pyrosetta.bindings.pose Namespace Reference

Classes
class	PoseResidueAccessor
class	ResidueLabelAccessor
class	PoseResidueLabelMaskAccessor
class	PoseResidueLabelAccessor
class	PoseScoreAccessor

Functions
def	__pose_getstate__ (pose)
def	residue_pairs (self, primary_residue_selector=TrueResidueSelector(), secondary_residue_selector=TrueResidueSelector(), neighborhood_distance_maximum=None, sequence_distance_minimum=None)
def	__residue_accessor (self)
def	__residue_accessor (self, accessor)
def	__reslabels_accessor (self)
def	__reslabels_accessor (self, accessor)
def	__scores_accessor (self)
def	__scores_accessor (self, accessor)
def	__cache_accessor (self)
def	__cache_accessor (self, accessor)
def	__getitem__ (self, key)
def	__iter__ (self)
def	__len__ (self)
def	pdb_rsd (self, chain_and_resNo)
def	apply_transform (self, xform)
def	translate (self, t)
def	rotate (self, R)
def	get_hbonds (self, calculate_derivative=False, exclude_bb=False, exclude_bsc=False, exclude_scb=False, exclude_sc=False)
def	display_secstruct (self, space=8, page=80)

Function Documentation

__cache_accessor() [1/2]

def pyrosetta.bindings.pose.__cache_accessor (   self )

private

Referenced by pyrosetta.bindings.pose.__cache_accessor().

__cache_accessor() [2/2]

def pyrosetta.bindings.pose.__cache_accessor (   self,   accessor  )

private

References pyrosetta.bindings.pose.__cache_accessor().

__getitem__()

def pyrosetta.bindings.pose.__getitem__	(		self,
			key
	)

Referenced by pyrosetta.bindings.warnings.setPoseExtraScore().

__iter__()

def pyrosetta.bindings.pose.__iter__

(

self

)

__len__()

def pyrosetta.bindings.pose.__len__

(

self

)

References ObjexxFCL.len().

__pose_getstate__()

def pyrosetta.bindings.pose.__pose_getstate__

(

pose

)

References pyrosetta.distributed.utility.pickle.__cereal_getstate__().

__residue_accessor() [1/2]

def pyrosetta.bindings.pose.__residue_accessor (   self )

private

Referenced by pyrosetta.bindings.pose.__residue_accessor().

__residue_accessor() [2/2]

def pyrosetta.bindings.pose.__residue_accessor (   self,   accessor  )

private

References pyrosetta.bindings.pose.__residue_accessor().

__reslabels_accessor() [1/2]

def pyrosetta.bindings.pose.__reslabels_accessor (   self )

private

Referenced by pyrosetta.bindings.pose.__reslabels_accessor().

__reslabels_accessor() [2/2]

def pyrosetta.bindings.pose.__reslabels_accessor (   self,   accessor  )

private

References pyrosetta.bindings.pose.__reslabels_accessor().

__scores_accessor() [1/2]

def pyrosetta.bindings.pose.__scores_accessor (   self )

private

Referenced by pyrosetta.bindings.pose.__scores_accessor().

__scores_accessor() [2/2]

def pyrosetta.bindings.pose.__scores_accessor (   self,   accessor  )

private

References pyrosetta.bindings.pose.__scores_accessor().

apply_transform()

def pyrosetta.bindings.pose.apply_transform	(		self,
			xform
	)

Apply a homogeneous transform to the current pose.

Args:
    xform (np.ndarray): A homogeneous transform.

References pyrosetta.bindings.homogeneous_transform.is_homog_xform().

display_secstruct()

def pyrosetta.bindings.pose.display_secstruct	(		self,
			space = 8,
			page = 80
	)

Use DSSP to assign secondary structure codes to each residue in a Pose,
store the result in the Pose, and display the result.

Args:
    space (int): Spacing of residue number labels in display.
        Defaults to 8.
    page (int): Number of characters per line in dispaly.
        Defaults to 80.

References basic::options::OptionKeys::stepwise.enumerate, join(), ObjexxFCL.len(), ObjexxFCL.ljust(), min(), print(), range, and str().

get_hbonds()

def pyrosetta.bindings.pose.get_hbonds	(		self,
			calculate_derivative = False,
			exclude_bb = False,
			exclude_bsc = False,
			exclude_scb = False,
			exclude_sc = False
	)

Return the HBondSet for all hydrogen bonds in the Pose.

Args:
    caclulate_derivative (bool): Defaults to False.
    exclube_bb (bool): Exclude backbone hydrogen bonds from the returned HBondSet.
        Defaults to False.
    exclube_bsc (bool):  Exclude backbone--side-chain hydrogen bonds from the returned HBondSet.
        Defaults to False.
    exclube_scb (bool):  Exclude side-chain--backbone hydrogen bonds from the returned HBondSet.
        Defaults to False.
    exclube_sc (bool):  Exclude side-chain hydrogen bonds from the returned HBondSet.
        Defaults to False.

Returns:
    pyrosetta.rosetta.core.scoring.hbonds.HBondSet: THe selected hydrogen bonds in the Pose.

pdb_rsd()

def pyrosetta.bindings.pose.pdb_rsd	(		self,
			chain_and_resNo
	)

Look up a specific PDB-numbered residue and return it.

Args:
    chain_and_resNo (tuple): a tuple representing the PDB description of the residue
        in the format (chainID, resNo). For example, residue 1 on chain A would be
        ("A", 1).

Returns:
    pyrosetta.core.conformation.Residue or None: the Residue instance in the Pose.
    returns `None` if the PDB residue identifier is invalid.

residue_pairs()

def pyrosetta.bindings.pose.residue_pairs	(		self,
			primary_residue_selector = TrueResidueSelector(),
			secondary_residue_selector = TrueResidueSelector(),
			neighborhood_distance_maximum = None,
			sequence_distance_minimum = None
	)

Iterate the permutations of residue pairs from two selections which are
within a cartesian and/or outside a sequence distance cutoff.

The method uses the PrimarySequenceNeighborhoodSelector and
NeighborhoodResidueSelector under the hood. Note that all _permutations_ of
residues are yielded, not _combinations_. If you prefer combinations simply
check `if residue_pair[0].sequence_position() > residue_pair[1].sequence_position():`.

primary_residue_selector - ResidueSelector
secondary_residue_selector - ResidueSelector
neighborhood_distance - float
sequence_distance - int

return - iterator(tuple(Residue, Residue))

Referenced by numeric::geometry::hashing::xyzStripeHash.clash_check_residue_pairs().

rotate()

def pyrosetta.bindings.pose.rotate	(		self,
			R
	)

Apply a rotation matrix to all of the coordinates in a Pose.

Args:
    p (Pose): The Pose instance to manipulate
    R (np.mat): A rotation matrix to apply to the Pose coordinates

Referenced by apply_rigid_body_settings(), define_states_test(), Link.move_phi(), Link.move_psi(), Link.set_phi(), Link.set_psi(), binder::Context.sort_binders(), and spinner_test().

translate()

def pyrosetta.bindings.pose.translate	(		self,
			t
	)

Apply a translation to all of the coordinates in a Pose.

Args:
    p (Pose): The Pose instance to manipulate
    t (np.array): A vector to add to the Pose coordinates