pyrosetta¶
- 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:
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()¶