Namespaces
	bindings

	distributed

	io

	logging_support

	mpi

	network

	numeric

	protocols

	PyMOLRosettaServer

	teaching

	tests

	toolbox

	utility

Classes
class	PyRosettaException
	Exception handling. More...

class	PythonPyExitCallback

class	EnergyMethod

Functions
def	_rosetta_database_from_env ()

def	_is_interactive ()

def	init (options='-ex1 -ex2aro', extra_options='', set_logging_handler=None, notebook=None, silent=False)

def	_version_string ()

def	version ()

def	_vector_extend_func (vec, othervec)
	Vector compatibility: Adding 'extend' to all utility.vector* functions. More...

def	Vector1 (list_in)

def	Set (list_in)

def	generate_nonstandard_residue_set (pose, params_list)
	New methods. More...

def	standard_task_factory ()

def	standard_packer_task (pose)

def	defineEnergyMethodCreator (class_, scoreType)

Variables
	vector1_string

	list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t

	vector_std_vector_double_std_allocator_double_t

	set_std_string_std_less_std_string_std_allocator_std_string_t

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

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

	extend

list	_mem_EnergyMethods_ = []
	Decorator generation for custom PyRosetta energy methods. More...

list	_mem_EnergyCreators_ = []

	CD = namedtuple("CD", "base first last methods")

list	_ScoreTypesRegistryByType_

dictionary	ScoreTypesRegistry = {}

Function Documentation

◆ _is_interactive()

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().

◆ _rosetta_database_from_env()

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().

◆ _vector_extend_func()

def pyrosetta._vector_extend_func	(	vec,
		othervec
	)

private

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

◆ _version_string()

def pyrosetta._version_string ( )

private

References join().

Referenced by pyrosetta.distributed.cluster.converters._parse_pyrosetta_build(), and version().

◆ defineEnergyMethodCreator()

def pyrosetta.defineEnergyMethodCreator	(	class_,
		scoreType
	)

◆ generate_nonstandard_residue_set()

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().

◆ init()

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(), pyrosetta.protocols.h5_structure_store_provider.init_H5StructureStoreProvider(), print(), and version().

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

◆ Set()

def pyrosetta.Set ( list_in )

Creates a std::set object, deducing type from the given list.

References all, str(), and predPRE.t.

Referenced by operator>>().

◆ standard_packer_task()

def pyrosetta.standard_packer_task ( pose )

References standard_task_factory().

◆ standard_task_factory()

def pyrosetta.standard_task_factory ( )

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

◆ Vector1()

def pyrosetta.Vector1 ( list_in )

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

References all, str(), and predPRE.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().

◆ version()

def pyrosetta.version ( )

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

Referenced by init().

Variable Documentation

◆ _mem_EnergyCreators_

list pyrosetta._mem_EnergyCreators_ = []

private

◆ _mem_EnergyMethods_

list pyrosetta._mem_EnergyMethods_ = []

private

Decorator generation for custom PyRosetta energy methods.

◆ _ScoreTypesRegistryByType_

list pyrosetta._ScoreTypesRegistryByType_

private

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={}),
 ]

