Re: [PyMOL] How to tell from within a script if a plugin is loaded?

[Sampson, Jared M.]

Hi Thomas -

Thanks for the clarification on cmd.extend() and the difference between how 
commands and functions are made available. I hadn't thought to just add the 
function to cmd directly.  This will come in handy!

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 18, 2016, at 1:14 PM, Thomas Holder 
> wrote:

Hi Jared,

The plugin system isn't really tuned for API extension. As Tsjerk pointed out, 
cmd.extend only registers a command, not a cmd. function. Also, scripts 
which are installed as plugins get loaded asynchronously from the external GUI. 
I suggest you do the following:

1) Inside your plugin (Python module), do:

from pymol import cmd
def my_func(): ...
cmd.my_func = my_func
cmd.extend('my_func', my_func)

2) The plugin's __init_plugin__ (or __init__) function should only be 
responsible for adding Plugin menu entries, not for anything else.

3) Inside your test file, do:

from pymol import cmd
import pmg_tk.startup.my_plugin
# (now cmd.my_func should be available immediately)

Hope that helps.

Cheers,
 Thomas

On 17 Feb 2016, at 11:32, Sampson, Jared M. 
> wrote:

Hi Tsjerk -

Thanks for the suggestion.  I tried this with:

import time
from pymol import cmd
while not hasattr(cmd, 'my_func'):
time.sleep(0.5)

Unfortunately that also causes everything to hang.  I think I might need to do 
this in a separate thread.  I'll have to look into how to do that.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 2:47 PM, Tsjerk Wassenaar 
> wrote:

Hi Jared,

The extend function must set an attribute "my_func" on cmd. You can test for 
that with hasattr:

while not hasattr(cmd, "my_func"):
   # wait some more

Hope it helps,

Tsjerk

On Feb 16, 2016 20:07, "Sampson, Jared M." 
> wrote:
To my previous message I should add that it works fine if I do:

```
import pmg_tk.startup.my_plugin as mp
mp.my_func()
```

but I'd like to use the `cmd.my_func()` version, so that `my_func` will work in 
a .pml script.

>From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't include 
>"extended" functions, even after the function is loaded.

```
PyMOL>print 'ray' in cmd.kw_list
True
PyMOL>print 'my_func' in cmd.kw_list
False
```

Looking forward to any suggestions.  Thanks!

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 1:50 PM, Sampson, Jared M. 
> wrote:

Hi PyMOLers -

Maybe some more experienced users/developers can help me out here.  I'm trying 
to write some automated test scripts for the plugin I'm writing, but the test 
functions end up running before the plugin is loaded.  Is there a way to tell 
if a plugin has been loaded from within a .pml or .py script?  For example, if 
the plugin makes commands available via `cmd.extend('my_func', my_func)`, how 
can I run `cmd.myfunc()` from a script and not have it execute before the 
plugin finishes loading?

I've tried something like this:

```
import time
from pymol import cmd
loaded = 0
while not loaded:
   try:
   cmd.my_func()  # if it's loaded no exception will be raised
   loaded = 1
   except:
   time.sleep(0.5)
```

But this just hangs, as apparently `time.sleep()` halts the execution of all 
threads, so the plugin won't ever be loaded.

Thanks,
Jared

--
Jared Sampson
Columbia University

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

--
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Re: [PyMOL] How to tell from within a script if a plugin is loaded?

[Thomas Holder]

Hi Jared,

The plugin system isn't really tuned for API extension. As Tsjerk pointed out, 
cmd.extend only registers a command, not a cmd. function. Also, scripts 
which are installed as plugins get loaded asynchronously from the external GUI. 
I suggest you do the following:

1) Inside your plugin (Python module), do:

from pymol import cmd
def my_func(): ...
cmd.my_func = my_func
cmd.extend('my_func', my_func)

2) The plugin's __init_plugin__ (or __init__) function should only be 
responsible for adding Plugin menu entries, not for anything else.

3) Inside your test file, do:

from pymol import cmd
import pmg_tk.startup.my_plugin
# (now cmd.my_func should be available immediately)

Hope that helps.

