Namespaces
	basic

	core

	initialization

	logging_support

	numeric

	protocols

	PyMolLink

	utility

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	mpi_init

def	MPIJobDistributor

def	version

def	_Pose_residue_iterator
	Modifications to Rosetta. More...

def	_total_residue

def	_extend_func

def	_add_extend

def	new_vector1_init

def	replace_init

def	Vector1

def	Set

def	generate_nonstandard_residue_set

def	standard_task_factory

def	standard_packer_task

def	add_extra_options

def	pose_from_pdb

def	pose_from_sequence
	Modifications to Rosetta. More...

def	etable_atom_pair_energies

def	output_scorefile

def	defineEnergyMethodCreator

def	get_include

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

dictionary	config = {"low_memory_mode": False, "protocols": True, "core": True, "basic": True, "numeric": True, "utility": True, 'monolith': True}

tuple	config_file_name = os.path.join( os.path.split(__file__)[0], 'config.json' )

string	PyRosettaVersion = 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 src._add_extend ( vectype )

private

def src._extend_func	(	vec,
		othervec
	)

private

def src._Pose_residue_iterator ( obj )

private

Modifications to Rosetta.

Add iter property to Pose.

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

def src._total_residue ( self )

private

def src.add_extra_options ( )

def src.defineEnergyMethodCreator	(	class_,
		scoreType
	)

References BuildBindings.__init__().

def src.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 src.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 src.get_include ( )

Return the directory that contains the Rosetta header files.

Extension modules that need to compile against librosetta should use this
function to locate the appropriate include directory.

Example:
    When using ``distutils``, for example in ``setup.py``.

    import rosetta
    ...
    Extension('extension_name', ...
            include_dirs=[rosetta.get_include()])
    ...

References name, pose_from_sequence(), and basic::options::OptionKeys::relax::range.range.

def src.get_rosetta_database_path ( )

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

References rosetta_database_from_env(), and version().

Referenced by mpi_init().

def src.mpi_init	(	args,
		kargs
	)

References init().

def src.MPIJobDistributor	(	njobs,
		fun
	)

References ObjexxFCL.len(), and basic::options::OptionKeys::relax::range.range.

def src.new_vector1_init	(	self,
		arg1 = `None`,
		arg2 = `False`
	)

def src.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 app.pyrosetta_toolkit.modules.tools.output.dumpPDB(), etable_atom_pair_energies(), src.PyJobDistributor.output_decoy(), and app.pyrosetta_toolkit.modules.protocols.ProtocolBaseClass.ProtocolBaseClass.output_pose().

def src.pose_from_pdb ( filename )

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

Modifications to Rosetta.

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.

Referenced by demo.D030_Fold_tree.fold_tree(), and get_include().

def src.replace_init	(	cls,
		init
	)

def src.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 src.Set ( 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.

def src.standard_packer_task ( pose )

References standard_task_factory().

Referenced by app.surface_docking.movers.FullAtomRelax._setupPackertask(), app.pyrosetta_toolkit.modules.Region.Regions.get_packer_task(), demo.D090_Ala_scan.mutate_residue(), demo.D050_Packer_task.packer_task(), and demo.D070_Refinement.sample_refinement().

def src.standard_task_factory ( )

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

def src.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 app.pyrosetta_toolkit.modules.protocols.DockingProtocols.LowResWrapper.apply(), generate_nonstandard_residue_set(), app.pyrosetta_toolkit.modules.protocols.DockingProtocols.DockingProtocols.high_res_dock(), 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 src.version ( )

Referenced by init().

Variable Documentation

list src._mem_EnergyCreators_ = []

list src._mem_EnergyMethods_ = []

string src._PLATFORM = "linux"

src._python_py_exit_callback = None

src._ROSETTA_DATABASE_PATH_ = None

list src._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={}),
     ]

dictionary src.config = {"low_memory_mode": False, "protocols": True, "core": True, "basic": True, "numeric": True, "utility": True, 'monolith': True}

Referenced by basic::resource_manager::LazyResourceManager.add_resource_configuration(), add_rosetta_options_14(), add_rosetta_options_9(), BinderVisitor.BinderVisitor(), basic::resource_manager::LazyResourceManager.create_resource(), basic::resource_manager::LazyResourceManager.find_resource_configuration(), binder.is_binding_requested(), and binder.is_skipping_requested().

tuple src.config_file_name = os.path.join( os.path.split(__file__)[0], 'config.json' )

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

string src.PyRosettaVersion = version.commit_id+':'

Constants and globals.

dictionary src.ScoreTypesRegistry = {}

Namespaces

Classes

Functions

Variables

Function Documentation

Variable Documentation