src Namespace Reference

Namespaces
	logging_support
	numeric
	protocols
	PyMolLink
	utility
	version

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
def	etable_atom_pair_energies
def	output_scorefile
def	defineEnergyMethodCreator
def	_extendfunc
	Modifications to Rosetta. More...

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	__version__ = 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

Referenced by _extendfunc().

def src._extend_func (   vec,   othervec  )

private

def src._extendfunc (   vec,   othervec  )

private

Modifications to Rosetta.

Add iter property to Pose.

References _add_extend(), basic::options::OptionKeys::out::path.all, numeric.distance_squared(), etable_atom_pair_energies(), generate_nonstandard_residue_set(), name, new_vector1_init(), pose_from_sequence(), replace_init(), Set(), standard_packer_task(), standard_task_factory(), basic::options::OptionKeys::in::file.t, and Vector1().

def src._Pose_residue_iterator (   obj )

private

Modifications to Rosetta.

Add iter property to Pose.

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().

Referenced by _extendfunc().

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()

References Vector1().

Referenced by _extendfunc().

def src.get_rosetta_database_path

(

)

def src.init

(

)

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 src.PythonPyExitCallback.__init__(), and mpi_init().

def src.mpi_init	(		args,
			kargs
	)

References init().

Referenced by src.PythonPyExitCallback.__init__().

def src.MPIJobDistributor	(		njobs,
			fun
	)

References ObjexxFCL.len().

Referenced by src.PythonPyExitCallback.__init__().

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

Referenced by _extendfunc().

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_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_pdb()
    pose_from_rcsb()

References name.

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

def src.replace_init	(		cls,
			init
	)

Referenced by _extendfunc().

def src.rosetta_database_from_env

(

)

Read rosetta database directory from environment or standard install locations.

Returns database path if found, else None.

References basic::options::OptionKeys::els.vars.

Referenced by src.PythonPyExitCallback.__init__(), and 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.

Referenced by _extendfunc().

def src.standard_packer_task

(

pose

)

References standard_task_factory().

Referenced by _extendfunc(), 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

(

)

Referenced by _extendfunc(), 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 _extendfunc(), 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

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

Constants and globals.

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(), basic::resource_manager::LazyResourceManager.create_resource(), and basic::resource_manager::LazyResourceManager.find_resource_configuration().

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

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

dictionary src.ScoreTypesRegistry = {}