ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Bret Wallace
I was wondering when ADT / MGLTools will be updated to be compatibility with Mac OS 11 and higher? Until then, does anybody know of any work-arounds?

Thanks,

Bret


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

Reply | Threaded
Open this post in threaded view
|

Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Michel Sanner
Dear Bret

We have been looking into this but so far do not have a working version. Sadly, due to budgets cuts on our grants we have lost our programmer so at the current time I have not ETA for such a port. The only workaround I can think of is to run it in a virtual machine with Mac OS 10.13 (high Sierra or earlier).

-Michel

From: <[hidden email]> on behalf of Bret Wallace <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Monday, December 21, 2020 at 6:26 AM
To: "[hidden email]" <[hidden email]>
Subject: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

I was wondering when ADT / MGLTools will be updated to be compatibility with Mac OS 11 and higher? Until then, does anybody know of any work-arounds?

Thanks,

Bret


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

Reply | Threaded
Open this post in threaded view
|

Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Francois Berenger
Bonjour,

Vous devriez mettre le code sur github,
pour attirer des contributeurs externes.

Actuellemnt, on peut telecharger le code de Vina,
mais on dirait que c'est de "l'open-source behind closed walls".

Cdt,
F.

On 22/12/2020 02:01, Michel Sanner wrote:

> Dear Bret
>
> We have been looking into this but so far do not have a working
> version. Sadly, due to budgets cuts on our grants we have lost our
> programmer so at the current time I have not ETA for such a port. The
> only workaround I can think of is to run it in a virtual machine with
> Mac OS 10.13 (high Sierra or earlier).
>
> -Michel
>
> From: <[hidden email]> on behalf of Bret Wallace
> <[hidden email]>
> Reply-To: "[hidden email]" <[hidden email]>
> Date: Monday, December 21, 2020 at 6:26 AM
> To: "[hidden email]" <[hidden email]>
> Subject: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?
>
> I was wondering when ADT / MGLTools will be updated to be
> compatibility with Mac OS 11 and higher? Until then, does anybody know
> of any work-arounds?
>
> Thanks,
>
> Bret
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list 
> ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list 
> ---


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

Reply | Threaded
Open this post in threaded view
|

Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Michel Sanner
In reply to this post by Bret Wallace
Hello François

I do like the idea however, MGLTools is a  large collection of Python packages dome developed in my lab and some developed by others, some pure Python (easy) and some with C and C++ extensions. Building a functional version of MGLtols requires a compatible set of these packages (and not all packages are using the same version on all platforms because of platform-dependent bugs in third party packages). So it is quite challenging to get to work from source.
Years ago I tried it and I ended up spending more time answering questions from people asking about how to build it than I could afford.
All source code was available under our public CVS repository. When we switched to GIT we did not go through the pain of maintaining a public version as access to our CVS server was quasi-inexistant.
I’ll be happy to put the source of the C and C++ extensions on GitHub  if there is enough interest that I feel it is worth my time. It is just more work, and work for which we get relatively few brownie points as we are mainly funded to do research.

-Michel

From: <[hidden email]> on behalf of Francois Berenger <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Monday, December 21, 2020 at 4:57 PM
To: "[hidden email]" <[hidden email]>
Subject: Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Bonjour,

Vous devriez mettre le code sur github,
pour attirer des contributeurs externes.

Actuellemnt, on peut telecharger le code de Vina,
mais on dirait que c'est de "l'open-source behind closed walls".

Cdt,
F.

On 22/12/2020 02:01, Michel Sanner wrote:
Dear Bret

We have been looking into this but so far do not have a working
version. Sadly, due to budgets cuts on our grants we have lost our
programmer so at the current time I have not ETA for such a port. The
only workaround I can think of is to run it in a virtual machine with
Mac OS 10.13 (high Sierra or earlier).

-Michel

From: <[hidden email]<mailto:[hidden email]>> on behalf of Bret Wallace
<[hidden email]<mailto:[hidden email]>>
Reply-To: "[hidden email]<mailto:[hidden email]>" <[hidden email]<mailto:[hidden email]>>
Date: Monday, December 21, 2020 at 6:26 AM
To: "[hidden email]<mailto:[hidden email]>" <[hidden email]<mailto:[hidden email]>>
Subject: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

I was wondering when ADT / MGLTools will be updated to be
compatibility with Mac OS 11 and higher? Until then, does anybody know
of any work-arounds?

Thanks,

Bret


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
---


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Bret Wallace
In reply to this post by Michel Sanner
Ahh OK, understood! I’ll look into the virtual machine.

