pyrosetta Namespace Reference

Namespaces
	logging_support
	teaching
	toolbox

Classes
class	CD
class	EnergyMethod
class	PyJobDistributor
class	PyRosettaException
	Exception handling. More...
class	PythonPyExitCallback

Functions
def	rosetta_database_from_env
def	get_rosetta_database_path
def	init
def	version
def	_Pose_residue_iterator
	Modifications to Rosetta. More...
def	_vector_extend_func
def	Vector1
def	Set
def	generate_nonstandard_residue_set
def	standard_task_factory
def	standard_packer_task
def	pose_from_sequence
def	etable_atom_pair_energies
def	output_scorefile
def	defineEnergyMethodCreator

Variables
tuple	logger = logging.getLogger("rosetta")
	get_score_function = rosetta.core.scoring.get_score_function
	create_score_function = rosetta.core.scoring.ScoreFunctionFactory.create_score_function
tuple	rosetta_version = rosetta.utility.Version.commit_id()
	Constants and globals. More...
string	_PLATFORM = "linux"
	_python_py_exit_callback = None
	_ROSETTA_DATABASE_PATH_ = None
list	_mem_EnergyMethods_ = []
list	_mem_EnergyCreators_ = []
list	_ScoreTypesRegistryByType_
dictionary	ScoreTypesRegistry = {}

Function Documentation

def pyrosetta._Pose_residue_iterator (   obj )

private

Modifications to Rosetta.

Add iter property to Pose.

References basic::options::OptionKeys::relax::range.range.

def pyrosetta._vector_extend_func (   vec,   othervec  )

private

def pyrosetta.defineEnergyMethodCreator	(		class_,
			scoreType
	)

References BuildBindings.__init__().

def 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

References numeric.distance_squared(), and output_scorefile().

def pyrosetta.generate_nonstandard_residue_set

(

params_list

)

Generates a ResidueTypeSet from a list of .params filenames.

.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"]
    type_set = generate_nonstandard_residue_set(params)
    pose = pose_from_file(type_set, "TEM-1_with_substrates.pdb")
See also:
    ResidueTypeSet
    Vector1()
    pose_from_file()

References Vector1().

def pyrosetta.get_rosetta_database_path

(

)

def pyrosetta.init	(		options = '-ex1 -ex2aro',
			extra_options = '',
			set_logging_handler = True,
			notebook = os.getenv('JPY_PARENT_PID')
	)

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 True)

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 rosetta_database_from_env(), and version().

Referenced by pyrosetta.toolbox.load_ligand.add_cid_to_database(), and test.T007_TracerIO.MyPyTracer.output_callback().

def 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

References basic::database.open(), round(), and PyMOL_demo.scorefxn.

Referenced by etable_atom_pair_energies(), and pyrosetta.PyJobDistributor.output_decoy().

def pyrosetta.pose_from_sequence	(		seq,
			res_type = "fa_standard",
			auto_termini = True
	)

Returns a pose generated from a single-letter sequence of amino acid
residues in <seq> using the <res_type> ResidueType and creates N- and C-
termini if <auto_termini> is set to True.

Unlike make_pose_from_sequence(), this method generates a default PDBInfo
and sets all torsion angles to 180 degrees.

Example:
    pose = pose_from_sequence("THANKSEVAN")
See also:
    Pose
    make_pose_from_sequence()
    pose_from_file()
    pose_from_rcsb()

References name, and basic::options::OptionKeys::relax::range.range.

def pyrosetta.rosetta_database_from_env

(

)

Read rosetta database directory from environment or standard install locations.

Returns database path if found, else None.

Referenced by 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.mutate_residue().

def pyrosetta.standard_task_factory

(

)

Referenced by 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().

def pyrosetta.version

(

)

Referenced by init().

Variable Documentation

list pyrosetta._mem_EnergyCreators_ = []

list pyrosetta._mem_EnergyMethods_ = []

string pyrosetta._PLATFORM = "linux"

pyrosetta._python_py_exit_callback = None

pyrosetta._ROSETTA_DATABASE_PATH_ = None

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={}),
]

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

Referenced by app.pyrosetta_toolkit.modules.protocols.DockingProtocols.LowResWrapper.apply(), HDdesignMover.apply(), PeptoidDesignMover.apply(), DougsDockDesignMinimizeMagicMover.apply(), CaToAllAtom.CaToAllAtom(), compute_chem_shift_RMSD(), create_bp_jump_database_test(), create_cs_rosetta_rna_scorefxn(), create_scorefxn(), create_scoring_function(), create_scoring_function_ws_patch(), find_close_motifs(), app.pyrosetta_toolkit.modules.protocols.DockingProtocols.DockingProtocols.high_res_dock(), app.pyrosetta_toolkit.modules.protocols.DockingProtocols.DockingProtocols.low_res_dock(), mp_ddG.main(), predict_ddG.main(), main(), MC_run(), minimize_test(), minimize_with_constraints(), nucleobase_probe_score_test(), demo.D020_Pose_scoring.pose_scoring(), quick_score_test(), rebuild_test(), repack_test(), app.pyrosetta_toolkit.modules.tools.analysis.return_energy(), rna_build_helix_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(), app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl.scoreOption(), zinc1_homodimer_design.setup_scorefunctions(), and stepwise_monte_carlo().

pyrosetta.get_score_function = rosetta.core.scoring.get_score_function

Referenced by HbsDesignMover.apply(), OopDesignMover.apply(), supercharge.apply(), calc_scores(), CoupledMovesProtocol.CoupledMovesProtocol(), densityTools(), supercharge.design_supercharge(), supercharge.design_supercharge_AvNAPSA(), ExposedStrandMover.ExposedStrandMover(), fill_designable_set(), HDdesignMover.HDdesignMover(), HDmakerMover.HDmakerMover(), main(), make_fragments(), MC_run(), mg_modeler_test(), MyScoreMover.MyScoreMover(), nucleobase_probe_score_test(), pep_rmsd_analysis(), supercharge.prepack_input_structure(), PhProtocol.prepack_pose(), quick_score_test(), rebuild_test(), PhProtocol.relax_pose(), rna_build_helix_test(), rna_design_test(), rna_score_test(), ConsensusFragmentMover.run(), run_mc(), run_pep_prep(), RunPepSpec(), sequence_tolerance_main(), MinimizerBenchmark< sft, TScale >.setUp(), NBuriedUnsatsCalcultor.setup(), zinc2_homodimer_setup.setup_filter_clashes(), zinc1_homodimer_design.setup_scorefunctions(), zinc2_homodimer_design.setup_taskfactory_scorefunction_movers(), stepwise_monte_carlo(), PhProtocol.titrate_pH(), UBQ_E2Mover.UBQ_E2Mover(), UBQ_GTPase_disulfide_Mover.UBQ_GTPase_disulfide_Mover(), and UBQ_GTPaseMover.UBQ_GTPaseMover().

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

tuple pyrosetta.rosetta_version = rosetta.utility.Version.commit_id()

Constants and globals.

dictionary pyrosetta.ScoreTypesRegistry = {}