Structure

Align principal axes	Aligning the principal inertia or geometric axes of a molecular system over a reference coordinates axes
Center	Centering a molecular system
Flip	Flipping a molecular system over a plane
Get angles	Getting the angles between specific triplets of atoms of a molecular system
Get center	Getting the center of a molecular system
Get contacts	Getting the contact matrix of specific elements of a molecular system or two different molecular systems
Get dihedral angles	Getting the dihedral angles of a molecular system
Get distances	Getting the distance between specific elements of a molecular system or two different molecular systems
Get least RMSD	Getting the least RMSD of a molecular system from a reference molecular system
Get maximum distances	Getting the maximum distance between specific groups of elements of a molecular system or two different molecular systems
Get minimum distances	Getting the minimum distance between specific groups of elements of a molecular system or two different molecular systems
Get neighbors	Getting the list of neighboring elements or groups of elements of a molecular system from specific elements or group of elements of another molecular system
Get least squares plane	Fitting unweighted planes and measuring planarity of selected atom groups
Get principal axes	Getting the principal inertia or geometric axes of a molecular system
Get radius of gyration	Getting radius of gyration of a molecular system
Get RMSD	Getting the RMSD of a molecular system from a reference molecular system
Get RMSF	Getting per-atom root-mean-square fluctuations over a trajectory
Get secondary structure	Assigning secondary structure elements to amino acid residues across molecular structures
Least RMSD align	Aligning the structure of a molecular system over a reference molecular system
Least RMSD fit	Fitting the structure of a molecular system over a reference molecular system
Move away	Moving away a molecular system from another molecular system
Principal component analysis	Principal component analysis
Rotate	Rotating a molecular system
Set dihedral angles	Setting new dihedral angles values in a molecular system
Shift dihedral angles	Shifting dihedral angles in a molecular system
Translate	Translating a molecular system