Groups of atoms

MDAnalysis has a hierarchy of Atom containers that are used throughout the code.

_images/classes.png

First and foremost is the AtomGroup. An AtomGroup is the primary Atom container; virtually everything can be accessed through it, as detailed in AtomGroup. This includes chemically meaningful groups of Atoms such as a Residue or a Segment.

Residues and Segments

A Residue is composed of Atoms, and a Segment is composed of Residues.

The corresponding container groups are ResidueGroup and SegmentGroup. These have similar properties and available methods as AtomGroup.

In [1]: import MDAnalysis as mda

In [2]: from MDAnalysis.tests.datafiles import TPR2019B3

In [3]: u = mda.Universe(TPR2019B3)

In [4]: ag = u.atoms.select_atoms('resname ARG and name CA')

In [5]: ag
Out[5]: <AtomGroup with 11 atoms>

Each of these container groups can be accessed through another. The behaviour of this differs by level. For example, the residues of the ag are the residues that the atoms of ag belong to.

In [6]: ag.residues
Out[6]: <ResidueGroup with 11 residues>

Accessing the atoms of those residues, however, returns all the atoms in the residues, not just those originally in ag.

In [7]: ag.residues.atoms
Out[7]: <AtomGroup with 264 atoms>

The same applies to segments.

In [8]: ag[:3].segments.atoms
Out[8]: <AtomGroup with 1960 atoms>

Similarly, an Atom has direct knowledge of the Residue and Segment it belongs to. Note that an Atom belongs to one Residue and the residue belongs to one Segment, but a Segment has multiple residues.

In [9]: a = u.atoms[0]

In [10]: a.residue
Out[10]: <Residue LYSH, 0>

In [11]: a.residue.segment
Out[11]: <Segment seg_0_Protein_A>

In [12]: a.residue.segment.residues
Out[12]: <ResidueGroup with 129 residues>

For information on adding custom Residues or Segments, have a look at Adding a Residue or Segment to a Universe.

Fragments

Certain analysis methods in MDAnalysis also make use of additional ways to group atoms. A key concept is a fragment. A fragment is what is typically considered a molecule: an AtomGroup where any atom is reachable from any other atom in the AtomGroup by traversing bonds, and none of its atoms is bonded to any atoms outside the AtomGroup. (A ‘molecule’ in MDAnalysis methods refers to a GROMACS-specific concept). The fragments of a Universe are determined by MDAnalysis as a derived quantity. They can only be determined if bond information is available.

The fragments of an AtomGroup are accessible via the fragments property. Below is a Universe from a GROMACS TPR file of lysozyme (PDB ID: 2LYZ) with 101 water molecules. While it has 230 residues, there are only 102 fragments: 1 protein and 101 water fragments.

In [12]: len(u.residues)
Out[12]: 230

In [13]: len(u.atoms.fragments)
Out[13]: 102

See Topology objects for more on bonds and which file formats give MDAnalysis bond information.

You can also look at which fragment a particular Atom belongs to:

In [9]: u.atoms[0].fragment  # first atom of lysozyme
Out[9]: <AtomGroup with 1960 atoms>

and see which fragments are associated with atoms in a smaller AtomGroup:

In [10]: u.atoms[1959:1961].fragments
Out[10]: (<AtomGroup with 1960 atoms>, <AtomGroup with 3 atoms>)

Note

AtomGroup.fragments returns a tuple of fragments with at least one Atom in the AtomGroup, not a tuple of fragments where all Atoms are in the AtomGroup.