Pyrolyse, modifying PyRosetta syntax

PyRosetta is a python API of Rosetta, a software intended for protein design.

Pyrolyse NEEDS PyRosetta to work.

This module also contains modified PyRosetta source code and documentation.

Pyrolyse mostly performs monkey-patching of existing classes in order to make PyRosetta feel more pythonic. There are also some dynamic definitions of new class attributes, and some useful new functions are created as well,

For example, in PyRosetta, to get psi of the first residue then set it to zero one would write:

print(pose.psi(1))
pose.set_psi(1, 0.)

While when using pyrolyse over PyRosetta, one could also write:

print(pose.psis[0])
pose.psis[0] = 0.

Which also permits to redefine several psis in a row with slices (although directly modifying torsion angles may not be the first goal when using PyRosetta). Other simple things consist in transforming most methods serving as read-only attributes into, well, read-only attributes, e.g. pose.size() becomes pose.size. This can be useful during autocompletion in notebooks or python interpreter to quickly grasp the usage of each proposition.

As PyRosetta and Rosetta are huge ever-growing softwares, not everything can be patched manually right away so that it gets a "pythonic" vibe. Which is why having an independant module doing it may be a good idea: while not needed to run PyRosetta, it can be imported over it to smoothen its use. If it is not yet patched or too buggy, the unpatched PyRosetta functions can always be used instead.

How to install

Get this repository on your computer using git clone https://github.com/OLaprevote/pyrolyse.git. Go inside, then run pip install -e .. The path of the module will hence be the pyrolyse directory, meaning any changes made there can directly be tested. Note that the environment in which it is installed must contain PyRosetta package, and setuptools to do pip. These are currently the only requirements.

Tests use pytest.

How to run

There are multiple ways to use pyrolyse:

• Keep importing everything from PyRosetta, then import pyrolyse.all to monkey-patch every objects and import new defined functions, like:

import pyrosetta as pyr
import pyrosetta.rosetta as ros
import pyrolyse.all as lys


lys.init() # Same as pyr.init excep set_logging_handler set to True.
pose_lys = lys.get_pose('5WRG')  # Swiss-army function to get pose
print(pose_lys.size, pose_lys.residue(1).natoms) 

# Former PyRosetta functions will also output monkey-patched classes
pose_pyr = pyr.pose_from_pdb('5WRG.pdb')
print(pose_pyr.size)

try:
    pose_error = pyr.pose_from_sequence('A'*12)
except:
    print('Sadly, some functions from PyRosetta crash')

# Although they should have an equivalent in pyrolyse
# For example either:
pose_seq = lys.get_pose('A'*12)
# Or:
pose_seq = lys.pose_from_sequence('A'*12)

• It is also possible to cherry-pick which classes to monkey-patch:

import pyrosetta as pyr
import pyrolyse.pose

pyr.init()

pose = pyr.pose_from_pdb('5WRG.pdb')
print(pose.size)
print(pose.residue(1).natoms())  # Residue class not monkey-patched

• Or to import some useful functions without changing PyRosetta behavior:

from pyrolyse.utils import get_pose

pose = get_pose('LYSE')  # Recognize it as a sequence

More examples are showcased in PyRosetta notebook directory.

Todo

• Include PyRosetta as a dependency in setup.py
• Write a setup.py with more than one line and add a version following semantic versioning.
• Then add a version tag on git. Or go clever parmed way and use the Versioneer.
• Patch Mover base class: hopefully its changes repercut on other movers.
• Probably not, though, but argument lists can then be imported and concatenated for each movers.
• Finish to process movers which were partially but not fully monkey-patched.
• Modify Movemap attributes.
• Enhance logging.
• Make Digest function.
• Stop writing explanatory notebooks and convert the rest of PyRosetta.
• Check if all python functions of PyRosetta work with current changes (most probably not).
• Not important and maybe not a good/simple idea: add torsion angles to residues, like pose.residue(1).psi.