extract_coords_pose

pyrosetta.toolbox.extract_coords_pose.pose_coords_as_cols(pack_or_pose, selection=[], atom_names=[])

Construct an ndarray of x, y, and z coordinates from all residues in selection

and atom names in <atom_names> from <pose> as columns and return it.

Args:

pack_or_pose (pyrosetta.rosetta.core.pose.Pose OR pyrosetta.distributed.packed_pose.PackedPose):

the Pose instance from which coordinates will be extracted.

selection (list): a list of residue numbers to use. Defaults to all residues. atom_names (list): a list of atom names to include. Defaults to all atoms.

Returns:

numpy.ndarray: a 3xN array of coordinates.

pyrosetta.toolbox.extract_coords_pose.pose_coords_as_rows(pack_or_pose, selection=[], atom_names=[])

Construct an ndarray of x, y, and z coordinates from all residues in selection

and atom names in <atom_names> from <pose> as rows and return it.

Args:

pack_or_pose (pyrosetta.rosetta.core.pose.Pose OR pyrosetta.distributed.packed_pose.PackedPose):

the Pose instance from which coordinates will be extracted.

selection (list): a list of residue numbers to use. Defaults to all residues. atom_names (list): a list of atom names to include. Defaults to all atoms.

Returns:

numpy.ndarray: an Nx3 array of coordinates.