Yes, one more question.
How to use all other "functions", like byres, "chain A" or "organic"?
Em seg, 5 de ago de 2019 12:36, Christian "Cole" French <
christian.fre...@schrodinger.com> escreveu:
> I see now. I updated the code at the link in my previous email to provide
> behavior which should allow you to do what you want. Here are your examples
> written using the command:
>
> select_with_filter sele, flag 8, lambda s: len(cmd.get_chains(s)) < 2
> select_with_filter sele, flag 8, lambda s: cmd.get_fastastr(s) < 2
> select_with_filter sele, flag 8 and chain A, lambda s: peplength(s) < 15
>
> If you want to write and use your own multi-line function, you can write a
> script and cmd.extend('your_function', your_function), then use
> your_function in select_with_filter.
>
> Please let me know if you have any further questions.
>
> Best,
> Cole
>
> On Mon, Aug 5, 2019 at 8:30 AM Pedro Lacerda <pslace...@gmail.com> wrote:
>
>> I expressed myself wrong, I'm looking something like:
>>
>> select peplength < 15 and chain A
>>
>> Where peplength is an user defined function like:
>>
>> def peplength(atom):
>> return compute_peplength(atom)
>>
>> I'm looking for the availability of user defined functions on selection
>> expressions. How to?
>>
>> Em sex, 2 de ago de 2019 às 15:44, Christian "Cole" French <
>> christian.fre...@schrodinger.com> escreveu:
>>
>>> Edit: remove the cmd. part when running select_with_filter. (Since it's
>>> a custom command, it doesn't belong to the cmd module.)
>>>
>>> On Fri, Aug 2, 2019 at 2:41 PM Christian "Cole" French <
>>> christian.fre...@schrodinger.com> wrote:
>>>
>>>> Hi Pedro Lacerda,
>>>>
>>>> Here is a link to a script I wrote which adds a command which does what
>>>> you ask:
>>>> https://gist.github.com/ColeFrench/6f68fa5f04a67bb6234f10c25debb865.
>>>> To use it, download the file to the directory where you run PyMOL from,
>>>> then open PyMOL and run run select_with_filter.py.
>>>>
>>>> For your examples, the commands would be
>>>> cmd.select_with_filter(predicate=lambda
>>>> s: len(cmd.get_chains(s)) < 2) and cmd.select_with_filter(predicate=lambda
>>>> s: cmd.get_fastastr(s) < 2).
>>>>
>>>> Commands which can be simply run are a convenience which allows you to
>>>> type less (e.g., select chain A instead of cmd.select('chain A')).
>>>> Some commands require different arguments and can only be run the longer
>>>> way, such as the one I wrote which takes a function as an argument.
>>>>
>>>> Hope this helps,
>>>> Cole
>>>>
>>>> On Fri, Aug 2, 2019 at 11:45 AM Pedro Lacerda <pslace...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi PyMOL users,
>>>>>
>>>>> It there any way to enhance the selecion algebra with functions? For
>>>>> instance:
>>>>>
>>>>> select len(get_chains(*)) < 2
>>>>>>
>>>>>
>>>>> Or even:
>>>>>
>>>>> select cmd.get_fastastr(*) < 2
>>>>>>
>>>>>
>>>>>
>>>>> By the way, why some commands we can simply run (like get_chains) and
>>>>> others are different (like cmd.get_fastastr())?
>>>>>
>>>>> --
>>>>> Pedro Sousa Lacerda
>>>>>
>>>>>
>>>>> *Laboratório de Bioinformática e Modelagem Molecular*
>>>>> *Faculdade de Farmácia / UFBA*
>>>>>
>>>>> *@pslacerda*
>>>>>
>>>>> *+55 71 9 9981-1856*
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>
>> --
>> Pedro Sousa Lacerda
>>
>>
>> *Laboratório de Bioinformática e Modelagem Molecular*
>> *Faculdade de Farmácia / UFBA*
>>
>> *@pslacerda*
>>
>> *+55 71 9 9981-1856*
>>
>
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