◆ CD

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

◆ create_score_function

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

Referenced by zinc_helix_cap.apply(), DougsDockDesignMinimizeMagicMover.apply(), PeptiodMovieMover.apply(), PeptoidRotamerRecoverer.apply(), CartRefineWrapperMover.apply(), CenRelaxMover.apply(), abbinding.apply(), PhDocking.apply(), B3AADihedralGrabber.apply(), LDConverterMover.apply(), SampleTiltProtocol.apply(), FindOptimalHydrophobicThk.apply(), MinCenrotMover.apply(), PeptoidDesignMover.apply(), HDdesignMover.apply(), MotifDock.apply(), MPFindInterfaceTestMover.apply(), MembraneMinMover.apply(), MembraneViewMover.apply(), MembraneDockingxMover.apply(), MembraneRelaxMover.apply(), MembraneSampleMover.apply(), MPInterfaceStatistics.apply(), MPDomainAssembly.apply(), complex_interface_optimize.apply(), run_score_patchdock_hotspot.apply(), run_score_hotspot.apply(), MinPackMin.backbone_minimization(), base_pair_to_base_pair_test(), benzene_pair_score_test(), block_stack_test(), bp_score_calibrate(), build_asn_motifs(), build_full_model_test(), build_next_nucleotide_test(), bzip_test(), calc_B_values(), calc_rmsf_and_avrg(), calculate_sasa(), capri_t033_trim_dock_test(), CaToAllAtom.CaToAllAtom(), cen_fold(), CenRotRBRelaxMover.CenRotRBRelaxMover(), CenRotRelaxMover.CenRotRelaxMover(), centroid_scores_destroys_pose(), check_interface_symmetry(), check_structures(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), compare_dna_energies(), compute_chem_shift_RMSD(), count_contacts(), create_bp_jump_database_test(), create_cs_rosetta_rna_scorefxn(), create_score_function_from_weights_and_refEs(), create_scorefxn(), delta_chi_correction_test(), derive(), design_test(), dinucleotide_test(), dna_dr_loop_test(), dna_specificity_test(), doit(), double_helix_test(), endo_test(), find_close_motifs(), Foldptn.Foldptn(), ga_main(), generate_combined_model(), protocols::abinitio::JumpSpecificAbrelax.generate_scorefxn(), get_rmsd(), get_stepwise_score_function(), graphics_main(), HbondZincBackbone.has_backbone_hbond(), helix_ST(), hessian_estimate(), HubDenovo.HubDenovo(), juke_sam_pos(), juke_sam_test(), lariat_modeling(), mp_ddG.main(), main(), make_sf(), MC_run(), methane_pair_score_test(), minimize_and_score(), minimize_test(), minimize_to_close(), minimize_with_constraints(), my_main(), nucleobase_probe_score_test(), one_chain_MC_sampling(), one_chain_ST_MC(), OPT_KEY(), pack_phosphates(), MinPackMin.pack_sidechains(), pdb_scoring(), pep_rmsd_analysis(), demo.D020_Pose_scoring.pose_scoring(), predict_AE(), process_for_motifs(), process_the_pose(), quick_score_test(), read_silent_input_as_library(), rebuild_centroid_test(), rebuild_test(), relax_cenrot_pose(), HbondZinc.repack(), HbondZincBackbone.repack(), repack_cluster(), repack_step(), repack_test(), resample_full_model_test(), rescore_test(), rna_build_helix_test(), rna_close_chainbreaks_test(), rna_fullatom_minimize_silent_test(), rna_lores_score_silent_test(), rna_lores_score_test(), rna_motif_test(), rna_protein_rb_test(), rna_torsion_check_test(), rotamerize(), rotamerize_rna_test(), run(), run_hh(), run_mc(), myspace::Scheduler.run_md(), run_parallel_docking(), run_pep_prep(), RunPepSpec(), demo.D110_DNA_interface.sample_dna_interface(), demo.D100_Docking.sample_docking(), demo.D120_Ligand_interface.sample_ligand_interface(), sample_rama_test(), demo.D080_Loop_modeling.sample_single_loop_modeling(), sample_state_to_state(), sample_trp_test(), myspace::Scheduler.Scheduler(), score_and_minimize(), score_rnp(), screen_phosphates(), TestQuickRelaxMover.set_defaults(), ZincMinimize.set_scorefunction(), abbinding.setup_RepulsiveRampMover(), setup_score_function(), zinc1_homodimer_design.setup_scorefunctions(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_scorefxns(), abbinding.setup_task_and_repack(), PhDocking.setup_task_and_repack(), soft_pack(), stepwise_lores_test(), stepwise_template_test(), superimpose_A_to_all(), swa_rna_sample(), SymmAbRelaxTest(), SymmDataTest(), SymmSilentFileTest(), test_membrane_scoring_highres(), test_membrane_scoring_lowres(), test_NMmin(), test_NMrelaxer(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_from_reproduce(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibility.test_reproducibility_minimizer_nstruct(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibility.test_reproducibility_packer_nstruct(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_packer_nstruct_multi(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_packer_nstruct_multi_decoy_ids(), pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibility.test_reproducibility_packer_separate(), test_scorefxn_io(), test_talaris(), tf_specificity_test(), thermal_sampler(), two_base_pairs_test(), viewer_main(), zf_test(), and zif268_test().

◆ extend

pyrosetta.extend

◆ list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t

pyrosetta.list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t

◆ logger

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

◆ ScoreTypesRegistry

dictionary pyrosetta.ScoreTypesRegistry = {}

◆ set_std_string_std_less_std_string_std_allocator_std_string_t

pyrosetta.set_std_string_std_less_std_string_std_allocator_std_string_t

◆ vector1_string

pyrosetta.vector1_string

◆ vector_std_vector_double_std_allocator_double_t

pyrosetta.vector_std_vector_double_std_allocator_double_t

Namespaces

Classes

Functions

Variables

Function Documentation

◆ _is_interactive()

◆ _rosetta_database_from_env()

◆ _vector_extend_func()

◆ _version_string()

◆ defineEnergyMethodCreator()

◆ generate_nonstandard_residue_set()

◆ init()

◆ Set()

◆ standard_packer_task()

◆ standard_task_factory()

◆ Vector1()

◆ version()

Variable Documentation

◆ _mem_EnergyCreators_

◆ _mem_EnergyMethods_

◆ _ScoreTypesRegistryByType_

◆ CD

◆ create_score_function

◆ extend

◆ list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t

◆ logger

◆ ScoreTypesRegistry

◆ set_std_string_std_less_std_string_std_allocator_std_string_t

◆ vector1_string

◆ vector_std_vector_double_std_allocator_double_t