Re: [PyMOL] pref_get() on library mode

[Pedro Lacerda]

It worked like a charm, thank you.

Em seg., 26 de out. de 2020 às 04:37, Thomas Holder <
thomas.hol...@schrodinger.com> escreveu:

> Hi Pedro,
>
> If you call `plugin_load` that will trigger initialization.
>
> pymol.plugins.plugin_load('yourplugin')
> value = pymol.plugins.pref_get('YOUPLUGIN_SOME_KEY')
>
>
> I feel like this plugin API is due for an overhaul, there are no great
> answers to your various questions :-/
>
> Cheers,
>   Thomas
>
>
> > On Oct 26, 2020, at 5:40 AM, Pedro Lacerda  wrote:
> >
> > Hi,
> >
> > How to use pref_get() on library mode.
> >
> > Or even better, how to use pref_get() even before library mode?
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular / UFBA
> > Mestrando em Ciências Farmácias / UEFS
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > http://lattes.cnpq.br/8338596525330907
> > ___
> > PyMOL-users mailing list
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> > Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular / UFBA
Mestrando em Ciências Farmácias / UEFS

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907
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[PyMOL] Generating list of polar contacts

[Marcelo Depólo]

Hi,

I have a set of protein structures and I want to quantify the amount of
internal H-bond, salt-bridges and non-polar interactions in each of them.

I was wondering if there is a way to use Pymol to provide a list of
internal H-bond and salt-bridges. Maybe with polar contacts?

Best regards,
--
Marcelo Depólo Polêto
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464
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Re: [PyMOL] pref_get() on library mode

[Thomas Holder]

Hi Pedro,

If you call `plugin_load` that will trigger initialization.

pymol.plugins.plugin_load('yourplugin')
value = pymol.plugins.pref_get('YOUPLUGIN_SOME_KEY')


I feel like this plugin API is due for an overhaul, there are no great answers 
to your various questions :-/

Cheers,
  Thomas


> On Oct 26, 2020, at 5:40 AM, Pedro Lacerda  wrote:
> 
> Hi,
> 
> How to use pref_get() on library mode.
> 
> Or even better, how to use pref_get() even before library mode?
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] Formatted output

[Thomas Holder]

Hi Pedro,

The Incentive PyMOL Qt GUI is able to handle a small subset of ANSI color codes.

pymol.colorprinting.error("Text in red")
pymol.colorprinting.warning("Text in magenta")
print("\033[31mRed \033[32mGreen \033[33mYellow\033[m Default")

https://en.wikipedia.org/wiki/ANSI_escape_code

Open-Source PyMOL will simply strip the color codes.

Cheers,
  Thomas


> On Oct 26, 2020, at 3:10 AM, Pedro Lacerda  wrote:
> 
> I see that probably you are using HTML for this.
> https://github.com/schrodinger/pymol-open-source/blob/69b1f0b53b4109c34604adcea3983e4d3886069e/modules/pymol/colorprinting.py
> 
> But printing HTML directly into the console didn't worked.
> 
> Em dom., 25 de out. de 2020 às 23:06, Pedro Lacerda  
> escreveu:
> Hi,
> 
> How can I print formatted output into the PyMOL console?
> 
> I see that on the incentive version the output is coloured (eg errors are 
> red).
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular / UFBA
> Mestrando em Ciências Farmácias / UEFS
> 
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] Problem In using Pymol 2.4 through IDLE -Python 3

[Dr. Vijay Masand]

Thank you, Dr. Christopher Gohlke
I downloaded and installed Microsoft Visual C++ Redistributable for
Visual Studio 2015, 2017 and 2019. This solved the problem. Now, PyMOL is
running without any problem. In fact, I just successfully ran PyMOL from
Portable Python 3.8 and also from IDLE.
Cheers

With Warm Regards
*Dr. Vijay H. Masand*
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/



On Sat, Oct 24, 2020 at 9:17 AM Christoph Gohlke  wrote:

> Try installing the Microsoft Visual C++ Redistributable for Visual
> Studio 2015, 2017 and 2019
> <
> https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads
> >
>
> Christoph
>
>
> On 10/23/2020 8:11 PM, Dr. Vijay Masand wrote:
> > Hello PyMOL users
> > I installed open source PyMOL 2.4 (Python 3.7) on Windows 10 (64 bit).
> > It strated without any problem when the icon was double clicked.But when
> > I tried to use it from IDLE (PYTHON 3.7- 64bit), it showed following
> error:
> > "ImportError: DLL load failed: The specified module could not be found."
> >
> > To find a solution, I installed Pymol 2.4 with Python 3.8, but Pymol did
> > not start at all. Then, I tried Pymol 2.4 with Python 3.9 also, again
> > PyMOL 2.4 did not start at all.
> > Finally, I tried Python 2.7 (using PyMOL 2.0), it worked perfectly and
> > was running from IDLE, as well.
> >
> > I need help to remove the error
> > "ImportError: DLL load failed: The specified module could not be found."
> > to run PyMOL 2.4 with Python 3 using IDLE?
> >
> > Thanks in advance.
> >
> > With Warm Regards
> > *Dr. Vijay H. Masand*
> > Department of Chemistry,
> > Vidya Bharati College, Amravati, 444 602
> > Maharashtra, India.
> > Phone number- +91-9403312628
> > https://sites.google.com/site/vijaymasand/
> > 
> >
> >
> >
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> >
>
>
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