Re: [PyMOL] Selection algebra

[Pedro Lacerda]

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

[Christian "Cole" French]

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*
>>>
>> ___
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> 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

[Pedro Lacerda]

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

[Christian "Cole" French]

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

[Pedro Lacerda]

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

[Christian "Cole" French]

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
>
>
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Re: [PyMOL] Selection algebra

[Christian "Cole" French]

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
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Re: [PyMOL] Grammar for PyMOL selection algebra

[Thomas Holder]

Hi Lukas,

All operators:
https://sourceforge.net/p/pymol/code/4159/tree/trunk/pymol/layer3/Selector.cpp#l455

Operator types (e.g. number of arguments) and priority (order of operation):
https://sourceforge.net/p/pymol/code/4159/tree/trunk/pymol/layer3/Selector.cpp#l365

Hope that helps.

Cheers,
  Thomas

On 19 Jul 2016, at 05:52, Lukáš Pravda  wrote:

> Dear PyMOL users,
>  
> I am trying to add support for pymol-like selection algebra into one of your 
> software tools. Therefore, I was wondering, if there is any formal 
> description of the language available in for example as context-free grammar. 
> I was trying to find something in the source code rather unsuccessfully.
>  
> All the best
>  
> Lukas Pravda
>  
> CEITEC | Central European Institute of Technology
> http://webchem.ncbr.muni.cz/

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Grammar for PyMOL selection algebra

[Lukáš Pravda]

Dear PyMOL users, 

 

I am trying to add support for pymol-like selection algebra into one of your
software tools. Therefore, I was wondering, if there is any formal
description of the language available in for example as context-free
grammar. I was trying to find something in the source code rather
unsuccessfully.

 

All the best

 

Lukas Pravda

 

CEITEC | Central European Institute of Technology

http://webchem.ncbr.muni.cz/

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[PyMOL] Selection algebra issue

[Katherine Sippel]

Hi all,

I'm trying to write a script to data mine the pdb. I'm want to look at the
ligands in a pdb file and fish out those that meet a certain criteria. I've
got a script that can look at the ligands all at once but I need to assess
each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
define them individually. I've tried variations on %s' % (resi) and
bymolec but I can't seem to figure out how to get them parsed separately
without specifying a number. I've also tried using index to create a tuples
list and iterating from that but I keep hitting the same issue. I've
attached a couple of the attempted scripts so you can laugh at my google
derived python skills.

I've been trying to figure this out for a week now and I'm completely
stumped. If anyone could nudge me in the right direction, even if it's some
Pymolwiki article I missed, I would appreciate it immensely.

Thanks for your time,
Katherine

-- 
Nil illegitimo carborundum* - *Didactylos
from pymol import cmd
from glob import glob

for file in glob(*.pdb):
cmd.load(file,'prot')
#some selection criteria. I've tried 'het and (not solvent) and %s' % (resi)
while cmd.count_atoms(solvent within 3.5 of sele) != 0
if cmd.count_atoms(solvent within 3.5 of het) == 0:
print file
break
cmd.delete(prot)


from pymol import cmd
from glob import glob

for file in glob(*.pdb):
cmd.load(file,'prot')
for a in cmd.index('het and (not solvent) and %s' % (resi)):
solvent.name = []
cmd.iterate('%a', count_atoms('solvent within 3.5 of %a'))
if cmd.count_atoms(solvent within 3.5 of %a) == 0:
print file
cmd.delete(prot)


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Re: [PyMOL] Selection algebra issue

[Schubert, Carsten [JRDUS]]

Katherine,

not sure if that is what you are looking for but you can select for non-polymer 
residues with:

select lig, prot and organic

That will select any non polymer (protein and R(D)NA) residues present in the 
pdb. You then would need to break the selection further into the individual 
constituents, by either chain Id and resid.

Hope this helps a bit.

Carsten

From: Katherine Sippel [mailto:katherine.sip...@gmail.com]
Sent: Friday, December 13, 2013 10:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selection algebra issue

Hi all,
I'm trying to write a script to data mine the pdb. I'm want to look at the 
ligands in a pdb file and fish out those that meet a certain criteria. I've got 
a script that can look at the ligands all at once but I need to assess each 
ligand individually. Since I'm looking at 40,000+ pdbs I need a way to define 
them individually. I've tried variations on %s' % (resi) and bymolec but I 
can't seem to figure out how to get them parsed separately without specifying a 
number. I've also tried using index to create a tuples list and iterating from 
that but I keep hitting the same issue. I've attached a couple of the attempted 
scripts so you can laugh at my google derived python skills.
I've been trying to figure this out for a week now and I'm completely stumped. 
If anyone could nudge me in the right direction, even if it's some Pymolwiki 
article I missed, I would appreciate it immensely.
Thanks for your time,
Katherine

--
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Re: [PyMOL] Selection algebra issue

[Katherine Sippel]

Hi Carsten,

Thanks for the help. I've tried variants of that selection and it works
great if there is only one ligand. Unfortunately it breaks down when there
are multiple ligands and they don't all fit the criteria. I'm surveying
almost half the PDB so these are all different proteins with different
binding sites and ligands. I was hoping for a way to get pymol to recognize
each individual ligand automatically by grouping common resids within the
non-solvent hetatm selection. Using the %s %(resi) seems to require an
explicit input.

