Re: [Rdkit-discuss] ipywidgets & py3Dmol
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 <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> 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
Re: [Rdkit-discuss] ipywidgets & py3Dmol
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 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 changes of the content of this message and any attachment thereto. Merck KGaA, 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 by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, Frenc
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 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 changes of the content of this message and > any attachment thereto. Merck KGaA, 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 by any virus transmitted > therewith. > > > > Click http://www.merckgroup.com/disclaimer to access the German, French, > Spanish and Portuguese versions of this disclaimer. > > > > > -- > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > > ___ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > > > 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,
Re: [Rdkit-discuss] ipywidgets & py3Dmol
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 resulting from any unauthorized changes of the content of this message and any attachment thereto. Merck KGaA, 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 by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 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 changes of the content of this message and any attachment thereto. Merck KGaA, 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 by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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): 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 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 changes of the content of this message and any attachment thereto. Merck KGaA, 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 by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimerto access the German, French, Spanish and Portuguese versions of this disclaimer. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] ipywidgets & py3Dmol
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 changes of the content of this message and any attachment thereto. Merck KGaA, 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 by any virus transmitted therewith. Click http://www.merckgroup.com/disclaimer to access the German, French, Spanish and Portuguese versions of this disclaimer. WidgetInsidepy3Dmol.ipynb Description: WidgetInsidepy3Dmol.ipynb -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
