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pyrosetta Namespace Reference

Namespaces

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

Classes

class  EnergyMethod
 
class  PyRosettaException
 Exception handling. More...
 
class  PythonPyExitCallback
 

Functions

def _rosetta_database_from_env
 
def _is_interactive
 
def init
 
def _version_string
 
def version
 
def _vector_extend_func
 Vector compatibility: Adding 'extend' to all utility.vector* functions. More...
 
def Vector1
 
def Set
 
def generate_nonstandard_residue_set
 New methods. More...
 
def standard_task_factory
 
def standard_packer_task
 
def defineEnergyMethodCreator
 

Variables

tuple logger = logging.getLogger("pyrosetta.rosetta")
 
 create_score_function = pyrosetta.rosetta.core.scoring.ScoreFunctionFactory.create_score_function
 
list _mem_EnergyMethods_ = []
 Decorator generation for custom PyRosetta energy methods. More...
 
list _mem_EnergyCreators_ = []
 
tuple CD = namedtuple("CD", "base first last methods")
 
list _ScoreTypesRegistryByType_
 
dictionary ScoreTypesRegistry = {}
 

Function Documentation

def pyrosetta._is_interactive ( )
private
Determine if in an interactive context.

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

Referenced by init(), and pyrosetta.distributed.maybe_init().

def pyrosetta._rosetta_database_from_env ( )
private
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.

Referenced by init().

def pyrosetta._vector_extend_func (   vec,
  othervec 
)
private

Vector compatibility: Adding 'extend' to all utility.vector* functions.

def pyrosetta._version_string ( )
private

References fmt.join().

Referenced by version().

def pyrosetta.defineEnergyMethodCreator (   class_,
  scoreType 
)

References DRRAFTER.type.

def pyrosetta.generate_nonstandard_residue_set (   pose,
  params_list 
)

New methods.

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()

References Vector1().

def 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

References _is_interactive(), _rosetta_database_from_env(), pyrosetta.protocols.h5_fragment_store_provider.init_H5FragmentStoreProvider(), fmt.print(), and version().

Referenced by pyrosetta.toolbox.load_ligand.add_cid_to_database(), pyrosetta.distributed.maybe_init(), and pyrosetta.mpi.mpi_init().

def pyrosetta.Set (   list_in)
Creates a std::set object, deducing type from the given list.

References basic::options::OptionKeys::out::path.all, and basic::options::OptionKeys::in::file.t.

def pyrosetta.standard_packer_task (   pose)
def pyrosetta.standard_task_factory ( )
def pyrosetta.Vector1 (   list_in)
def pyrosetta.version ( )

References _version_string(), and binder.split().

Referenced by init().

Variable Documentation

list pyrosetta._mem_EnergyCreators_ = []
list pyrosetta._mem_EnergyMethods_ = []

Decorator generation for custom PyRosetta energy methods.

list pyrosetta._ScoreTypesRegistryByType_
Initial value:
1 = [
2  CD(base=rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy,
3  first=rosetta.core.scoring.PyRosettaTwoBodyContextIndepenedentEnergy_first,
4  last=rosetta.core.scoring.PyRosettaTwoBodyContextIndepenedentEnergy_last,
5  methods={}),
6  CD(base=rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy,
7  first=rosetta.core.scoring.PyRosettaTwoBodyContextDependentEnergy_first,
8  last=rosetta.core.scoring.PyRosettaTwoBodyContextDependentEnergy_last,
9  methods={}),
10  CD(base=None,
11  first=rosetta.core.scoring.PyRosettaEnergy_first,
12  last=rosetta.core.scoring.PyRosettaEnergy_last,
13  methods={}),
14 ]
tuple CD
Definition: __init__.py:303
tuple pyrosetta.CD = namedtuple("CD", "base first last methods")
pyrosetta.create_score_function = pyrosetta.rosetta.core.scoring.ScoreFunctionFactory.create_score_function
tuple pyrosetta.logger = logging.getLogger("pyrosetta.rosetta")
dictionary pyrosetta.ScoreTypesRegistry = {}