Re: [PyMOL] Selection algebra
Thank you, it was really what I asked!
Em seg, 5 de ago de 2019 15:50, Christian "Cole" French <
christian.fre...@schrodinger.com> escreveu:
> select_with_filter allows you to make a selection as you would with the
> select command, so it supports all selection algebra including byres,
> chain, organic, etc. Here's a modified example from the wiki:
>
> # Select all residues within 5 Ang. of any organic small molecules whose
> x-coordinate is at least 50
> select_with_filter sele, br. all within 5 of (organic and flag 8), lambda
> s: cmd.get_extent(s)[0][0] >= 50
>
> Best,
> Cole
>
> On Mon, Aug 5, 2019 at 1:06 PM Pedro Lacerda wrote:
>
>> 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
>>> 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
>> 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*
>>> ___
>> 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
>
>
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Re: [PyMOL] Selection algebra
select_with_filter allows you to make a selection as you would with the
select command, so it supports all selection algebra including byres,
chain, organic, etc. Here's a modified example from the wiki:
# Select all residues within 5 Ang. of any organic small molecules whose
x-coordinate is at least 50
select_with_filter sele, br. all within 5 of (organic and flag 8), lambda
s: cmd.get_extent(s)[0][0] >= 50
Best,
Cole
On Mon, Aug 5, 2019 at 1:06 PM Pedro Lacerda wrote:
> 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 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
> 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*
>>>
>> ___
> 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
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Re: [PyMOL] Selection algebra
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 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
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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Re: [PyMOL] Selection algebra
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 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
>>> 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*
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>>>
>>>
>
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>
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Re: [PyMOL] Selection algebra
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
>> 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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