Bret

> On Dec 21, 2020, at 12:01 PM, Michel Sanner <[hidden email]> wrote:
>
> Dear Bret
>
> We have been looking into this but so far do not have a working version. Sadly, due to budgets cuts on our grants we have lost our programmer so at the current time I have not ETA for such a port. The only workaround I can think of is to run it in a virtual machine with Mac OS 10.13 (high Sierra or earlier).
>
> -Michel
>
> From: <[hidden email]> on behalf of Bret Wallace <[hidden email]>
> Reply-To: "[hidden email]" <[hidden email]>
> Date: Monday, December 21, 2020 at 6:26 AM
> To: "[hidden email]" <[hidden email]>
> Subject: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?
>
> I was wondering when ADT / MGLTools will be updated to be compatibility with Mac OS 11 and higher? Until then, does anybody know of any work-arounds?
>
> Thanks,
>
> Bret
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Rick Sheridan
In reply to this post by Michel Sanner
In addition to virtual machines, the other Mac OS workaround I’m aware of
is ‘upgrading’ to an earlier OS version after booting via an external
bootable drive.

While we’re on the topic though, any guidance about anticipated M1
compatibility? (Assuming use of VM’s
or downgraded OS’s).

Best,
Rick

On Tue, 22 Dec 2020 at 4:10 AM, Michel Sanner <[hidden email]> wrote:

> Hello François
>
> I do like the idea however, MGLTools is a  large collection of Python
> packages dome developed in my lab and some developed by others, some pure
> Python (easy) and some with C and C++ extensions. Building a functional
> version of MGLtols requires a compatible set of these packages (and not all
> packages are using the same version on all platforms because of
> platform-dependent bugs in third party packages). So it is quite
> challenging to get to work from source.
> Years ago I tried it and I ended up spending more time answering questions
> from people asking about how to build it than I could afford.
> All source code was available under our public CVS repository. When we
> switched to GIT we did not go through the pain of maintaining a public
> version as access to our CVS server was quasi-inexistant.
> I’ll be happy to put the source of the C and C++ extensions on GitHub  if
> there is enough interest that I feel it is worth my time. It is just more
> work, and work for which we get relatively few brownie points as we are
> mainly funded to do research.
>
> -Michel
>
> From: <[hidden email]> on behalf of Francois Berenger <
> [hidden email]>
> Reply-To: "[hidden email]" <[hidden email]>
> Date: Monday, December 21, 2020 at 4:57 PM
> To: "[hidden email]" <[hidden email]>
> Subject: Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?
>
> Bonjour,
>
> Vous devriez mettre le code sur github,
> pour attirer des contributeurs externes.
>
> Actuellemnt, on peut telecharger le code de Vina,
> mais on dirait que c'est de "l'open-source behind closed walls".
>
> Cdt,
> F.
>
> On 22/12/2020 02:01, Michel Sanner wrote:
> Dear Bret
>
> We have been looking into this but so far do not have a working
> version. Sadly, due to budgets cuts on our grants we have lost our
> programmer so at the current time I have not ETA for such a port. The
> only workaround I can think of is to run it in a virtual machine with
> Mac OS 10.13 (high Sierra or earlier).
>
> -Michel
>
> From: <[hidden email]<mailto:[hidden email]>>
> on behalf of Bret Wallace
> <[hidden email]<mailto:[hidden email]>>
> Reply-To: "[hidden email]<mailto:[hidden email]>" <
> [hidden email]<mailto:[hidden email]>>
> Date: Monday, December 21, 2020 at 6:26 AM
> To: "[hidden email]<mailto:[hidden email]>" <
> [hidden email]<mailto:[hidden email]>>
> Subject: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?
>
> I was wondering when ADT / MGLTools will be updated to be
> compatibility with Mac OS 11 and higher? Until then, does anybody know
> of any work-arounds?
>
> Thanks,
>
> Bret
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

--
--
********************************************************************
Rick Sheridan
********************************************************************
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Navan Chauhan
People have been able to run Windows 10 on M1 Macs, which means you can run
32/64 bit apps in emulated mode. I don't know how much a hit the
performance will take but the M1 runs Windows 10 better than Qualcomm's ARM
chips.

Another way is to use CrossOver. I used to use it to run PyRx but the
docking performance was slower than natively running AutoDock-Vina.

