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	_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_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 = {}

Detailed Description

(c) Copyright Rosetta Commons Member Institutions.
(c) This file is part of the Rosetta software suite and is made available under
(c) license.
(c) The Rosetta software is developed by the contributing members of the
(c) Rosetta Commons.
(c) For more information, see http://www.rosettacommons.org.
(c) Questions about this can be addressed to University of Washington UW
(c) TechTransfer, email: license@u.washington.edu.

Function Documentation

def src._add_extend ( vectype )

private

Definition at line 435 of file __init__.py.

def src._extend_func	(	vec,
		othervec
	)

private

Definition at line 430 of file __init__.py.

def src._Pose_residue_iterator ( obj )

private

Modifications to Rosetta.

Add iter property to Pose.

Definition at line 400 of file __init__.py.

def src.add_extra_options ( )

Definition at line 543 of file __init__.py.

def src.defineEnergyMethodCreator	(	class_,
		scoreType
	)

Definition at line 735 of file __init__.py.

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

Definition at line 583 of file __init__.py.

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_pdb(type_set, "TEM-1_with_substrates.pdb")
See also:
    ResidueTypeSet
    Vector1()
    pose_from_pdb()

Definition at line 499 of file __init__.py.

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()])
    ...

Definition at line 28 of file __init__.py.

References name, and pose_from_sequence().

def src.get_rosetta_database_path ( )

Definition at line 291 of file __init__.py.

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

Definition at line 294 of file __init__.py.

References rosetta_database_from_env(), and version().

Referenced by mpi_init().

def src.mpi_init	(	args,
		kargs
	)

Definition at line 342 of file __init__.py.

References init().

def src.MPIJobDistributor	(	njobs,
		fun
	)

Definition at line 355 of file __init__.py.

References ObjexxFCL.len().

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

Definition at line 444 of file __init__.py.

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

Definition at line 617 of file __init__.py.

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_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_pdb()
    pose_from_rcsb()

Definition at line 549 of file __init__.py.

References name.

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

def src.replace_init	(	cls,
		init
	)

Definition at line 453 of file __init__.py.

def src.rosetta_database_from_env ( )

Read rosetta database directory from environment or standard install locations.

Returns database path if found, else None.

Definition at line 245 of file __init__.py.

Referenced by init().

def src.Set ( list_in )

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

Definition at line 481 of file __init__.py.

References utility::options::OptionKeys::options.all.

def src.standard_packer_task ( pose )

Definition at line 537 of file __init__.py.

References standard_task_factory().

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

def src.standard_task_factory ( )

Definition at line 529 of file __init__.py.

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.

Definition at line 458 of file __init__.py.

References utility::options::OptionKeys::options.all.

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 ( )

Definition at line 390 of file __init__.py.

Referenced by init().

Variable Documentation

list src._mem_EnergyCreators_ = []

Definition at line 700 of file __init__.py.

list src._mem_EnergyMethods_ = []

Definition at line 699 of file __init__.py.

string src._PLATFORM = "linux"

Definition at line 211 of file __init__.py.

src._python_py_exit_callback = None

Definition at line 223 of file __init__.py.

src._ROSETTA_DATABASE_PATH_ = None

Definition at line 290 of file __init__.py.

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={}),
     ]

Definition at line 717 of file __init__.py.

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

Definition at line 33 of file __init__.py.

Referenced by basic::resource_manager::LazyResourceManager.add_resource_configuration(), basic::resource_manager::LazyResourceManager.create_resource(), basic::resource_manager::LazyResourceManager.find_resource_configuration(), and register_options().

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

Definition at line 35 of file __init__.py.

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

Definition at line 20 of file __init__.py.

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

Constants and globals.

Definition at line 207 of file __init__.py.

dictionary src.ScoreTypesRegistry = {}

Definition at line 732 of file __init__.py.

Namespaces

Classes

Functions

Variables

Detailed Description

Function Documentation

Variable Documentation