Hi Cun Zhuang,
I think what you need to do is adding one line in the end of mathexpr.py:
cmd.extend("SelectByExpr",Select)
then you can type in command line
SelectByExpr x>5
see the following page for more explanation:
http://www.pymolwiki.org/index.php/Simple_Scripting
hongbo
On 12/13/2010 11:00 AM, Tsjerk Wassenaar wrote:
> Ni Hao Cun Zhang
>
> The real 'problem' is that Pymol does not allow selection based on
> coordinates. Probably this should be on the wish list (and easy to
> implement). Expressions are allowed, for instance selecting based on
> b-factor or occupancy.
>
> In your script, you can use some shortcuts. Maybe something like:
>
> def cselect(selection="all",expression=lambda (x,y,z): True):
> return [i.id for i in cmd.get_model(selection).atom if
> expression(i.coord)]
>
> The expression can be a predefined function, or a lambda function,
> like here. You could then say:
>
> ids = cselect("n. ca",lambda (x,y,z): x<10 and y>5)
> cmd.show("spheres","id %s"%",".join([str(i) for i in ids]))
>
> Hope it helps :)
>
> Cheers,
>
> Tsjerk
>
>
>
> On Mon, Dec 13, 2010 at 9:44 AM, Cun Zhang<apzc2...@gmail.com> wrote:
>> Hi,all
>>
>> I haven't found any pymol script supports using math expression to select
>> atoms,
>> so I spend several hours to write one function to do it.
>>
>> I write a script(mathexpr.py) containing this function, then run
>> mathexpr.py,
>> function 'Select' now can be called. Can anybody tell me how to combine this
>> function into pymol,
>> or 'select' command, so it can be called like 'select x>5'.
>> Hope it useful for you.
>>
>> Thank you!
>>
>> Yours,
>> Cun Zhang
>>
>>
>> def Select(expr='x>5',sel='all'):
>> """
>> A function which supports selection by math expressions.
>> example:
>> x=Select('x>5 and y<2','name C')
>> """
>> ATOMS=cmd.get_model(sel)
>> vec,index=ATOMS.get_coord_list(),cmd.identify(sel)
>> command='[index[vec.index([x,y,z])] for x,y,z in vec if '+expr+']'
>> ID=eval(command) #list type
>> return ID
>>
>> --
>> ========================================
>> Cun Zhang
>> Ph.D. Candidate
>> LNM,Institute of Mechanics
>> Chinese Academy of Sciences
>> Beijing, 100190, China
>> Tel:86-10-82544204
>> http://www.edwardpku.com/cun
>> ========================================
>>
>> ------------------------------------------------------------------------------
>> Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL,
>> new data types, scalar functions, improved concurrency, built-in packages,
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>
>
>
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