pyrosetta Namespace Reference

Namespaces
	bindings
	io
	logging_support
	mpi
	teaching
	toolbox

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

Functions
def	_rosetta_database_from_env
def	_is_interactive
def	init
def	version
def	_vector_extend_func
def	Vector1
def	Set
def	generate_nonstandard_residue_set
def	standard_task_factory
def	standard_packer_task
def	etable_atom_pair_energies
def	dump_atom_pair_energy_table
def	print_atom_pair_energy_table
def	dump_residue_pair_energies
def	print_residue_pair_energies
def	output_scorefile
def	defineEnergyMethodCreator
def	rrange

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.package()
	Constants and globals. More...
string	_PLATFORM = "linux"
	_python_py_exit_callback = None
list	_mem_EnergyMethods_ = []
list	_mem_EnergyCreators_ = []
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

def pyrosetta.defineEnergyMethodCreator	(		class_,
			scoreType
	)

References DRRAFTER.type.

def pyrosetta.dump_atom_pair_energy_table	(		sfxn,
			score_type,
			residue_1,
			residue_2,
			output_filename
	)

Usage: dump_atom_pair_energy_table(sfxn, score_type, residue_1, residue_2, output_filename)
    Description: dumps a csv formatted table (saved as "output_filename")
    of all pairwise atom pair energies for the complete list of atoms contained 
    by residue_1 and residue_2 using a specified score_type in the provided sfxn.

References etable_atom_pair_energies(), basic::database.open(), fmt.print(), and basic::options::OptionKeys::relax::range.range.

def pyrosetta.dump_residue_pair_energies	(		res,
			pose,
			sfxn,
			score_type,
			output_filename
	)

Usage: dump_residue_pair_energies(res, pose, sfxn, score_type, output_filename)
    Description: dumps a csv formatted table (saved as "output_filename")
    of the interactions of a single residue (res) with all other residues in the
    specified pose using a specified score_type in the provided sfxn.

References ObjexxFCL.abs(), basic::database.open(), and basic::options::OptionKeys::relax::range.range.

def pyrosetta.etable_atom_pair_energies	(		res1,
			atom_index_1,
			res2,
			atom_index_2,
			sfxn
	)

Usage: lj_atr, lj_rep, solv=etable_atom_pair_energies(res1, atom_index_1, res2, atom_index_2, sfxn)
    Description: given a pair of atoms (specified using a pair of residue objects and 
    atom indices) and scorefunction, use the precomputed 'etable' to return 
    LJ attractive, LJ repulsive, and LK solvation energies

References numeric.distance_squared().

Referenced by dump_atom_pair_energy_table(), and print_atom_pair_energy_table().

def 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()

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 version().

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

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 basic::options::OptionKeys::DisulfideInsertion.scorefxn.

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

def pyrosetta.print_atom_pair_energy_table	(		sfxn,
			score_type,
			residue_1,
			residue_2,
			threshold
	)

Usage: print_atom_pair_energy_table(sfxn, score_type, residue_1, residue_2, threshold)
    Description: outputs a formatted table to the commandline of all pairwise atom 
    pair energies for the complete list of atoms contained by residue_1 and residue_2 
    using a specified score_type in the provided sfxn. Only interactions with
    an absolute value energy above the threshold are printed 

References ObjexxFCL.abs(), etable_atom_pair_energies(), fmt.format(), fmt.print(), and basic::options::OptionKeys::relax::range.range.

def pyrosetta.print_residue_pair_energies	(		res,
			pose,
			sfxn,
			score_type,
			threshold
	)

Usage: print_residue_pair_energies(res, pose, sfxn, score_type, threshold)
    Description: outputs a formatted table to the commandline 
    of the interactions of a single residue (res) with all other residues in the
    specified pose using a specified score_type in the provided sfxn. 
    Only interactions with an absolute value energy above the threshold are 
    printed 

References ObjexxFCL.abs(), fmt.format(), output_scorefile(), fmt.print(), and basic::options::OptionKeys::relax::range.range.

def pyrosetta.rrange

(

n

)

Return an iterator from 1 to n inclusive

References basic::options::OptionKeys::relax::range.range, and DRRAFTER.type.

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(), 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.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

(

)

Referenced by init().

Variable Documentation

list pyrosetta._mem_EnergyCreators_ = []

list pyrosetta._mem_EnergyMethods_ = []

string pyrosetta._PLATFORM = "linux"

pyrosetta._python_py_exit_callback = 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 HDdesignMover.apply(), PeptoidDesignMover.apply(), MPDomainAssembly.apply(), DougsDockDesignMinimizeMagicMover.apply(), calc_rmsf_and_avrg(), calculate_sasa(), CaToAllAtom.CaToAllAtom(), compute_chem_shift_RMSD(), create_bp_jump_database_test(), create_cs_rosetta_rna_scorefxn(), create_scorefxn(), BuildFullModel.fill_and_sample_full_model(), 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().

pyrosetta.get_score_function = rosetta.core.scoring.get_score_function

Referenced by HbsDesignMover.apply(), OopDesignMover.apply(), supercharge.apply(), calc_rama_scores(), calc_scores(), calculate_average_residue_scores(), densityTools(), supercharge.design_supercharge(), supercharge.design_supercharge_AvNAPSA(), ExposedStrandMover.ExposedStrandMover(), fill_designable_set(), get_stepwise_score_function(), 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(), DockGlycansProtocol.prepare_scoring_function(), quick_score_test(), rebuild_test(), PhProtocol.relax_pose(), resample_full_model_test(), 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(), setup_score_function(), zinc1_homodimer_design.setup_scorefunctions(), zinc2_homodimer_design.setup_taskfactory_scorefunction_movers(), thermal_sampler(), 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.package()

Constants and globals.

dictionary pyrosetta.ScoreTypesRegistry = {}