Cheers,
  Thomas

On 17 Feb 2016, at 11:32, Sampson, Jared M.  wrote:

> Hi Tsjerk - 
> 
> Thanks for the suggestion.  I tried this with:
> 
> import time
> from pymol import cmd
> while not hasattr(cmd, 'my_func'):  
> time.sleep(0.5)
> 
> Unfortunately that also causes everything to hang.  I think I might need to 
> do this in a separate thread.  I'll have to look into how to do that.
> 
> Cheers,
> Jared
> 
> --
> Jared Sampson
> Columbia University
> 
>> On Feb 16, 2016, at 2:47 PM, Tsjerk Wassenaar  wrote:
>> 
>> Hi Jared,
>> 
>> The extend function must set an attribute "my_func" on cmd. You can test for 
>> that with hasattr:
>> 
>> while not hasattr(cmd, "my_func"):
>> # wait some more
>> 
>> Hope it helps,
>> 
>> Tsjerk
>> 
>> On Feb 16, 2016 20:07, "Sampson, Jared M."  wrote:
>> To my previous message I should add that it works fine if I do:
>> 
>> ```
>> import pmg_tk.startup.my_plugin as mp
>> mp.my_func()
>> ```
>> 
>> but I'd like to use the `cmd.my_func()` version, so that `my_func` will work 
>> in a .pml script.
>> 
>> From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't include 
>> "extended" functions, even after the function is loaded.
>> 
>> ```
>> PyMOL>print 'ray' in cmd.kw_list
>> True
>> PyMOL>print 'my_func' in cmd.kw_list
>> False
>> ```
>> 
>> Looking forward to any suggestions.  Thanks!
>> 
>> Cheers,
>> Jared
>> 
>> --
>> Jared Sampson
>> Columbia University
>> 
>>> On Feb 16, 2016, at 1:50 PM, Sampson, Jared M.  
>>> wrote:
>>> 
>>> Hi PyMOLers - 
>>> 
>>> Maybe some more experienced users/developers can help me out here.  I'm 
>>> trying to write some automated test scripts for the plugin I'm writing, but 
>>> the test functions end up running before the plugin is loaded.  Is there a 
>>> way to tell if a plugin has been loaded from within a .pml or .py script?  
>>> For example, if the plugin makes commands available via 
>>> `cmd.extend('my_func', my_func)`, how can I run `cmd.myfunc()` from a 
>>> script and not have it execute before the plugin finishes loading?
>>> 
>>> I've tried something like this:
>>> 
>>> ```
>>> import time
>>> from pymol import cmd
>>> loaded = 0
>>> while not loaded:
>>> try:
>>> cmd.my_func()  # if it's loaded no exception will be raised
>>> loaded = 1
>>> except:
>>> time.sleep(0.5)
>>> ```
>>> 
>>> But this just hangs, as apparently `time.sleep()` halts the execution of 
>>> all threads, so the plugin won't ever be loaded.
>>> 
>>> Thanks,
>>> Jared
>>> 
>>> --
>>> Jared Sampson
>>> Columbia University

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] How to tell from within a script if a plugin is loaded?

[Sampson, Jared M.]

Hi Tsjerk -

Thanks for the suggestion.  I tried this with:

import time
from pymol import cmd
while not hasattr(cmd, 'my_func'):
time.sleep(0.5)

Unfortunately that also causes everything to hang.  I think I might need to do 
this in a separate thread.  I'll have to look into how to do that.

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 2:47 PM, Tsjerk Wassenaar 
> wrote:


Hi Jared,

The extend function must set an attribute "my_func" on cmd. You can test for 
that with hasattr:

while not hasattr(cmd, "my_func"):
# wait some more

Hope it helps,

Tsjerk

On Feb 16, 2016 20:07, "Sampson, Jared M." 
> wrote:
To my previous message I should add that it works fine if I do:

```
import pmg_tk.startup.my_plugin as mp
mp.my_func()
```

but I'd like to use the `cmd.my_func()` version, so that `my_func` will work in 
a .pml script.

>From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't include 
>"extended" functions, even after the function is loaded.

```
PyMOL>print 'ray' in cmd.kw_list
True
PyMOL>print 'my_func' in cmd.kw_list
False
```

Looking forward to any suggestions.  Thanks!

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 1:50 PM, Sampson, Jared M. 
> wrote:

Hi PyMOLers -

Maybe some more experienced users/developers can help me out here.  I'm trying 
to write some automated test scripts for the plugin I'm writing, but the test 
functions end up running before the plugin is loaded.  Is there a way to tell 
if a plugin has been loaded from within a .pml or .py script?  For example, if 
the plugin makes commands available via `cmd.extend('my_func', my_func)`, how 
can I run `cmd.myfunc()` from a script and not have it execute before the 
plugin finishes loading?

I've tried something like this:

```
import time
from pymol import cmd
loaded = 0
while not loaded:
try:
cmd.my_func()  # if it's loaded no exception will be raised
loaded = 1
except:
time.sleep(0.5)
```

But this just hangs, as apparently `time.sleep()` halts the execution of all 
threads, so the plugin won't ever be loaded.

Thanks,
Jared

--
Jared Sampson
Columbia University

--
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Re: [PyMOL] How to tell from within a script if a plugin is loaded?

