Re: [PyMOL] Common atoms in two selections (and their indices)

[Thomas Holder]

Hi Tsjerk, Spencer, Osvaldo,

cmd.get_raw_alignment() might be what you are looking for.

http://pymolwiki.org/index.php/Get_raw_alignment

Cheers,
  Thomas

On 27 Oct 2015, at 12:49, Spencer Bliven  wrote:

> Tsjerk–
> 
> You might be able to extract the ids of the aligned residues from an 
> alignment object:
> 
> cmd.align(sele1,sele2copy,object="aln")
> [a.id for a in cmd.get_model('aln').atom]
> 
> Since the alignment is sequential, I think this should contain all the 
> aligned atoms from sele1 concatenated with the aligned atoms from sele2. 
> However, as far as I know the internals of the alignment objects aren't 
> documented, so I'm not sure if this can be relied upon.
> 
> -Spencer
> 
> 
> On Tue, Oct 27, 2015 at 12:22 PM, Tsjerk Wassenaar  wrote:
> Hi Osvaldo,
> 
> Probably that's the trick, although I'd need the indices, but that's simple 
> enough.
> The 'equivalence' one is still standing though :)
> 
> Thanks,
> 
> Tsjerk
> 
> On Tue, Oct 27, 2015 at 11:44 AM, Osvaldo Martin  
> wrote:
> So, you want to know the best way to do this?
> 
> Z = [at_x for at_x in X for at_y in Y if at_x.id == at_y.id
> ]
> 
> Or am I still not getting it right?
> 
> Cheers,
> Osvaldo.
> 
> On Tue, Oct 27, 2015 at 10:56 AM, Tsjerk Wassenaar  wrote:
> 
> 
> 
> Hi Osvaldo,
> 
> I could have been more clear I guess. First of all, let's say I have obtained 
> the atom list of a selection:
> 
> X = cmd.get_model(selection1).atom
> 
> I'm doing stuff with that (PCA, to be exact), but now I want to display the 
> result only for a subselection. Probably getting the intersection of the 
> selections and then check which atoms there match with the original selection 
> is an approach. The question there is what the best way is for checking 
> identity of the atoms.
> 
> The second issue is when there is no intersection of the selections, but 
> there may be correspondence, as in alignment.
> 
> Thanks for thinking along,
> 
> Tsjerk
> 
> On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin  
> wrote:
> Hi Tsjerk,
> 
> Do you mean something like this?
> 
> cmd.index("sel_1 and sel_2")
> 
> I do not get the differences between your two cases. Whats the difference 
> between “atoms which are both in selection 1 and 2” and “matching atoms in 
> the two selections”
> 
> Cheers,
> 
> Osvaldo.
> 
> On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar  wrote:
> 
> 
> 
> 
> Hi Thomas e.a.,
> 
> Given two selections, would there be an easy way to 
> 
> 1. find the atoms which are both in selection 1 and 2, and the indices of 
> those in the selections
> 
> and 
> 
> 2. find the matching atoms in the two selections, like align does, and the 
> indices of those in the selections
> 
> Thanks,
> 
> Tsjerk
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Common atoms in two selections (and their indices)

[Tsjerk Wassenaar]

Hi Osvaldo,

I could have been more clear I guess. First of all, let's say I have
obtained the atom list of a selection:

X = cmd.get_model(selection1).atom

I'm doing stuff with that (PCA, to be exact), but now I want to display the
result only for a subselection. Probably getting the intersection of the
selections and then check which atoms there match with the original
selection is an approach. The question there is what the best way is for
checking identity of the atoms.

The second issue is when there is no intersection of the selections, but
there may be correspondence, as in alignment.

