[PyMOL] About legal/copyright issue with developing PyMOL plugin

[William Tao]

Hi PyMOL community,

I am planning to develop a PyMOL plugin based on PyMOL 2.x versions with
PyQt.

However, I am not quite clear about the legal implications and copyright
issues if I would like to make my plugin open-source in future.

First, PyMOL has incentive version and open-source version. I have an
educational license for incentive version and open-source version. If I am
going to describe my plugin in a scientific article or website, which
version of PyMOL version am I allowed to use?

Second, the PyQt requires the code based on it must also be open-source
according to GPL.

These two factors make me confused about the possibility of publishing a
plugin for PyMOL in future.

If anybody has experience in this aspect, please feel free to advise.

Many thanks.

William
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Re: [PyMOL] About legal/copyright issue with developing PyMOL plugin

[William Tao]

Hi Dr. Holder,

Thank you for your detailed explanation. Your answer is very helpful.

Best,

William

Thomas Holder  于2019年3月6日周三 上午4:04写道：

> Hi William,
>
> You can use any version of PyMOL, the plugin API is the same in all of
> them (Open-Source, Incentive with edu/academic/commercial license).
>
> Your own code, if open-sourced, needs a GPL-compatible license. You're in
> the same situation as the person asking "can I release my SW under the MIT
> license in situation 3?" (answer: Yes) here:
> https://riverbankcomputing.com/pipermail/pyqt/2016-September/038129.html
>
> Only if you are going to sell your plugin, you need to purchase a
> commercial PyQt license. See
> https://riverbankcomputing.com/commercial/license-faq
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> > On Mar 4, 2019, at 7:03 PM, William Tao  wrote:
> >
> > Hi PyMOL community,
> >
> > I am planning to develop a PyMOL plugin based on PyMOL 2.x versions with
> PyQt.
> >
> > However, I am not quite clear about the legal implications and copyright
> issues if I would like to make my plugin open-source in future.
> >
> > First, PyMOL has incentive version and open-source version. I have an
> educational license for incentive version and open-source version. If I am
> going to describe my plugin in a scientific article or website, which
> version of PyMOL version am I allowed to use?
> >
> > Second, the PyQt requires the code based on it must also be open-source
> according to GPL.
> >
> > These two factors make me confused about the possibility of publishing a
> plugin for PyMOL in future.
> >
> > If anybody has experience in this aspect, please feel free to advise.
> >
> > Many thanks.
> >
> > William
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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Re: [PyMOL] Plugin upload.

[William Tao]

Hi Wael,

I'm somehow curious whether you have used PyQt in your plugin.

Nowadays, people usually upload released code onto repositories like
GitHub. But I'm not sure which open source license we need to use if PyQt
is used.

Hope anyone who is familiar with this issue could help.

Many thanks.

Will


Wael Azzam via PyMOL-users  于2019年7月9日周二
上午3:11写道：

> To whom it may concern,
>
> I am writing to you in the hopes of knowing how to upload a PyMol plugin
> that I developed on the page PyMolWiki ?
>
> Best regards,
>
> Wael Azzam
> B.S in Bioinformatics
> Lebanese American University, Beirut
>
>
>
>
>
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Re: [PyMOL] Pymol install on CentoOS7

[William Tao]

Hi Yanni,

If you have root access (su), it might be easier to try "Open-Source PyMOL
in Linux Distros" (
https://pymolwiki.org/index.php/Linux_Install#Open-Source_PyMOL_in_Linux_Distros).
This approach saves the process of compiling the code manually.

Best,

Y. Tao

Yanni G  于2020年10月7日周三 上午5:21写道：

> Hello everyone
>
> I'm having difficulty installing pymol on my Centos7 machine. I have
> followed the instructions on the Pymol wiki page but when I try to
> build+install, I get this error:
>
> python3 setup.py build install --home=/opt/pymol-osbuild
>
>   File "setup.py", line 227
>
> out.write(f'set PYMOL_PATH={pymol_path}' + os.linesep)
>
>^
>
> SyntaxError: invalid syntax
>
> Has anyone seen this before? If you have any suggestions please let me
> know. I'm stuck at the moment.
>
> Many thanks
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[PyMOL] PyVibMS - New PyMOL plugin

[William Tao]

Dear colleagues,

We are very glad to announce the first version of PyVibMS -- a PyMOL plugin
designed to visualize vibrations in molecules and solids, and the code has
been deposited in GitHub (https://github.com/smutao/PyVibMS).

PyVibMS has two major functionalities

   - Visualize the structure of molecules and solids (with lattice vector
   information), chemical bonding will be automatically detected based on
   distance
   - Animate vibrations with or without arrows, these animations can be
   exported via PyMOL's encoder interface

Current version of PyVibMS can natively process the vibrational analysis
result calculated by (1) Gaussian 09/16, (2) Q-Chem, (3) CRYSTAL17 and (4)
VASP. Other quantum chemical packages are supported in a generic way with a
formatted mode input file.

This plugin used a cgo-arrow script (
https://pymolwiki.org/index.php/Cgo_arrow) made by Dr. Thomas Holder. And
we also like to thank other PyMOL developers who made this plugin based on
PyQT possible.

If you find PyVibMS plugin useful in your research, please cite our work "Tao,
Y., et al., J. Mol. Model. 2020, 26, 290
". If you
have any comments and suggestions, we are more than happy to hear your
thoughts.

Best regards,

Y. Tao
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