[Tsjerk Wassenaar]

Hi Jared,

The extend function must set an attribute "my_func" on cmd. You can test
for that with hasattr:

while not hasattr(cmd, "my_func"):
# wait some more

Hope it helps,

Tsjerk
On Feb 16, 2016 20:07, "Sampson, Jared M." 
wrote:

> To my previous message I should add that it works fine if I do:
>
> ```
> import pmg_tk.startup.my_plugin as mp
> mp.my_func()
> ```
>
> but I'd like to use the `cmd.my_func()` version, so that `my_func` will
> work in a .pml script.
>
> From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't
> include "extended" functions, even after the function is loaded.
>
> ```
> PyMOL>print 'ray' in cmd.kw_list
> True
> PyMOL>print 'my_func' in cmd.kw_list
> False
> ```
>
> Looking forward to any suggestions.  Thanks!
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Columbia University
>
> On Feb 16, 2016, at 1:50 PM, Sampson, Jared M. 
> wrote:
>
> Hi PyMOLers -
>
> Maybe some more experienced users/developers can help me out here.  I'm
> trying to write some automated test scripts for the plugin I'm writing, but
> the test functions end up running before the plugin is loaded.  Is there a
> way to tell if a plugin has been loaded from within a .pml or .py script?
> For example, if the plugin makes commands available via
> `cmd.extend('my_func', my_func)`, how can I run `cmd.myfunc()` from a
> script and not have it execute before the plugin finishes loading?
>
> I've tried something like this:
>
> ```
> import time
> from pymol import cmd
> loaded = 0
> while not loaded:
> try:
> cmd.my_func()  # if it's loaded no exception will be raised
> loaded = 1
> except:
> time.sleep(0.5)
> ```
>
> But this just hangs, as apparently `time.sleep()` halts the execution of
> all threads, so the plugin won't ever be loaded.
>
> Thanks,
> Jared
>
> --
> Jared Sampson
> Columbia University
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151=/4140___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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Re: [PyMOL] How to tell from within a script if a plugin is loaded?

[Sampson, Jared M.]

To my previous message I should add that it works fine if I do:

```
import pmg_tk.startup.my_plugin as mp
mp.my_func()
```

but I'd like to use the `cmd.my_func()` version, so that `my_func` will work in 
a .pml script.

>From `help(cmd)` I found `cmd.kw_list`, but this apparently doesn't include 
>"extended" functions, even after the function is loaded.

```
PyMOL>print 'ray' in cmd.kw_list
True
PyMOL>print 'my_func' in cmd.kw_list
False
```

Looking forward to any suggestions.  Thanks!

Cheers,
Jared

--
Jared Sampson
Columbia University

On Feb 16, 2016, at 1:50 PM, Sampson, Jared M. 
> wrote:

Hi PyMOLers -

Maybe some more experienced users/developers can help me out here.  I'm trying 
to write some automated test scripts for the plugin I'm writing, but the test 
functions end up running before the plugin is loaded.  Is there a way to tell 
if a plugin has been loaded from within a .pml or .py script?  For example, if 
the plugin makes commands available via `cmd.extend('my_func', my_func)`, how 
can I run `cmd.myfunc()` from a script and not have it execute before the 
plugin finishes loading?

I've tried something like this:

```
import time
from pymol import cmd
loaded = 0
while not loaded:
try:
cmd.my_func()  # if it's loaded no exception will be raised
loaded = 1
except:
time.sleep(0.5)
```

But this just hangs, as apparently `time.sleep()` halts the execution of all 
threads, so the plugin won't ever be loaded.

Thanks,
Jared

--
Jared Sampson
Columbia University

--
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[PyMOL] How to tell from within a script if a plugin is loaded?

[Sampson, Jared M.]

Hi PyMOLers -

Maybe some more experienced users/developers can help me out here.  I'm trying 
to write some automated test scripts for the plugin I'm writing, but the test 
functions end up running before the plugin is loaded.  Is there a way to tell 
if a plugin has been loaded from within a .pml or .py script?  For example, if 
the plugin makes commands available via `cmd.extend('my_func', my_func)`, how 
can I run `cmd.myfunc()` from a script and not have it execute before the 
plugin finishes loading?

I've tried something like this:

```
import time
from pymol import cmd
loaded = 0
while not loaded:
try:
cmd.my_func()  # if it's loaded no exception will be raised
loaded = 1
except:
time.sleep(0.5)
```

But this just hangs, as apparently `time.sleep()` halts the execution of all 
threads, so the plugin won't ever be loaded.

Thanks,
Jared

--
Jared Sampson
Columbia University

--
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