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Classes | Functions
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 
)
def pyrosetta.bindings.pose.__iter__ (   self)
def pyrosetta.bindings.pose.__len__ (   self)
def pyrosetta.bindings.pose.__pose_getstate__ (   pose)
def pyrosetta.bindings.pose.__residue_accessor (   self)
private
def pyrosetta.bindings.pose.__residue_accessor (   self,
  accessor 
)
private
def pyrosetta.bindings.pose.__reslabels_accessor (   self)
private
def pyrosetta.bindings.pose.__reslabels_accessor (   self,
  accessor 
)
private
def pyrosetta.bindings.pose.__scores_accessor (   self)
private
def pyrosetta.bindings.pose.__scores_accessor (   self,
  accessor 
)
private
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().