Thanks for thinking along,

Tsjerk

On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin 
wrote:

> Hi Tsjerk,
>
> Do you mean something like this?
>
> cmd.index("sel_1 and sel_2")
>
> I do not get the differences between your two cases. Whats the difference
> between “atoms which are both in selection 1 and 2” and “matching atoms in
> the two selections”
>
> Cheers,
>
> Osvaldo.
>
> On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar 
> wrote:
>
>
>> Hi Thomas e.a.,
>>
>> Given two selections, would there be an easy way to
>>
>> 1. find the atoms which are both in selection 1 and 2, and the indices of
>> those in the selections
>>
>> and
>>
>> 2. find the matching atoms in the two selections, like align does, and
>> the indices of those in the selections
>>
>> Thanks,
>>
>> Tsjerk
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>>
>> --
>>
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
> ​
>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [PyMOL] Common atoms in two selections (and their indices)

[Osvaldo Martin]

Hi Tsjerk,

Do you mean something like this?

cmd.index("sel_1 and sel_2")

I do not get the differences between your two cases. Whats the difference
between “atoms which are both in selection 1 and 2” and “matching atoms in
the two selections”

Cheers,

Osvaldo.

On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar 
wrote:


> Hi Thomas e.a.,
>
> Given two selections, would there be an easy way to
>
> 1. find the atoms which are both in selection 1 and 2, and the indices of
> those in the selections
>
> and
>
> 2. find the matching atoms in the two selections, like align does, and the
> indices of those in the selections
>
> Thanks,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
> --
>
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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Re: [PyMOL] Common atoms in two selections (and their indices)

[Osvaldo Martin]

So, you want to know the best way to do this?

Z = [at_x for at_x in X for at_y in Y if at_x.id == at_y.id]

Or am I still not getting it right?

Cheers,
Osvaldo.

On Tue, Oct 27, 2015 at 10:56 AM, Tsjerk Wassenaar 
wrote:

Hi Osvaldo,
>
> I could have been more clear I guess. First of all, let's say I have
> obtained the atom list of a selection:
>
> X = cmd.get_model(selection1).atom
>
> I'm doing stuff with that (PCA, to be exact), but now I want to display
> the result only for a subselection. Probably getting the intersection of
> the selections and then check which atoms there match with the original
> selection is an approach. The question there is what the best way is for
> checking identity of the atoms.
>
> The second issue is when there is no intersection of the selections, but
> there may be correspondence, as in alignment.
>
> Thanks for thinking along,
>
> Tsjerk
>
> On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin 
> wrote:
>
>> Hi Tsjerk,
>>
>> Do you mean something like this?
>>
>> cmd.index("sel_1 and sel_2")
>>
>> I do not get the differences between your two cases. Whats the difference
>> between “atoms which are both in selection 1 and 2” and “matching atoms in
>> the two selections”
>>
>> Cheers,
>>
>> Osvaldo.
>>
>> On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar 
>> wrote:
>>
>>
>>> Hi Thomas e.a.,
>>>
>>> Given two selections, would there be an easy way to
>>>
>>> 1. find the atoms which are both in selection 1 and 2, and the indices
>>> of those in the selections
>>>
>>> and
>>>
>>> 2. find the matching atoms in the two selections, like align does, and
>>> the indices of those in the selections
>>>
>>> Thanks,
>>>
>>> Tsjerk
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>>
>>>
>>> --
>>>
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>> ​
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> ​
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Re: [PyMOL] Common atoms in two selections (and their indices)

[Tsjerk Wassenaar]

Hi Osvaldo,

Probably that's the trick, although I'd need the indices, but that's simple
enough.
The 'equivalence' one is still standing though :)

Thanks,

Tsjerk

On Tue, Oct 27, 2015 at 11:44 AM, Osvaldo Martin 
wrote:

