pyrosetta

• io
• logging_support
• method_bindings
• mpi
• teaching
• toolbox
• util

class pyrosetta.CD(**entries)

Bases: object

Class to represent named tuples.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class pyrosetta.EnergyMethod(scoreName=None, scoreType=None, version=1)

Bases: object

Decorator function for custom EnergyMethods in PyRosetta.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

pyrosetta.Set(list_in)

Creates a std::set object, deducing type from the given list.

pyrosetta.Vector1(list_in)

Creates a Vector1 object, deducing type from the given list.

pyrosetta._rosetta_database_from_env()

Read rosetta database directory from environment or standard install locations.

Database resolution proceeds by first searching the current installation for a ‘database’ or ‘rosetta_database’ path. If not found the search then continues to the users’s home dir, cygwin, and osx standard installation locations.

Returns database path if found, else None.

pyrosetta.etable_atom_pair_energies(atom1, atom2, sfxn)

Usage: lj_atr, lj_rep, solv=etable_atom_pair_energies(atom1, atom2, sfxn)

Description: given a pair of atoms and scorefunction, use the precomputed ‘etable’ to return LJ attractive, LJ repulsive, and LK solvation energies

pyrosetta.generate_nonstandard_residue_set(pose, params_list)

Places the ResidueTypes corresponding to a list of .params filenames into a given pose

.params files must be generated beforehand. Typically, one would obtain a molfile (.mdl) generated from the xyz coordinates of a residue, small molecule, or ion. The script molfile_to_params.py can be used to convert to a Rosetta-readable .params file. It can be found in the /test/tools folder of your PyRosetta installation or downloaded from the Rosetta Commons.

Example:

params = [“penicillin.params”, “amoxicillin.params”] pose = Pose() generate_nonstandard_residue_set(pose, params) pose_from_file(pose, “TEM-1_with_substrates.pdb”)

See also:

ResidueTypeSet Vector1() pose_from_file()

pyrosetta.init(options='-ex1 -ex2aro', extra_options='', set_logging_handler=None, notebook=None)

Initialize Rosetta. Includes core data and global options.

options string with default Rosetta command-line options args.

(default: ‘-ex1 -ex2aro’)

kargs -

extra_options - Extra command line options to pass rosetta init.

(default None)

set_logging_handler - Route rosetta tracing through logging logger ‘rosetta’.

(default None)

Examples:

init() # uses default flags init(extra_options=’-pH’) # adds flags to supplement the default init(‘-pH -database /home/me/pyrosetta/rosetta_database’) # overrides default flags - be sure to include the dB last

pyrosetta.output_scorefile(pose, pdb_name, current_name, scorefilepath, scorefxn, nstruct, native_pose=None, additional_decoy_info=None)

Moved from PyJobDistributor (Jared Adolf-Bryfogle) Creates a scorefile if none exists, or appends the current one. Calculates and writes CA_rmsd if native pose is given, as well as any additional decoy info

pyrosetta.rrange(n)

Return an iterator from 1 to n inclusive