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Generating random number using numeric.random

Submitted by resiros on Thu, 2014-10-23 09:25
Category: 
PyRosetta

Hello,

I'm developing a new protocol using PyRosetta. I hoped to use Rosetta's built-in random functions (numeric::random::gaussian for example) but couldn't find them in PyRosetta under numeric (numeric.random does not exist)
Is there a way to access them?
I remember reading that having a good random generator for stochastic highly-parallelized application is quite important. Does it make sense to use Python's built-in random class in case it did not work with Rosetta's?

Thank you!

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Enumerating torsion (dihedral) angles

Submitted by ajasja on Wed, 2014-10-01 09:10
Category: 
PyRosetta

Is it perhaps possible to get a list of all torsion angles in the pose? I’m using the pyrosetta with the CHARMM force filed to do some monte-carlo simulations of spin-label rotamers. This works very well, except that it turns out I need to apply the CMAP correction as well. This correction is basically a 24x24 lookup table for the energy between two dihedral angles.
Parsing and loading the CMAP from the parameter file is (almost) trivial in python. But now I have to map the mm_atom_name(s) to the correct two torsions.
For example I have to map

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Residue.set_chi() does not update internal state?

Submitted by ajasja on Wed, 2014-09-24 09:19
Category: 
PyRosetta

Under Residue.chi() there is a warning

CAUTION: This function does not cause updating to any internal coordinate data. See Residue::set_chi() and Residue::set_all_chi() functions for versions which handle coordinate updates.

But in code it seems that Residue::set_chi() and Residue::set_all_chi()  (at least in pyrosetta) do not update internal data as well. Is this a bug or a feature?

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Displaying side-chain rotamers in PyMol

Submitted by ajasja on Wed, 2014-09-24 08:57
Category: 
PyRosetta

What is the most elegant way to display rotamers in PyMol?

This is a spin-off from this question.
I have a basic implementation working here. I had the most problems since doing r.pose_from_sequence('Z') was not working.
Any suggestions about improving this are welcome.

_______________________

def display_rotamers(pose, rotamers,  pymol_mover):

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Iterating over graph edges in PyRosetta.

Submitted by ajasja on Mon, 2014-09-22 07:21
Category: 
PyRosetta

I would like to get all residues that are close to any chosen residue in my pose. (I need a list of all residues whose side chains could potentially interact with the side chain of my chosen residue.)

I’m guessing the information is available in `pose.energies().tenA_neighbor_graph()`, but I can’t seem to access it in PyRosetta.

calling:

    for l in pose.energies().tenA_neighbor_graph().get_node(1).edge_list_begin():
        pass

returns:

    TypeError: 'EdgeListIterator' object is not iterable

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Forum webpage not working

Submitted by ajasja on Mon, 2014-09-22 06:14
Category: 
PyRosetta

This is probably not the right place to post this, but I did not find any better palce:

I'm having trouble posting a reply to this question (https://www.rosettacommons.org/node/3777). Upon saving a reply the site returns an uninformative error message "Unexpected error". Also a blank reply is saved. I have also tried posting from a different computer, but that did not improve the situation.

The message I'm trying to post is below:

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Getting chi rotamers

Submitted by ajasja on Tue, 2014-08-26 12:11
Category: 
Non-Canonical Peptides
PyRosetta

Hi!

Is there a way to get rotamers in PyRosetta? I googled around and found this old post, but the conclusion seemed to be, that it might be easier to implement the parsing of the rotamer libraries again. Is this still the case?

I tried to explore on my own (see ipython notebook), but the most promising function

pose.residue(6).chi_rotamers(1)

returns

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PyRosetta - General

Can I export command line & result from iPython PyRosetta shell to a text file?

Submitted by lanselibai on Mon, 2014-08-25 04:05
Category: 
PyRosetta

Dear Sir or Madam,
I know we can use cmd.exe to export command line by using

python name.py > name.txt

However, we cannot see anything in the cmd.exe if we do that.

I am thinking can we export result from iPython to a text file? I was trying

run name.py > name.txt

But I think the file of "name.txt" has not been created.

Can you please help me? Thank you very much.

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Large Memory usage in Windows r10 Build

Submitted by ajasja on Fri, 2014-08-22 09:09
Category: 
PyRosetta

Dear all,

When running simple scripts such as these, the memory usage of the python interpreter under windows goes to about 5.5 GB. Im using the r10 version of PyRosetta.Is such high memory usage normal?

Under linux (version '56891:56891:6efc58f8abb54611ace5a6cdd7e69e6c970a01ef') the same script takes about 1 GB.

Does this perhaps have something to do with the monolith (win) vs namespace (linux) release?

Best regards,
Ajasja

 

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