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The topology system

MDAnalysis groups static data about a :class:`~MDAnalysis.core.universe.Universe` into its topology. This is typically loaded from a topology file. Topology information falls into 3 categories:

Users will almost never interact directly with a :class:`~MDAnalysis.core.topology.Topology`. Modifying atom containers or topology attributes is typically done through :class:`~MDAnalysis.core.universe.Universe`. Methods for viewing containers or topology attributes, or for calculating topology object values, are accessed through :class:`~MDAnalysis.core.groups.AtomGroup`.

Topology attributes

MDAnalysis supports a range of topology attributes for each :class:`~MDAnalysis.core.groups.Atom` and :class:`~MDAnalysis.core.groups.AtomGroup`. If an attribute is defined for an Atom, it will be for an AtomGroup, and vice versa -- however, they are accessed with singular and plural versions of the attribute specifically.

Canonical attributes

These attributes are derived for every :class:`~MDAnalysis.core.universe.Universe`, including Universes created with :meth:`~MDAnalysis.core.universe.Universe.empty`. They encode the MDAnalysis order of each object.

Atom AtomGroup Description
index indices MDAnalysis canonical atom index (from 0)
resindex resindices MDAnalysis canonical residue index (from 0)
segindex segindices MDAnalysis segment index (from 0)

The following attributes are read or guessed from every format supported by MDAnalysis.

Atom AtomGroup Description
id ids atom serial (from 1, except PSF/DMS/TPR formats)
mass masses atom mass (guessed, default: 0.0)
resid resids residue number (from 1, except for TPR)
resnum resnums alias of resid
segid segids names of segments (default: 'SYSTEM')
type types atom name, atom element, or force field atom type

Format-specific attributes

The table below lists attributes that are read from supported formats. These can also be :ref:`added to a Universe <add-topologyattrs>` created from a file that does not support them.

Connectivity information

MDAnalysis can also read connectivity information, if the file provides it. These become available as :ref:`topology-objects`, which have additional functionality.

Adding TopologyAttrs

Each of the attributes above can be added to a Universe if it was not available in the file with :meth:`~MDAnalysis.core.universe.Universe.add_TopologyAttr`.

:meth:`~MDAnalysis.core.universe.Universe.add_TopologyAttr` takes two arguments:

  • topologyattr : the singular or plural name of a TopologyAttr, or a MDAnalysis TopologyAttr object. This must already have been defined as a :class:`~MDAnalysis.core.topologyattrs.TopologyAttr` (see :ref:`custom-topologyattrs` for an example of adding a custom topology attribute).
  • values (optional) : if topologyattr is a string, the values for that attribute. This can be None if the attribute has default values defined, e.g. tempfactors.
.. ipython:: python
    :okwarning:

    import MDAnalysis as mda
    from MDAnalysis.tests.datafiles import PSF
    psf = mda.Universe(PSF)
    hasattr(psf.atoms, 'tempfactors')
    psf.add_TopologyAttr('tempfactors')
    psf.atoms.tempfactors

One way to modify topology attributes is to simply replace them with :meth:`~MDAnalysis.core.universe.Universe.add_TopologyAttr`:

.. ipython:: python

    psf.add_TopologyAttr('tempfactors', range(len(psf.atoms)))
    psf.atoms.tempfactors

The number of values provided should correspond with the "level" of the attribute. For example, B-factors are atomic-level information. However, residue names and residue ids apply to residues. See a :ref:`table of attribute levels and default values <topologyattr-defaults>` for more information.

Modifying TopologyAttrs

Existing topology attributes can be directly modified by assigning new values.

.. ipython:: python
    :okwarning:

    import MDAnalysis as mda
    from MDAnalysis.tests.datafiles import PDB
    pdb = mda.Universe(PDB)
    pdb.residues[:3].resnames
    pdb.residues[:3].resnames = ['RES1', 'RES2', 'RES3']
    pdb.residues[:3].atoms.resnames

Note

This method cannot be used with connectivity attributes, i.e. bonds, angles, dihedrals, and impropers.

Similarly to adding topology attributes with :meth:`~MDAnalysis.core.universe.Universe.add_TopologyAttr`, the "level" of the attribute matters. Residue attributes can only be assigned to attributes at the Residue or ResidueGroup level. The same applies to attributes for Atoms and Segments. For example, we would get a NotImplementedError if we tried to assign resnames to an AtomGroup.

