pyrosetta Namespace Reference

Namespaces
	bindings
	distributed
	io
	logging_support
	mpi
	numeric
	protocols
	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().

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
	)

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':
        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(), and fmt.print().

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

)

References standard_task_factory().

Referenced by pyrosetta.toolbox.mutants.mutate_residue(), demo.D090_Ala_scan.mutate_residue(), demo.D050_Packer_task.packer_task(), and demo.D070_Refinement.sample_refinement().

def pyrosetta.standard_task_factory

(

)

Referenced by demo.D090_Ala_scan.calc_binding_energy(), and standard_packer_task().

def pyrosetta.Vector1

(

list_in

)

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

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

Referenced by generate_nonstandard_residue_set(), pyrosetta.toolbox.mutants.mutate_residue(), pyrosetta.toolbox.load_ligand.pose_from_params(), demo.D110_DNA_interface.sample_dna_interface(), demo.D100_Docking.sample_docking(), demo.D120_Ligand_interface.sample_ligand_interface(), and demo.D090_Ala_scan.scanning().

def pyrosetta.version

(

)

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

Variable Documentation

list pyrosetta._mem_EnergyCreators_ = []

list pyrosetta._mem_EnergyMethods_ = []

Decorator generation for custom PyRosetta energy methods.

list pyrosetta._ScoreTypesRegistryByType_

Initial value:

= [
    CD(base=rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy,
       first=rosetta.core.scoring.PyRosettaTwoBodyContextIndepenedentEnergy_first,
       last=rosetta.core.scoring.PyRosettaTwoBodyContextIndepenedentEnergy_last,
       methods={}),
    CD(base=rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy,
       first=rosetta.core.scoring.PyRosettaTwoBodyContextDependentEnergy_first,
       last=rosetta.core.scoring.PyRosettaTwoBodyContextDependentEnergy_last,
       methods={}),
    CD(base=None,
       first=rosetta.core.scoring.PyRosettaEnergy_first,
       last=rosetta.core.scoring.PyRosettaEnergy_last,
       methods={}),
]

tuple pyrosetta.CD = namedtuple("CD", "base first last methods")

pyrosetta.create_score_function = pyrosetta.rosetta.core.scoring.ScoreFunctionFactory.create_score_function

Referenced by HDdesignMover.apply(), PeptoidDesignMover.apply(), MPDomainAssembly.apply(), DougsDockDesignMinimizeMagicMover.apply(), build_full_model_test(), calc_rmsf_and_avrg(), calculate_sasa(), CaToAllAtom.CaToAllAtom(), compute_chem_shift_RMSD(), create_bp_jump_database_test(), create_cs_rosetta_rna_scorefxn(), create_scorefxn(), find_close_motifs(), get_stepwise_score_function(), RNA_DeNovoJobQueen.initialize_scorefxn(), mp_ddG.main(), main(), MC_run(), minimize_test(), minimize_with_constraints(), nucleobase_probe_score_test(), demo.D020_Pose_scoring.pose_scoring(), quick_score_test(), read_silent_input_as_library(), rebuild_test(), repack_test(), resample_full_model_test(), rna_build_helix_test(), rna_motif_test(), rna_score_test(), run_pep_prep(), RunPepSpec(), demo.D110_DNA_interface.sample_dna_interface(), demo.D100_Docking.sample_docking(), demo.D120_Ligand_interface.sample_ligand_interface(), demo.D080_Loop_modeling.sample_single_loop_modeling(), setup_score_function(), zinc1_homodimer_design.setup_scorefunctions(), and thermal_sampler().

tuple pyrosetta.logger = logging.getLogger("pyrosetta.rosetta")

dictionary pyrosetta.ScoreTypesRegistry = {}