>>> ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2
>>> ../../../lib/libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization
>>> ../../../lib/libRDKitCatalogs.so.1.2017.03.2
>>> ../../../lib/libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread
>>> -lboost_system -lpthread -Wl,-rpath,/opt/rdkit/rdkit-Re
>>> lease_2017_03_2/build/lib
>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>>> to `boost::archive::text_iarchive_impl>> chive>::load_override(boost::archive::class_name_type&)'
>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>>> to 
>>> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
>>> const&)'
>>> collect2: error: ld returned 1 exit status
>>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
>>> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
>>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
>>> make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
>>> CMakeFiles/Makefile2:4157: recipe for target
>>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
>>> make[1]: *** [Code/GraphMol/ChemReactions/C
>>> MakeFiles/testReaction.dir/all] Error 2
>>> make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
>>> Makefile:160: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>>
>>> /opt/boost_1_61_0/lib is also the first path in 

Re: [Rdkit-discuss] setting valence of choice to S and P atoms in rdkit

[Ling Chan]

Hello Janusz,

Perhaps you have answered your own question? You can start with Smiles like
"[H][SH3](C)[SH5]".

Otherwise you could use the SetNumExplicitHs() function. For example,

  m = Chem.MolFromSmiles('CS')
  m.GetAtomWithIdx(1).SetNumExplicitHs(5)
  AllChem.SanitizeMol(m)
  print Chem.AddHs(m).GetNumAtoms()

will inform you that there is a total of 10 atoms. But if you comment out
the line with SetNumExplicitHs, it will inform you that the total number of
atoms is 6.

The above seems to work without the SanitizeMol() function but I think it
is better to call it for safety, to clean up the molecule.

Ling Chan




On Tue, Jun 20, 2017 at 7:37 AM, Janusz Petkowski  wrote:

> Dear RDKit Community,
>
> I have a quick question regarding a possibility of setting valence of an
> atom in rdkit.
>
> Let's say that I have a molecule like this (smiles notation): PPC or SSC
> and I would like to change the valence of one or more S or P atoms from
> default II for S or III for P to let's say SIV or SVI and PV. As a result I
> would like to have the following molecules (as an example):
> [H][SH3](C)[SH5], [H][SH2]SC, [H][SH3](C)[SH3] or [H][PH3]PC, [H][PH3][PH3]C
>
> Is it possible to output such molecules using SSC or PPC molecules as
> inputs, using one of rdkit methods (modules)?
>
> Thank you very much for your help,
>
> Best regards,
>
> Dr Janusz Petkowski
>
> Research Fellow at MIT EAPS 
>
> Tel:  +1 (617) 258 - 6910 <%28857%29%20777-6977>
>
> 
> --
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>
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[Rdkit-discuss] Definition of HBA differs from pipeline pilot

[Hongbin Yang]

Hi, Rdkiters,
? ?The definition of HBA in rdkit is (by Lipinski) :
32  HAcceptorSmarts = Chem.MolFromSmarts('[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),' + 
33   
'$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),' + 
34   '$([nH0,o,s;+0])]') 

? ? But in pipeline pilot (3.5), there are two HBA definitions, one of which is 
Lipinsk's. I guess the other is the "first edition", which is defined as:22  # 
HAcceptor  '[$([!#6;+0]);!$([F,Cl,Br,I]); 
23  # !$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]' 
? ?Does it mean that we should use the newest edition of HBA and?get rid of the 
default definition in pipeline pilot. These may change the?datasets filtered by 
rules such RO5.
(I am not sure whether the HBA defined in PP is the same as defined in Line 
22-23. I made a test.?Abacavir have 7 (current edition) and 6 (old) 
respectively. And in PP, it also returned these two results).

reference:?http://www.rdkit.org/docs/api/rdkit.Chem.Lipinski-pysrc.html#NumHAcceptors?

Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology?


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[Rdkit-discuss] setting valence of choice to S and P atoms in rdkit

[Janusz Petkowski]

Dear RDKit Community,

I have a quick question regarding a possibility of setting valence of an atom 
in rdkit.

Let's say that I have a molecule like this (smiles notation): PPC or SSC and I 
would like to change the valence of one or more S or P atoms from default II 
for S or III for P to let's say SIV or SVI and PV. As a result I would like to 
have the following molecules (as an example): [H][SH3](C)[SH5], [H][SH2]SC, 
[H][SH3](C)[SH3] or [H][PH3]PC, [H][PH3][PH3]C

Is it possible to output such molecules using SSC or PPC molecules as inputs, 
using one of rdkit methods (modules)?

Thank you very much for your help,

Best regards,

Dr Janusz Petkowski

Research Fellow at MIT EAPS

Tel:  +1 (617) 258 - 6910
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Re: [Rdkit-discuss] ipywidgets & py3Dmol

[Malitha Kabir]

Dear Paul,

>From your response, I think your ipywidgets is working fine. Now, you are
facing trouble with py3Dmol.

py3Dmol basically generates JavaScript codes (3Dmol.js) and IPython injects
those in web browser. So, will you kindly share what error printed in your
browser console?

Off topic: The following link shows how to see browser console from Google
Chrome https://developers.google.com/web/tools/chrome-devtools/console/

Best regards,
Malitha



On Tue, Jun 20, 2017 at 3:33 PM, Paul Czodrowski <
paul.czodrow...@merckgroup.com> wrote:

> 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 <+49%206151%20723218>
>
> E-mail: paul.czodrow...@merckgroup.com | 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 
> *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> 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]
> *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
>
>
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have 

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 | 
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 
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 
> 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]
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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Re: [Rdkit-discuss] ipywidgets & py3Dmol

[Malitha Kabir]

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> 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]
> *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
>
>
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have received this transmission in error, please
> notify the sender immediately and delete the message and any attachment
> from your system. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not accept liability for any omissions or errors in this
> message which may arise as a result of E-Mail-transmission or for damages
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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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Re: [Rdkit-discuss] ipywidgets & py3Dmol

[Axel Pahl]

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):

python 3.5.3
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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or otherwise protected from disclosure. If you are not the intended 
recipient, you must not copy this message or attachment or disclose 
the contents to any other person. If you have received this 
transmission in error, please notify the sender immediately and delete 
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Darmstadt, Germany and any of its subsidiaries do not accept liability 
for any omissions or errors in this message which may arise as a 
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unauthorized changes of the content of this message and any attachment 
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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




This message and any attachment are confidential and may be privileged or 
otherwise protected from disclosure. If you are not the intended recipient, you 
must not copy this message or attachment or disclose the contents to any other 
person. If you have received this transmission in error, please notify the 
sender immediately and delete the message and any attachment from your system. 
Merck KGaA, Darmstadt, Germany and any of its subsidiaries do not accept 
liability for any omissions or errors in this message which may arise as a 
result of E-Mail-transmission or for damages resulting from any unauthorized 
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Darmstadt, Germany and any of its subsidiaries do not guarantee that this 
message is free of viruses and does not accept liability for any damages caused 
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WidgetInsidepy3Dmol.ipynb
Description: WidgetInsidepy3Dmol.ipynb
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