pyrosetta

• PyMOLRosettaServer
• bindings
• distributed
• io
• logging_support
• mpi
• network
• numeric
• protocols
• teaching
• tests
• toolbox
• utility

class pyrosetta.CD(base, first, last, methods)

Bases: tuple

_asdict()

Return a new OrderedDict which maps field names to their values.

_fields = ('base', 'first', 'last', 'methods')

classmethod _make(iterable, new=<built-in method __new__ of type object at 0x891d20>, len=<built-in function len>)

Make a new CD object from a sequence or iterable

_replace(**kwds)

Return a new CD object replacing specified fields with new values

_source = "from builtins import property as _property, tuple as _tuple\nfrom operator import itemgetter as _itemgetter\nfrom collections import OrderedDict\n\nclass CD(tuple):\n    'CD(base, first, last, methods)'\n\n    __slots__ = ()\n\n    _fields = ('base', 'first', 'last', 'methods')\n\n    def __new__(_cls, base, first, last, methods):\n        'Create new instance of CD(base, first, last, methods)'\n        return _tuple.__new__(_cls, (base, first, last, methods))\n\n    @classmethod\n    def _make(cls, iterable, new=tuple.__new__, len=len):\n        'Make a new CD object from a sequence or iterable'\n        result = new(cls, iterable)\n        if len(result) != 4:\n            raise TypeError('Expected 4 arguments, got %d' % len(result))\n        return result\n\n    def _replace(_self, **kwds):\n        'Return a new CD object replacing specified fields with new values'\n        result = _self._make(map(kwds.pop, ('base', 'first', 'last', 'methods'), _self))\n        if kwds:\n            raise ValueError('Got unexpected field names: %r' % list(kwds))\n        return result\n\n    def __repr__(self):\n        'Return a nicely formatted representation string'\n        return self.__class__.__name__ + '(base=%r, first=%r, last=%r, methods=%r)' % self\n\n    def _asdict(self):\n        'Return a new OrderedDict which maps field names to their values.'\n        return OrderedDict(zip(self._fields, self))\n\n    def __getnewargs__(self):\n        'Return self as a plain tuple.  Used by copy and pickle.'\n        return tuple(self)\n\n    base = _property(_itemgetter(0), doc='Alias for field number 0')\n\n    first = _property(_itemgetter(1), doc='Alias for field number 1')\n\n    last = _property(_itemgetter(2), doc='Alias for field number 2')\n\n    methods = _property(_itemgetter(3), doc='Alias for field number 3')\n\n"

property base

Alias for field number 0

count(value) → integer -- return number of occurrences of value

property first

Alias for field number 1

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

property last

Alias for field number 2

property methods

Alias for field number 3

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

Bases: object

Decorator function for custom EnergyMethods in PyRosetta.

exception pyrosetta.PyRosettaException

Bases: Exception

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class pyrosetta.PythonPyExitCallback

Bases: pyrosetta.rosetta.utility.py.PyExitCallback

assign(self: pyrosetta.rosetta.utility.py.PyExitCallback, : pyrosetta.rosetta.utility.py.PyExitCallback) → pyrosetta.rosetta.utility.py.PyExitCallback

C++: utility::py::PyExitCallback::operator=(const class utility::py::PyExitCallback &) –> class utility::py::PyExitCallback &

exit_callback(self: pyrosetta.rosetta.utility.py.PyExitCallback) → None

C++: utility::py::PyExitCallback::exit_callback() –> void

static get_static_int() → int

C++: utility::py::PyExitCallback::get_static_int() –> int

static get_static_string() → str

C++: utility::py::PyExitCallback::get_static_string() –> std::string

static get_static_string_const() → str

C++: utility::py::PyExitCallback::get_static_string_const() –> const std::string

static set_PyExitCallBack(exit_callback_object: pyrosetta.rosetta.utility.py.PyExitCallback) → None

C++: utility::py::PyExitCallback::set_PyExitCallBack(class std::shared_ptr<class utility::py::PyExitCallback>) –> void

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._is_interactive()

Determine if in an interactive context.

See: https://stackoverflow.com/questions/2356399/tell-if-python-is-in-interactive-mode

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._vector_extend_func(vec, othervec)

pyrosetta._version_string()

pyrosetta.defineEnergyMethodCreator(class_, scoreType)

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, silent=False)

Initialize Rosetta. Includes core data and global options.

options string with default Rosetta command-line options args.

(default: ‘-ex1 -ex2aro’)

kwargs -

extra_options - Extra command line options to pass rosetta init.

(default None)

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

None - Set handler if interactive, otherwise not. False - Write logs via c++-level filehandles. “interactive” - Register python log handling and make visible if not. “logging” - Register python log handling, do not update logging config. True - Register python log handling, make visible if logging isn’t configured.

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.standard_packer_task(pose)

pyrosetta.standard_task_factory()

pyrosetta.version()