In [15]: pdb.residues[0].atoms.resnames = ['new_name']

NotImplementedErrorTraceback (most recent call last)
<ipython-input-15-0f99b0dc5f49> in <module>
----> 1 pdb.residues[0].atoms.resnames = ['new_name']
...
NotImplementedError: Cannot set resnames from AtomGroup. Use 'AtomGroup.residues.resnames = '

Default values and attribute levels

Topology information in MDAnalysis is always associated with a level: one of atom, residue, or segment. For example, indices is Atom information, resindices is Residue information, and segindices is Segment information. Many topology attributes also have default values, so that they can be :ref:`added to a Universe without providing explicit values <add-topologyattrs>`, and expected types. The table below lists which attributes have default values, what they are, and the information level.

Topology objects

MDAnalysis defines four types of :class:`~MDAnalysis.core.topologyobjects.TopologyObject` by connectivity:

The value of each topology object can be calculated with :func:`value`.

Each :class:`~MDAnalysis.core.topologyobjects.TopologyObject` also contains the following attributes:

Groups of these are held in :class:`~MDAnalysis.core.topologyobjects.TopologyGroup`s. The master groups of TopologyObjects are :ref:`accessible as properties of a Universe <universe-properties>`. TopologyObjects are typically read from a file with connectivity information (:ref:`see the supported formats here <topologyobject-attr>`). However, they can be created in two ways: by adding them to a Universe, or by creating them from an :class:`~MDAnalysis.core.groups.AtomGroup`. Bonds can be guessed based on distance and Van der Waals' radii with :meth:`AtomGroup.guess_bonds <MDAnalysis.core.groups.AtomGroup.guess_bonds>`.

Adding to a Universe

As of version 0.21.0, there are specific methods for adding :class:`~MDAnalysis.core.topologyobjects.TopologyObject`s to a :class:`~MDAnalysis.core.universe.Universe`:

These accept the following values:

Prior to version 0.21.0, objects could be added to a Universe with :meth:`~MDAnalysis.core.universe.Universe.add_TopologyAttr`.

.. ipython:: python
    :okwarning:

    hasattr(pdb, 'angles')
    pdb.add_TopologyAttr('angles', [(0, 1, 2), (2, 3, 4)])
    pdb.angles

Both of these methods add the new objects to the associated master :class:`~MDAnalysis.core.topologyobjects.TopologyGroup` in the :class:`~MDAnalysis.core.universe.Universe`.

Creating with an AtomGroup

An :class:`~MDAnalysis.core.groups.AtomGroup` can be represented as a bond, angle, dihedral angle, or improper angle :class:`~MDAnalysis.core.topologyobjects.TopologyObject` through the respective properties:

The :class:`~MDAnalysis.core.groups.AtomGroup` must contain the corresponding number of atoms, in the desired order. For example, a bond cannot be created from three atoms.

In [18]: pdb.atoms[[3, 4, 2]].bond

ValueErrorTraceback (most recent call last)
<ipython-input-21-e59c36ab66f4> in <module>
----> 1 pdb.atoms[[3, 4, 2]].bond
...
ValueError: bond only makes sense for a group with exactly 2 atoms

However, the angle Atom 2 ----- Atom 4 ------ Atom 3 can be calculated, even if the atoms are not connected with bonds.

.. ipython:: python

    a = pdb.atoms[[3, 4, 2]].angle
    print(a.value())

These AtomGroup :class:`~MDAnalysis.core.topologyobjects.TopologyObject`s are not added to the associated master :class:`~MDAnalysis.core.topologyobjects.TopologyGroup` in the :class:`~MDAnalysis.core.universe.Universe`.

Deleting from a Universe

As of version 0.21.0, there are specific methods for deleting :class:`~MDAnalysis.core.topologyobjects.TopologyObject`s from a :class:`~MDAnalysis.core.universe.Universe`:

Topology-specific methods

A number of analysis and transformation methods are defined for :class:`~MDAnalysis.core.groups.AtomGroup`, :class:`~MDAnalysis.core.groups.ResidueGroup`, and :class:`~MDAnalysis.core.groups.SegmentGroup` that require specific properties to be available. The primary requirement is the positions attribute. With positions, you can easily compute a center of geometry:

>>> u.atoms.center_of_geometry()
array([-0.04223882,  0.01418196, -0.03504874])

The following methods all require coordinates.

Other methods are made available when certain topology attributes are defined in the Universe. These are listed below.