From cmncri at ibmb.csic.es  Mon Jul 25 11:26:25 2016
From: cmncri at ibmb.csic.es (=?UTF-8?Q?Claudia_Mill=C3=A1n_Nebot?=)
Date: Mon, 25 Jul 2016 12:26:25 +0100
Subject: [Biopython] Problem when adding a residue
Message-ID: <CAPBAO+AnN-ZWVtNJot-EwSTvsF229C+=nXdMzKYWbybWSL1O+g@mail.gmail.com>

Dear all,

I am using Biopython to parse a pdb model extracted from a larger pdb and
if a condition is met, complete it with some residues from the original pdb
model. The residue object that I am trying to add was saved when parsing
the original larger pdb, but when I am trying to add it to the new model I
am getting this error:

  File
"/Library/Python/2.7/site-packages/biopython-1.66-py2.7-macosx-10.11-intel.egg/Bio/PDB/PDBIO.py",
line 187, in save

    fp.write("MODEL      %s\n" % model.serial_num)

AttributeError: 'Residue' object has no attribute 'serial_num'


The pdb model that I am completing might have some changes in the chain
nomenclature, could that be the reason for the error? But apparently is
raised for something related with the model... so I am not sure what is
happening.

This is the relevant piece of code where the error happens:

                        if add==True and checkres!=resi.get_full_id()[-1]:

                              ncheckres=checkres[1]

                              print "Adding ncheckres",ncheckres

                              print
"dictio_template[ncheckres]['residue_object']",dictio_template[ncheckres][
'residue_object']

                              checkresobj=dictio_template[ncheckres][
'residue_object']

                              #print "resi.serial_num",resi.serial_num()

                              #print
"list_res[i+1].serial_num",list_res[i+1].serial_num()

                              #print
"checkresobj.serial_num",checkresobj.serial_num()

                              structure.add(dictio_template[ncheckres][
'residue_object'])

Thanks in advance,


Claudia
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From arklenna at gmail.com  Mon Jul 25 13:08:56 2016
From: arklenna at gmail.com (Lenna Peterson)
Date: Mon, 25 Jul 2016 09:08:56 -0400
Subject: [Biopython] Problem when adding a residue
In-Reply-To: <CAPBAO+AnN-ZWVtNJot-EwSTvsF229C+=nXdMzKYWbybWSL1O+g@mail.gmail.com>
References: <CAPBAO+AnN-ZWVtNJot-EwSTvsF229C+=nXdMzKYWbybWSL1O+g@mail.gmail.com>
Message-ID: <CAHQkFdfBBbL2aPCmQ606Ep13TO44ednBHNAdcnmPrSYqxO1Naw@mail.gmail.com>

Hi Claudia,

Rather than add the residue directly to the structure, you need to add it
to a chain. So you will want to do something like
`structure[0]["A"].add(...)` (depending on the models/chains in your
structure).

The PDB object in Biopython has 5 hierarchical levels:
Structure
Model
Chain
Residue
Atom

The error occurred because the `PDBIO.save` method expects the child of a
`Structure` object to be a `Model` object, which has the attribute
`serial_num`.

Let me know if you still run into any problems.

Cheers,

Lenna

On Mon, Jul 25, 2016 at 7:26 AM, Claudia Mill?n Nebot <cmncri at ibmb.csic.es>
wrote:

> Dear all,
>
> I am using Biopython to parse a pdb model extracted from a larger pdb and
> if a condition is met, complete it with some residues from the original pdb
> model. The residue object that I am trying to add was saved when parsing
> the original larger pdb, but when I am trying to add it to the new model I
> am getting this error:
>
>   File
> "/Library/Python/2.7/site-packages/biopython-1.66-py2.7-macosx-10.11-intel.egg/Bio/PDB/PDBIO.py",
> line 187, in save
>
>     fp.write("MODEL      %s\n" % model.serial_num)
>
> AttributeError: 'Residue' object has no attribute 'serial_num'
>
>
> The pdb model that I am completing might have some changes in the chain
> nomenclature, could that be the reason for the error? But apparently is
> raised for something related with the model... so I am not sure what is
> happening.
>
> This is the relevant piece of code where the error happens:
>
>                         if add==True and checkres!=resi.get_full_id()[-1]:
>
>                               ncheckres=checkres[1]
>
>                               print "Adding ncheckres",ncheckres
>
>                               print
> "dictio_template[ncheckres]['residue_object']",dictio_template[ncheckres][
> 'residue_object']
>
>                               checkresobj=dictio_template[ncheckres][
> 'residue_object']
>
>                               #print "resi.serial_num",resi.serial_num()
>
>                               #print
> "list_res[i+1].serial_num",list_res[i+1].serial_num()
>
>                               #print
> "checkresobj.serial_num",checkresobj.serial_num()
>
>                               structure.add(dictio_template[ncheckres][
> 'residue_object'])
>
> Thanks in advance,
>
>
> Claudia
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
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From cmncri at ibmb.csic.es  Mon Jul 25 14:56:55 2016
From: cmncri at ibmb.csic.es (=?UTF-8?Q?Claudia_Mill=C3=A1n_Nebot?=)
Date: Mon, 25 Jul 2016 15:56:55 +0100
Subject: [Biopython] Problem when adding a residue
In-Reply-To: <CAHQkFdfBBbL2aPCmQ606Ep13TO44ednBHNAdcnmPrSYqxO1Naw@mail.gmail.com>
References: <CAPBAO+AnN-ZWVtNJot-EwSTvsF229C+=nXdMzKYWbybWSL1O+g@mail.gmail.com>
 <CAHQkFdfBBbL2aPCmQ606Ep13TO44ednBHNAdcnmPrSYqxO1Naw@mail.gmail.com>
Message-ID: <CAPBAO+AGeXxeBpYnOL2TQX8QQOWCqn=Ts9j4KgysXWigOG4R2g@mail.gmail.com>

