pyrosetta.bindings.pose Namespace Reference

Classes
class	PoseResidueAccessor
class	PoseResidueLabelAccessor
class	PoseResidueLabelMaskAccessor
class	PoseScoreAccessor
class	ResidueLabelAccessor

Functions
def	__pose_getstate__
def	residue_pairs
def	__residue_accessor
def	__residue_accessor
def	__reslabels_accessor
def	__reslabels_accessor
def	__scores_accessor
def	__scores_accessor
def	__getitem__
def	__iter__
def	__len__
def	pdb_rsd
def	apply_transform
def	translate
def	rotate
def	get_hbonds
def	display_secstruct

Function Documentation

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

References pyrosetta.bindings.utility.bind_method().

def pyrosetta.bindings.pose.__iter__

(

self

)

References pyrosetta.bindings.utility.bind_method().

def pyrosetta.bindings.pose.__len__

(

self

)

References pyrosetta.bindings.utility.bind_method(), and ObjexxFCL.len().

def pyrosetta.bindings.pose.__pose_getstate__

(

pose

)

References pyrosetta.distributed.utility.pickle.__cereal_getstate__(), pyrosetta.bindings.utility.bind_method(), and pyrosetta.bindings.pose.residue_pairs().

def pyrosetta.bindings.pose.__residue_accessor (   self )

private

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

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

private

References pyrosetta.bindings.pose.__residue_accessor().

def pyrosetta.bindings.pose.__reslabels_accessor (   self )

private

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

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

private

References pyrosetta.bindings.pose.__reslabels_accessor().

def pyrosetta.bindings.pose.__scores_accessor (   self )

private

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

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

private

References pyrosetta.bindings.pose.__scores_accessor(), and pyrosetta.bindings.utility.bind_method().

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.utility.bind_method(), and pyrosetta.bindings.homogeneous_transform.is_homog_xform().

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, fmt.join(), ObjexxFCL.len(), ObjexxFCL.ljust(), min(), fmt.print(), and basic::options::OptionKeys::relax::range.range.

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.

References pyrosetta.bindings.utility.bind_method().

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

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.

References pyrosetta.bindings.utility.bind_method().

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 pyrosetta.bindings.pose.__pose_getstate__().

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

References pyrosetta.bindings.utility.bind_method(), and pyrosetta.bindings.pose.get_hbonds().

Referenced by LigandDockBench.apply(), and binder::Context.sort_binders().

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

References pyrosetta.bindings.utility.bind_method().

Referenced by LigandDockBench.apply(), DougsDockDesignMinimizeMagicMover.apply(), and mp_ddG.print_score_labels_to_file().