TopologyDataStructures

Richard Gowers edited this page May 25, 2015 · 4 revisions

Overview

MDAnalysis primarily uses a list of Atoms to identify particles in the system. Topology information (i.e. connectivity through bonds and force-field relevant higher order connectivities such as angles (3) and torsions (dihedrals, 4)) is partially available. This depends on the topology parser (e.g. the PSFParser and TPRParser can read this information from the topology file).

Bond information can also be guessed from a distance search using topology.core.guess_bonds(). Once bond information is in place, angles and torsions can be determined using topology.core.guess_angles() and guess_torsions().

This page together with the Developer Notes on Topologies in the online docs serves as a starting point for discussions and to spell out a number of implementation details that so far have not been explicitly defined.

The structure dict

Currently, the topology information is stored in an ad-hoc manner in the attribute Universe._topology. This is a dict with entries

  • atoms
  • bonds
  • guessed_bonds
  • bond_order
  • angles
  • torsions
  • impropers

Only atoms must be present and it contains a list of AtomGroup.Atom instances. All other entries must be a list of tuples containing the identity number of Atoms in the bonds. Eg 'bonds' = [(0, 1), (1, 2), (2, 3)]

Universe has .bonds .angles .torsions and .impropers attributes which are loaded lazily into _cache the first time they are called. This can be forced using universe.build_topology(). Building topology calls a relevant universe._init* method. This method reads from the appropriate field in u._topology, and creates TopologyObjects. On initialisation, TopologyObjects append themselves to Atom objects.

Numbering

There are different numbering schemes for Atom instances in simultaneous use:

  • Atom.number uniquely identifies an Atom in MDAnalysis. No two Atoms should ever have the same number!
  • Atom.serial is typically atom.number+1 but really can be set by the parser. This isn't used internally in MDAnalysis
  • Atom.id is the atom number inside a residue, starting at 0. It is not unique globally, and is only unique within an Atom's Residue. The Atom.number is the unique identifier for an atom.

Topology Group

Basics

TopologyGroup objects are designed to be a container for many TopologyObjects analogous to AtomGroups containing Atoms. The Universe attributes detailed above are master versions of these TopologyGroups, with all other TopologyGroups being subsets of these. AtomGroups can then build their own ones lazily from their Atoms.

A single TopologyGroup can only contain a single type of TopologyObject, eg only Bonds, not a mix of Bonds and Angles.

Topology Dict

TopologyGroups have a lazily created .topDict attribute which categorises TopologyObjects based on their .type, which is a tuple of the contained Atom.types. TopologyGroups of bonds can then be selected based on types, eg:

tg = u.bonds  # all bonds in universe as object
tg.types()  # view available bonds
tg.selectBonds(('C', 'H'))  # select all C-H bonds in from the topology group.

ag = u.atoms[100:200]
tg2 = ag.angles.selectBonds(('C', 'C', 'O'))  # select all C-C-O angles in an AtomGroup.

Atomgroup intersection

TopologyGroups and AtomGroups can be intersected as if they were sets

ag = u.atoms[0:100]  # select some atoms
tg = u.bonds.selectBonds(('C', 'O'))  # select a type of bond
tg.atomgroup_intersection(ag)

# this is identical to ag.bonds.selectBonds(('C', 'O'))!

By default, bonds will be included in an AtomGroup if at least one Atom has a bond. To only include bonds which have all their atoms within the AtomGroups, there is a keyword strict

ag = u.atoms[0:100]  # select some atoms
tg = u.bonds.selectBonds(('C', 'O'))  # select a type of bond
tg.atomgroup_intersection(ag, strict=True)

Calculations

Cython functions have been written for bond length, angle size and torsion size including the use of periodic boundary conditions. These are callable from TopologyGroups using the .bonds(), .angles() and .torsions() methods.

Topology Objects

All bonds/angles/etc are a subclass of TopologyObject. This is a container which stores Atom objects in a tuple in .atoms. This then supports operations such as __getitem__ __contains__ __eq__ operating on the tuple of atoms.

Bonds

Bonds are 1-2 interactions between two atoms.

Data structures

  1. Universe._topology['bonds']
  2. Universe.bonds
  3. AtomGroup.bonds

Angles

Angles are 1-2-3 interactions between three atoms. The atom 2 is at the apex of an angle.

Data structures

  1. Universe._topology['angles']
  2. Universe.angles
  3. AtomGroup.angles

Dihedrals

Dihedrals or torsions are 1-2-3-4 interactions between four atoms. They describe the angle between the planes formed by atoms 1-2-3 and 2-3-4. (Proper and improper dihedrals are computed in the same manner; only the order of atoms differs.)

Data structures

  1. Universe._topology['torsions']
  2. Universe.torsions
  3. AtomGroup.torsions
  4. Universe._topology['impropers']
  5. Universe.impropers
  6. AtomGroup.impropers

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