Hi Lenna,

thanks for the quick answer. It makes perfect sense and now is working.

Best,

Claudia

2016-07-25 14:08 GMT+01:00 Lenna Peterson <arklenna at gmail.com>:

> Hi Claudia,
>
> Rather than add the residue directly to the structure, you need to add it
> to a chain. So you will want to do something like
> `structure[0]["A"].add(...)` (depending on the models/chains in your
> structure).
>
> The PDB object in Biopython has 5 hierarchical levels:
> Structure
> Model
> Chain
> Residue
> Atom
>
> The error occurred because the `PDBIO.save` method expects the child of a
> `Structure` object to be a `Model` object, which has the attribute
> `serial_num`.
>
> Let me know if you still run into any problems.
>
> Cheers,
>
> Lenna
>
> On Mon, Jul 25, 2016 at 7:26 AM, Claudia Mill?n Nebot <cmncri at ibmb.csic.es
> > wrote:
>
>> Dear all,
>>
>> I am using Biopython to parse a pdb model extracted from a larger pdb and
>> if a condition is met, complete it with some residues from the original pdb
>> model. The residue object that I am trying to add was saved when parsing
>> the original larger pdb, but when I am trying to add it to the new model I
>> am getting this error:
>>
>>   File
>> "/Library/Python/2.7/site-packages/biopython-1.66-py2.7-macosx-10.11-intel.egg/Bio/PDB/PDBIO.py",
>> line 187, in save
>>
>>     fp.write("MODEL      %s\n" % model.serial_num)
>>
>> AttributeError: 'Residue' object has no attribute 'serial_num'
>>
>>
>> The pdb model that I am completing might have some changes in the chain
>> nomenclature, could that be the reason for the error? But apparently is
>> raised for something related with the model... so I am not sure what is
>> happening.
>>
>> This is the relevant piece of code where the error happens:
>>
>>                         if add==True and checkres!=resi.get_full_id()[-1
>> ]:
>>
>>                               ncheckres=checkres[1]
>>
>>                               print "Adding ncheckres",ncheckres
>>
>>                               print
>> "dictio_template[ncheckres]['residue_object']"
>> ,dictio_template[ncheckres]['residue_object']
>>
>>                               checkresobj=dictio_template[ncheckres][
>> 'residue_object']
>>
>>                               #print "resi.serial_num",resi.serial_num()
>>
>>                               #print
>> "list_res[i+1].serial_num",list_res[i+1].serial_num()
>>
>>                               #print
>> "checkresobj.serial_num",checkresobj.serial_num()
>>
>>                               structure.add(dictio_template[ncheckres][
>> 'residue_object'])
>>
>> Thanks in advance,
>>
>>
>> Claudia
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
>
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From tra at popgen.net  Thu Jul 28 21:39:17 2016
From: tra at popgen.net (Tiago Antao)
Date: Thu, 28 Jul 2016 15:39:17 -0600
Subject: [Biopython] Deprecating simcoal and fdisk content in PopGen
Message-ID: <3d1da74384f6ab554eced103c36cf226@webmail.webfaction.com>

Dear all,

I would like to deprecate a big part of PopGen, that is:
- All the simcoal stuff
- All the fdist stuff.

Simcoal comes from the lack of source code and a free license.
fdist from a lack of license.

In simcoal case, I do not think we should support black box code (unless 
it is something very very popular which is definitely not the case).

For the fdist case I suspect that 99%+ of the users are via my own 
applications, and I will take care of that myself. We would benefit my 
reducing Biopython's complexity a little bit.

For simcoal, I understand that there might be a few (handful at most?) 
users, but I think the trade-off is well worth it.

Any opinions?

Regards,
Tiago