> So, you want to know the best way to do this?
>
> Z = [at_x for at_x in X for at_y in Y if at_x.id == at_y.id]
>
> Or am I still not getting it right?
>
> Cheers,
> Osvaldo.
>
> On Tue, Oct 27, 2015 at 10:56 AM, Tsjerk Wassenaar 
> wrote:
>
> Hi Osvaldo,
>>
>> I could have been more clear I guess. First of all, let's say I have
>> obtained the atom list of a selection:
>>
>> X = cmd.get_model(selection1).atom
>>
>> I'm doing stuff with that (PCA, to be exact), but now I want to display
>> the result only for a subselection. Probably getting the intersection of
>> the selections and then check which atoms there match with the original
>> selection is an approach. The question there is what the best way is for
>> checking identity of the atoms.
>>
>> The second issue is when there is no intersection of the selections, but
>> there may be correspondence, as in alignment.
>>
>> Thanks for thinking along,
>>
>> Tsjerk
>>
>> On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin 
>> wrote:
>>
>>> Hi Tsjerk,
>>>
>>> Do you mean something like this?
>>>
>>> cmd.index("sel_1 and sel_2")
>>>
>>> I do not get the differences between your two cases. Whats the
>>> difference between “atoms which are both in selection 1 and 2” and
>>> “matching atoms in the two selections”
>>>
>>> Cheers,
>>>
>>> Osvaldo.
>>>
>>> On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar 
>>> wrote:
>>>
>>>
 Hi Thomas e.a.,

 Given two selections, would there be an easy way to

 1. find the atoms which are both in selection 1 and 2, and the indices
 of those in the selections

 and

 2. find the matching atoms in the two selections, like align does, and
 the indices of those in the selections

 Thanks,

 Tsjerk

 --
 Tsjerk A. Wassenaar, Ph.D.



 --

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>>> ​
>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> ​
>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [PyMOL] Common atoms in two selections (and their indices)

[Spencer Bliven]

Tsjerk–

You might be able to extract the ids of the aligned residues from an
alignment object:

cmd.align(sele1,sele2copy,object="aln")
[a.id for a in cmd.get_model('aln').atom]

Since the alignment is sequential, I think this should contain all the
aligned atoms from sele1 concatenated with the aligned atoms from sele2.
However, as far as I know the internals of the alignment objects aren't
documented, so I'm not sure if this can be relied upon.

-Spencer


On Tue, Oct 27, 2015 at 12:22 PM, Tsjerk Wassenaar 
wrote:

> Hi Osvaldo,
>
> Probably that's the trick, although I'd need the indices, but that's
> simple enough.
> The 'equivalence' one is still standing though :)
>
> Thanks,
>
> Tsjerk
>
> On Tue, Oct 27, 2015 at 11:44 AM, Osvaldo Martin 
> wrote:
>
>> So, you want to know the best way to do this?
>>
>> Z = [at_x for at_x in X for at_y in Y if at_x.id == at_y.id]
>>
>> Or am I still not getting it right?
>>
>> Cheers,
>> Osvaldo.
>>
>> On Tue, Oct 27, 2015 at 10:56 AM, Tsjerk Wassenaar 
>> wrote:
>>
>> Hi Osvaldo,
>>>
>>> I could have been more clear I guess. First of all, let's say I have
>>> obtained the atom list of a selection:
>>>
>>> X = cmd.get_model(selection1).atom
>>>
>>> I'm doing stuff with that (PCA, to be exact), but now I want to display
>>> the result only for a subselection. Probably getting the intersection of
>>> the selections and then check which atoms there match with the original
>>> selection is an approach. The question there is what the best way is for
>>> checking identity of the atoms.
>>>
>>> The second issue is when there is no intersection of the selections, but
>>> there may be correspondence, as in alignment.
>>>
>>> Thanks for thinking along,
>>>
>>> Tsjerk
>>>
>>> On Tue, Oct 27, 2015 at 10:44 AM, Osvaldo Martin 
>>> wrote:
>>>
 Hi Tsjerk,

 Do you mean something like this?

 cmd.index("sel_1 and sel_2")

 I do not get the differences between your two cases. Whats the
 difference between “atoms which are both in selection 1 and 2” and
 “matching atoms in the two selections”

 Cheers,

 Osvaldo.

 On Mon, Oct 26, 2015 at 10:33 AM, Tsjerk Wassenaar 
 wrote:


> Hi Thomas e.a.,
>
> Given two selections, would there be an easy way to
>
> 1. find the atoms which are both in selection 1 and 2, and the indices
> of those in the selections
>
> and
>
> 2. find the matching atoms in the two selections, like align does, and
> the indices of those in the selections
>
> Thanks,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
> --
>
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
 ​

>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> ​
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
> --
>
> ___
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