11.3.1. Core Topology object — MDAnalysis.core.topology
¶
New in version 0.16.0.
Topology
is the core object that holds all topology information.
TODO: Add indepth discussion.
Notes
For developers: In MDAnalysis 0.16.0 this new topology system was introduced and discussed as issue #363; this issue contains key information and discussions on the new system. The issue number 363 is also being used as a shorthand in discussions to refer to the new topology system.
11.3.1.1. Classes¶

class
MDAnalysis.core.topology.
Topology
(n_atoms=1, n_res=1, n_seg=1, attrs=None, atom_resindex=None, residue_segindex=None)[source]¶ Inmemory, arraybased topology database.
The topology model of MDanalysis features atoms, which must each be a member of one residue. Each residue, in turn, must be a member of one segment. The details of maintaining this heirarchy, and mappings of atoms to residues, residues to segments, and viceversa, are handled internally by this object.
Parameters:  n_atoms (int) – number of atoms in topology. Must be larger then 1 at each level
 n_residues (int) – number of residues in topology. Must be larger then 1 at each level
 n_segments (int) – number of segments in topology. Must be larger then 1 at each level
 attrs (TopologyAttr objects) – components of the topology to be included
 atom_resindex (array) – 1D array giving the resindex of each atom in the system
 residue_segindex (array) – 1D array giving the segindex of each residue in the system

add_Residue
(segment, **new_attrs)[source]¶ Returns: Return type: residx of the new Residue Raises: NoDataError
– If not all data was provided. This error is raised before any

add_TopologyAttr
(topologyattr)[source]¶ Add a new TopologyAttr to the Topology.
Parameters: topologyattr (TopologyAttr) –

del_TopologyAttr
(topologyattr)[source]¶ Remove a TopologyAttr from the Topology.
If it is not present, nothing happens.
Parameters: topologyattr (TopologyAttr) – New in version 2.0.0.

guessed_attributes
¶ A list of the guessed attributes in this topology

read_attributes
¶ A list of the attributes read from the topology

class
MDAnalysis.core.topology.
TransTable
(n_atoms, n_residues, n_segments, atom_resindex=None, residue_segindex=None)[source]¶ Membership tables with methods to translate indices across levels.
There are three levels; Atom, Residue and Segment. Each Atom must belong in a Residue, each Residue must belong to a Segment.
When translating upwards, eg finding which Segment a Residue belongs in, a single numpy array is returned. When translating downwards, two options are available; a concatenated result (suffix _1) or a list for each parent object (suffix _2d).
Parameters:  n_atoms (int) – number of atoms in topology
 n_residues (int) – number of residues in topology
 n_segments (int) – number of segments in topology
 atom_resindex (1D array) – resindex for each atom in the topology; the number of unique values in this array must be <= n_residues, and the array must be length n_atoms; giving None defaults to placing all atoms in residue 0
 residue_segindex (1D array) – segindex for each residue in the topology; the number of unique values in this array must be <= n_segments, and the array must be length n_residues; giving None defaults to placing all residues in segment 0

size
¶ tuple describing the shape of the TransTable

atoms2residues
(aix)[source] Get residue indices for each atom.
Parameters: aix (array) – atom indices Returns: rix – residue index for each atom Return type: array

atoms2segments
(aix)[source] Get segment indices for each atom.
Parameters: aix (array) – atom indices Returns: rix – segment index for each atom Return type: array

residues2atoms_1d
(rix)[source] Get atom indices collectively represented by given residue indices.
Parameters: rix (array) – residue indices Returns: aix – indices of atoms present in residues, collectively Return type: array

residues2atoms_2d
(rix)[source] Get atom indices represented by each residue index.
Parameters: rix (array) – residue indices Returns: raix – each element corresponds to a residue index, in order given in rix, with each element being an array of the atom indices present in that residue Return type: list

residues2segments
(rix)[source] Get segment indices for each residue.
Parameters: rix (array) – residue indices Returns: six – segment index for each residue Return type: array

segments2atoms_1d
(six)[source] Get atom indices collectively represented by given segment indices.
Parameters: six (array) – segment indices Returns: aix – sorted indices of atoms present in segments, collectively Return type: array

segments2atoms_2d
(six)[source] Get atom indices represented by each segment index.
Parameters: six (array) – residue indices Returns: saix – each element corresponds to a segment index, in order given in six, with each element being an array of the atom indices present in that segment Return type: list

segments2residues_1d
(six)[source] Get residue indices collectively represented by given segment indices
Parameters: six (array) – segment indices Returns: rix – sorted indices of residues present in segments, collectively Return type: array

segments2residues_2d
(six)[source] Get residue indices represented by each segment index.
Parameters: six (array) – residue indices Returns: srix – each element corresponds to a segment index, in order given in six, with each element being an array of the residue indices present in that segment Return type: list

size
The shape of the table, (n_atoms, n_residues, n_segments)
11.3.1.2. Helper functions¶

MDAnalysis.core.topology.
make_downshift_arrays
(upshift, nparents)[source]¶ From an upwards translation table, create the opposite direction
Turns a many to one mapping (eg atoms to residues) to a one to many mapping (residues to atoms)
Parameters:  upshift (array_like) – Array of integers describing which parent each item belongs to
 nparents (integer) – Total number of parents that exist.
Returns: downshift – An array of arrays, each containing the indices of the children of each parent. Length nparents + 1
Return type: array_like (dtype object)
Examples
To find the residue to atom mappings for a given atom to residue mapping:
>>> atom2res = np.array([0, 1, 0, 2, 2, 0, 2]) >>> make_downshift_arrays(atom2res) array([array([0, 2, 5]), array([1]), array([3, 4, 6]), None], dtype=object)
Entry 0 corresponds to residue 0 and says that this contains atoms 0, 2 & 5
Notes
The final entry in the return array will be
None
to ensure that the dtype of the array isobject
.Warning
This means negative indexing should never be used with these arrays.