Works perfectly, thanks a lot!
On 30.01.2015 21:31, Thomas Holder wrote:
> Hi Christian,
>
> the pymol.session variable is not really part of the API -- means,
> not intended to be modified or accessed by the user. However, it's
> all Python and obviously not hidden, so you can mess around with it,
> if you do it right. Short answer is: Always access it as
> "pymol.session", don't do "from pymol import session". This works:
>
> --- script.py --- import pymol from pymol import cmd
>
> @cmd.extend def print_session_id(): print id(pymol.session)
>
> @cmd.extend def set_foo(value): pymol.session.foo = value
>
> @cmd.extend def print_foo(): print pymol.session.foo --- end
> script.py ---
>
> Cheers, Thomas
>
> On 29 Jan 2015, at 20:20, Christian Becke
> <christian.be...@fu-berlin.de> wrote:
>
>> Dear pymol experts,
>>
>> I found some odd behaviour when trying to use pymol.session in my
>> script. I'm using open source pymol 1.7.4.0 (built from svn) on
>> linux. Here comes a minimal example:
>>
>> 1) Create a directory, containing the following 2 files:
>>
>> --- script.py --- from pymol import cmd, session
>>
>> def print_session_id(): print id(session)
>> cmd.extend("print_session_id", print_session_id)
>>
>> def set_foo(value): session.foo = value cmd.extend("set_foo",
>> set_foo)
>>
>> def print_foo(): print session.foo cmd.extend("print_foo",
>> print_foo) --- end script.py ---
>>
>> --- .pymolrc.py --- import script --- end .pymolrc.py ---
>>
>> 2) Change to this directory and start pymol.
>>
>> 3) In the pymol CLI, do:
>>
>> script_set_foo bar script_print_foo script_session_id python print
>> id(session) print session.foo session.foo = "foo" python end
>> script_print_foo save test.pse
>>
>> This produces the output given below. Note that the id of the
>> session object is the same when printed from the script and from
>> within the pymol session, and how the script reflects changes made
>> to the session.foo variable from the pymol CLI and vice versa.
>>
>> --- pymol log --- PyMOL>script_set_foo bar PyMOL>script_print_foo
>> bar PyMOL>script_session_id 139958033268464 PyMOL>python
>> PyMOL>print id(session) 1:print id(session) PyMOL>print
>> session.foo 2:print session.foo PyMOL>session.foo = "foo"
>> 3:session.foo = "foo" PyMOL>python end PyMOL>python end
>> 139958033268464 bar PyMOL>script_print_foo foo PyMOL>save test.pse
>> Save: Please wait -- writing session file... Save: wrote
>> "test.pse". PyMOL>quit PyMOL: normal program termination. --- end
>> pymol log ---
>>
>> 4) If I now start pymol, load test.pse and run the following
>> commands in the pymol CLI:
>>
>> script_print_foo script_session_id script_set_foo bar python print
>> id(session) print session.foo python end
>>
>> I get the following results:
>>
>> --- pymol log --- Executive: Loading version 1.740 session...
>> PyMOL>script_print_foo Traceback (most recent call last): File
>> "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256, in
>> parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File
>> "script.py", line 12, in script_print_foo print session.foo
>> AttributeError: Session_Storage instance has no attribute 'foo'
>> PyMOL>script_session_id 139950852452080 PyMOL>script_set_foo bar
>> PyMOL>python PyMOL>print id(session) 1:print id(session)
>> PyMOL>print session.foo 2:print session.foo PyMOL>python end
>> PyMOL>python end 139950603504528 foo PyMOL>script_print_foo bar ---
>> end pymol log ---
>>
>> Note that the ids of the session objects differ when printed from
>> the script or from the pymol CLI, and the contents of the variable
>> session.foo differs between pymol CLI and script.
>>
>> If I do not import script.py from .pymolrc.py, everything works as
>> expected.
>>
>> Apparently, loading of a new session file creates a new instance of
>> the pymol.session object. Shouldn't the pymol.session instance be
>> created once upon startup, so it can be shared between all scripts?
>> And only values assigned to this instance upon loading a session
>> from file?
>>
>> Is there a way to import scripts from .pymolrc.py, load a session
>> file *and* get the correct pymol.session object within the script?
>> Or is there an alternative way to get custom data saved in session
>> files that can be used in scripts?
>>
>>
>> Best,
>>
>> Christian
>
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