Also, I have been tinkering with the MGLTools app on macOS 11. I decompiled
the run(?) script. ( command for PMV: osadecompile
/Applications/MGLTools-1.5.6/PMV-1.5.6.app/Contents/Resources/Scripts/main.scpt
)

Output:

(*Author: Sargis Dallakyan <[hidden email]>*)


do shell script "

ps -wx -ocommand | grep -e '[X]11' > dev/null;

if [ \"$?\" != \"0\" -a ! -f ~/.xinitrc ]; then

    echo \"rm -f ~/.xinitrc\" > ~/.xinitrc

    sed 's/xterm/# xterm/' /usr/X11R6/lib/X11/xinit/xinitrc >> ~/.xinitrc

fi;

"

tell application "Finder"

launch application "XQuartz"

end tell

do shell script "

MGL_ROOT=\"/Library/MGLTools/1.5.6\";

export MGL_ROOT;


MGL_ARCHOSV=`$MGL_ROOT/bin/archosv`;

export MGL_ARCHOSV;


PATH=\"$MGL_ROOT/bin:$PATH\"

export PATH;

TCL_LIBRARY=\"$MGL_ROOT/tcl8.4\";

export TCL_LIBRARY;


TK_LIBRARY=\"$MGL_ROOT/tk8.4\";

export TK_LIBRARY;


DYLD_LIBRARY_PATH=\"$MGL_ROOT/lib${DYLD_LIBRARY_PATH:+:$DYLD_LIBRARY_PATH}\";

export DYLD_LIBRARY_PATH;


unset PYTHONHOME;

PYTHONHOME=\"$MGL_ROOT\";

export PYTHONHOME;

PYTHONPATH=\"$MGL_ROOT/MGLToolsPckgs\";

export PYTHONPATH;

python=\"$MGL_ROOT/bin/python\";

cd ~;

if [ ! \"$DISPLAY\" ]; then

DISPLAY=:0.0;

export DISPLAY;

fi

$python $MGL_ROOT/MGLToolsPckgs/Pmv/bin/runPmv.py;
"dc

Now, after creating a virtual environment with Python2.7 ( To run MGLTools
you need oldnumerical functionality in NumPy which was removed around
version 1.9, so I created a virtual environment to install numpy==1.8.0 )

Once you activate your virtual environment, you will also need to export
the PYTHONPATH for your instance to pick up the Python modules (export
PYTHONPATH="/Library/MGLTools/1.5.6/MGLToolsPckgs")

Running python /Library/MGLTools/1.5.6/MGLToolsPckgs/Pmv/bin/runPmv.py almost
worked.

Attached the screenshot. Error:

ImportError:
dlopen(/Library/MGLTools/1.5.6/MGLToolsPckgs/opengltk/extent/_gllib.so, 2):
no suitable image found.  Did find:

/Library/MGLTools/1.5.6/MGLToolsPckgs/opengltk/extent/_gllib.so: mach-o,
but wrong architecture

/Library/MGLTools/1.5.6/MGLToolsPckgs/opengltk/extent/_gllib.so: mach-o,
but wrong architecture

hit enter to continue

I haven't been able to compile pyopengltk
[image: image.png]

I haven't been able to compile OpenGlTk from source as SWIG is throwing an
error and I am not familiar with it ( reference:
http://mgltools.scripps.edu/api/opengltk/opengltk-module.html ).

Error while running python setup.py install:

building 'extent._gllib' extension

swigging opengltk/extent/gllib.i to opengltk/extent/gllib_wrap.c

swig -python -o opengltk/extent/gllib_wrap.c opengltk/extent/gllib.i

opengltk/extent/gl_i.h:2380: Error: Syntax error - possibly a missing
semicolon.

error: command 'swig' failed with exit status 1

(venv) *➜  **opengltk-1.5.6* swig -v -includeall -python -o
opengltk/extent/gllib_wrap.c opengltk/extent/gllib.i

Language subdirectory: python

Search paths:

   ./

   ./swig_lib/python/

   /usr/local/Cellar/swig/4.0.2/share/swig/4.0.2/python/

   ./swig_lib/

   /usr/local/Cellar/swig/4.0.2/share/swig/4.0.2/

Preprocessing...

opengltk/extent/gl_i.h:41: Error: Unable to find 'OpenGL/gltypes.h'

opengltk/extent/gl_i.h:44: Error: Unable to find 'OpenGL/glext.h'

opengltk/extent/gl_i.h:46: Error: Unable to find
'OpenGL/OpenGLAvailability.h'

(venv) *➜  **opengltk-1.5.6*


If someone manages to fix this, please let me know.

Rewriting the source from Python2 to Python3 will take a really long time,
but for now making it work with Python2.7 should be easy.


