API Structure

align_principal_axes(molecular_system[, ...])	Aligning selected atoms to reference principal axes.
center(molecular_system[, selection, ...])	Translate a selection of atoms so that a reference center lies at a target point.
flip(molecular_system[, vector, point, ...])	Reflect (flip) atomic coordinates of a selection through a plane defined by a vector and a point.
get_angles(molecular_system, triplets[, ...])	Calculating bond angles for given atom triplets.
get_center(molecular_system[, selection, ...])	Computing centers (centroids or weighted centers) of atom selections.
get_contacts(molecular_system[, selection, ...])	Compute a boolean contact map between two sets of atoms (or atom-group centers).
get_dihedral_angles(molecular_system[, ...])	Compute dihedral angles for a set of atom quartets over one or more structures.
get_distances(molecular_system[, selection, ...])	Computing distances between atoms or centers of selections.
get_least_rmsd(molecular_system[, ...])	Compute the least-RMSD (optimal superposition RMSD) between structures.
get_maximum_distances(molecular_system[, ...])	Find the maximum pairwise distances between two sets of atoms (or atom-group centers).
get_minimum_distances(molecular_system[, ...])	Find the minimum pairwise distances between two sets of atoms (or atom-group centers).
get_neighbors(molecular_system[, selection, ...])	Find the neighbors of each atom (or group center) within a cutoff or by count.
get_principal_axes(molecular_system[, ...])	Computing principal axes for a selection of atoms.
get_radius_of_gyration(molecular_system[, ...])	Computing the radius of gyration over one or more structures.
get_rmsd(molecular_system[, selection, ...])	Compute the RMSD between structures without prior superposition.
least_rmsd_align(molecular_system[, ...])	Align a molecular system to a reference using sequence alignment followed by least-RMSD fitting.
least_rmsd_fit([molecular_system, ...])	Superpose a molecular system onto a reference using the Kabsch least-RMSD algorithm.
move_away(molecular_system[, selection, ...])	Translate a selection of atoms away from a reference center by a fixed distance.
principal_component_analysis(molecular_system)	Computing covariance eigenvectors and eigenvalues for selected atoms.
rotate(molecular_system[, rotation, ...])	Rotate atomic coordinates of a selection by a given rotation.
set_dihedral_angles(molecular_system[, ...])	Set dihedral angles to specified target values by rotating covalent blocks.
shift_dihedral_angles(molecular_system[, ...])	Shift (increment/decrement) dihedral angles by specified amounts.
show_contacts(molecular_system[, selection, ...])	Visualize the contact map between two sets of atoms as a 2-D heatmap.
translate(molecular_system[, translation, ...])	Apply a translation vector to atomic coordinates of a selection.