I might be able to extract an explicit chain/resi designation for each file
from the het portion of the pdb header, though I'm not sure how to automate
this. I suppose it's back to the script repository for me.

Cheers,
Katherine


On Fri, Dec 13, 2013 at 2:50 PM, Schubert, Carsten [JRDUS] 
cschu...@its.jnj.com wrote:

  Katherine,



 not sure if that is what you are looking for but you can select for
 non-polymer residues with:



 select lig, prot and organic



 That will select any non polymer (protein and R(D)NA) residues present in
 the pdb. You then would need to break the selection further into the
 individual constituents, by either chain Id and resid.



 Hope this helps a bit.



 Carsten



 *From:* Katherine Sippel [mailto:katherine.sip...@gmail.com]
 *Sent:* Friday, December 13, 2013 10:28 AM
 *To:* pymol-users@lists.sourceforge.net
 *Subject:* [PyMOL] Selection algebra issue



 Hi all,

 I'm trying to write a script to data mine the pdb. I'm want to look at the
 ligands in a pdb file and fish out those that meet a certain criteria. I've
 got a script that can look at the ligands all at once but I need to assess
 each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
 define them individually. I've tried variations on %s' % (resi) and
 bymolec but I can't seem to figure out how to get them parsed separately
 without specifying a number. I've also tried using index to create a tuples
 list and iterating from that but I keep hitting the same issue. I've
 attached a couple of the attempted scripts so you can laugh at my google
 derived python skills.

 I've been trying to figure this out for a week now and I'm completely
 stumped. If anyone could nudge me in the right direction, even if it's some
 Pymolwiki article I missed, I would appreciate it immensely.

 Thanks for your time,
 Katherine


 --

 Nil illegitimo carborundum* - *Didactylos




-- 
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Re: [PyMOL] Selection algebra issue

[Jason Vertrees]

Hi Katherine,

PyMOL can do what you want. I've done this exact task before.

Here's the idea. If you have a PDB with multiple ligands and you use,

  select allLigands, organic and myProtein

you create the selection allLigands which contains all the ligand
atoms in myProtein. What you need to do is extract each ligand,
molecule by molecule, from the allLigands selection using selection
algebra until myLigands is empty. It's done like this:

# create a selection containing the atoms of all ligands

select allLigands, organic and myProtein

# create a selection to use later as we iterate across
# all ligands, this will hold individual ligands we extract
# from allLigands

select current_ligand, none

# enter a Python block so we can use Python while-loop
# and other Python syntax

python

# loop until allLigands is not empty

while cmd.count_atoms(myLigands)  0:

  # copy the first ligand selection, by molecule, into
  # the, current_ligand

  cmd.select(current_ligand, bm. first allLigands)

  # do something with current_ligand, like finding all ligands
  # without waters nearby

  if cmd.count_atoms(solvent within 5 of current_ligand) == 0:

print This is an interesting ligand.

  # now remove current_ligand from allLigands
  # and loop again

  cmd.select(allLigands, allLigands and not current_ligand)

python end

Good luck!

Cheers,

-- Jason


On Fri, Dec 13, 2013 at 4:58 PM, Katherine Sippel
katherine.sip...@gmail.com wrote:
 Hi Carsten,

 Thanks for the help. I've tried variants of that selection and it works
 great if there is only one ligand. Unfortunately it breaks down when there
 are multiple ligands and they don't all fit the criteria. I'm surveying
 almost half the PDB so these are all different proteins with different
 binding sites and ligands. I was hoping for a way to get pymol to recognize
 each individual ligand automatically by grouping common resids within the
 non-solvent hetatm selection. Using the %s %(resi) seems to require an
 explicit input.

 I might be able to extract an explicit chain/resi designation for each file
 from the het portion of the pdb header, though I'm not sure how to automate
 this. I suppose it's back to the script repository for me.

 Cheers,
 Katherine


 On Fri, Dec 13, 2013 at 2:50 PM, Schubert, Carsten [JRDUS]
 cschu...@its.jnj.com wrote:

 Katherine,



 not sure if that is what you are looking for but you can select for
 non-polymer residues with:



 select lig, prot and organic



 That will select any non polymer (protein and R(D)NA) residues present in
 the pdb. You then would need to break the selection further into the
 individual constituents, by either chain Id and resid.



 Hope this helps a bit.



 Carsten



 From: Katherine Sippel [mailto:katherine.sip...@gmail.com]
 Sent: Friday, December 13, 2013 10:28 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Selection algebra issue



 Hi all,

 I'm trying to write a script to data mine the pdb. I'm want to look at the
 ligands in a pdb file and fish out those that meet a certain criteria. I've
 got a script that can look at the ligands all at once but I need to assess
 each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
 define them individually. I've tried variations on %s' % (resi) and
 bymolec but I can't seem to figure out how to get them parsed separately
 without specifying a number. I've also tried using index to create a tuples
 list and iterating from that but I keep hitting the same issue. I've
 attached a couple of the attempted scripts so you can laugh at my google
 derived python skills.

 I've been trying to figure this out for a week now and I'm completely
 stumped. If anyone could nudge me in the right direction, even if it's some
 Pymolwiki article I missed, I would appreciate it immensely.

 Thanks for your time,
 Katherine


 --

 Nil illegitimo carborundum - Didactylos




 --
 Nil illegitimo carborundum - Didactylos

 --
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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