On Thu, 24 Dec 2020 at 14:28, Rick Sheridan <[hidden email]> wrote:

> In addition to virtual machines, the other Mac OS workaround I’m aware of
> is ‘upgrading’ to an earlier OS version after booting via an external
> bootable drive.
>
> While we’re on the topic though, any guidance about anticipated M1
> compatibility? (Assuming use of VM’s
> or downgraded OS’s).
>
> Best,
> Rick
>
> On Tue, 22 Dec 2020 at 4:10 AM, Michel Sanner <[hidden email]> wrote:
>
> > Hello François
> >
> > I do like the idea however, MGLTools is a  large collection of Python
> > packages dome developed in my lab and some developed by others, some pure
> > Python (easy) and some with C and C++ extensions. Building a functional
> > version of MGLtols requires a compatible set of these packages (and not
> all
> > packages are using the same version on all platforms because of
> > platform-dependent bugs in third party packages). So it is quite
> > challenging to get to work from source.
> > Years ago I tried it and I ended up spending more time answering
> questions
> > from people asking about how to build it than I could afford.
> > All source code was available under our public CVS repository. When we
> > switched to GIT we did not go through the pain of maintaining a public
> > version as access to our CVS server was quasi-inexistant.
> > I’ll be happy to put the source of the C and C++ extensions on GitHub  if
> > there is enough interest that I feel it is worth my time. It is just more
> > work, and work for which we get relatively few brownie points as we are
> > mainly funded to do research.
> >
> > -Michel
> >
> > From: <[hidden email]> on behalf of Francois Berenger <
> > [hidden email]>
> > Reply-To: "[hidden email]" <[hidden email]>
> > Date: Monday, December 21, 2020 at 4:57 PM
> > To: "[hidden email]" <[hidden email]>
> > Subject: Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?
> >
> > Bonjour,
> >
> > Vous devriez mettre le code sur github,
> > pour attirer des contributeurs externes.
> >
> > Actuellemnt, on peut telecharger le code de Vina,
> > mais on dirait que c'est de "l'open-source behind closed walls".
> >
> > Cdt,
> > F.
> >
> > On 22/12/2020 02:01, Michel Sanner wrote:
> > Dear Bret
> >
> > We have been looking into this but so far do not have a working
> > version. Sadly, due to budgets cuts on our grants we have lost our
> > programmer so at the current time I have not ETA for such a port. The
> > only workaround I can think of is to run it in a virtual machine with
> > Mac OS 10.13 (high Sierra or earlier).
> >
> > -Michel
> >
> > From: <[hidden email]<mailto:[hidden email]
> >>
> > on behalf of Bret Wallace
> > <[hidden email]<mailto:[hidden email]>>
> > Reply-To: "[hidden email]<mailto:[hidden email]>" <
> > [hidden email]<mailto:[hidden email]>>
> > Date: Monday, December 21, 2020 at 6:26 AM
> > To: "[hidden email]<mailto:[hidden email]>" <
> > [hidden email]<mailto:[hidden email]>>
> > Subject: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?
> >
> > I was wondering when ADT / MGLTools will be updated to be
> > compatibility with Mac OS 11 and higher? Until then, does anybody know
> > of any work-arounds?
> >
> > Thanks,
> >
> > Bret
> >
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> > ---
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> > ---
> >
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> --
> --
> ********************************************************************
> Rick Sheridan
> ********************************************************************
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?

Navan Chauhan
In reply to this post by Michel Sanner
Is there a link to the source code for MGLTools 1.5.7 ( Can only find for
1.5.6), I am trying to patch for 1.5.6 and only a few packages remain but
it would be easier if I was working on the latest version of the source
perhaps?

The major issue I was facing was compiling OpenGLTk, fiddled with the
deprecation messages and applied a few patches. I plan on fixing geomutils
when I have some more time next.

Screenshot of Running CADD: https://i.imgur.com/wlLZQNm.jpg



On Mon, 21 Dec 2020 at 22:32, Michel Sanner <[hidden email]> wrote:

> Dear Bret
>
> We have been looking into this but so far do not have a working version.
> Sadly, due to budgets cuts on our grants we have lost our programmer so at
> the current time I have not ETA for such a port. The only workaround I can
> think of is to run it in a virtual machine with Mac OS 10.13 (high Sierra
> or earlier).
>
> -Michel
>
> From: <[hidden email]> on behalf of Bret Wallace <
> [hidden email]>
> Reply-To: "[hidden email]" <[hidden email]>
> Date: Monday, December 21, 2020 at 6:26 AM
> To: "[hidden email]" <[hidden email]>
> Subject: ADL: AutoDockTools / MGLTools Compatability with Mac OS 11?
>
> I was wondering when ADT / MGLTools will be updated to be compatibility
> with Mac OS 11 and higher? Until then, does anybody know of any
> work-arounds?
>
> Thanks,
>
> Bret
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---