11.3.2. Core Topology Objects — MDAnalysis.core.topologyobjects¶

The building blocks for MDAnalysis’ description of topology

class MDAnalysis.core.topologyobjects.Angle(ix, universe, type=None, guessed=False, order=None)[source]

An angle between three Atom instances. Atom 2 is the apex of the angle

New in version 0.8.

Changed in version 0.9.0: Now a subclass of TopologyObject; now uses __slots__ and stores atoms in atoms attribute

Create a topology object

Parameters: ix (numpy array) – indices of the Atoms universe (MDAnalysis.Universe) – type (optional) – Type of the bond guessed (optional) – If the Bond is guessed
angle(pbc=True)[source]

Returns the angle in degrees of this Angle.

Angle between atoms 0 and 2 with apex at 1:

   2
/
/
1------0


Note

The numerical precision is typically not better than 4 decimals (and is only tested to 3 decimals).

New in version 0.9.0.

Changed in version 0.17.0: Fixed angles close to 180 giving NaN

Changed in version 0.19.0: Added pbc keyword, default True

value(pbc=True)

Returns the angle in degrees of this Angle.

Angle between atoms 0 and 2 with apex at 1:

   2
/
/
1------0


Note

The numerical precision is typically not better than 4 decimals (and is only tested to 3 decimals).

New in version 0.9.0.

Changed in version 0.17.0: Fixed angles close to 180 giving NaN

Changed in version 0.19.0: Added pbc keyword, default True

class MDAnalysis.core.topologyobjects.Bond(ix, universe, type=None, guessed=False, order=None)[source]

A bond between two Atom instances.

Two Bond instances can be compared with the == and != operators. A bond is equal to another if the same atom numbers are connected and they have the same bond order. The ordering of the two atom numbers is ignored as is the fact that a bond was guessed.

The presence of a particular atom can also be queried:

>>> Atom in Bond


will return either True or False.

Changed in version 0.9.0: Now a subclass of TopologyObject. Changed class to use __slots__ and stores atoms in atoms attribute.

Create a topology object

Parameters: ix (numpy array) – indices of the Atoms universe (MDAnalysis.Universe) – type (optional) – Type of the bond guessed (optional) – If the Bond is guessed
length(pbc=True)[source]

Length of the bond.

Changed in version 0.11.0: Added pbc keyword

Changed in version 0.19.0: Changed default of pbc to True

partner(Atom)[source]
Returns: the other Atom in this bond
value(pbc=True)

Length of the bond.

Changed in version 0.11.0: Added pbc keyword

Changed in version 0.19.0: Changed default of pbc to True

class MDAnalysis.core.topologyobjects.CMap(ix, universe, type=None, guessed=False, order=None)[source]

Coupled-torsion correction map term between five Atom instances.

New in version 1.0.0.

Create a topology object

Parameters: ix (numpy array) – indices of the Atoms universe (MDAnalysis.Universe) – type (optional) – Type of the bond guessed (optional) – If the Bond is guessed
class MDAnalysis.core.topologyobjects.Dihedral(ix, universe, type=None, guessed=False, order=None)[source]

Dihedral (dihedral angle) between four Atom instances.

The dihedral is defined as the angle between the planes formed by Atoms (1, 2, 3) and (2, 3, 4).

New in version 0.8.

Changed in version 0.9.0: Now a subclass of TopologyObject; now uses __slots__ and stores atoms in atoms attribute.

Changed in version 0.11.0: Renamed to Dihedral (was Torsion)

Create a topology object

Parameters: ix (numpy array) – indices of the Atoms universe (MDAnalysis.Universe) – type (optional) – Type of the bond guessed (optional) – If the Bond is guessed
dihedral(pbc=True)[source]

Calculate the dihedral angle in degrees.

Dihedral angle around axis connecting atoms 1 and 2 (i.e. the angle between the planes spanned by atoms (0,1,2) and (1,2,3)):

        3
|
1-----2
/
0


Note

The numerical precision is typically not better than 4 decimals (and is only tested to 3 decimals).

New in version 0.9.0.

Changed in version 0.19.0: Added pbc keyword, default True

value(pbc=True)

Calculate the dihedral angle in degrees.

Dihedral angle around axis connecting atoms 1 and 2 (i.e. the angle between the planes spanned by atoms (0,1,2) and (1,2,3)):

        3
|
1-----2
/
0


Note

The numerical precision is typically not better than 4 decimals (and is only tested to 3 decimals).

New in version 0.9.0.

Changed in version 0.19.0: Added pbc keyword, default True

class MDAnalysis.core.topologyobjects.ImproperDihedral(ix, universe, type=None, guessed=False, order=None)[source]

Improper Dihedral (improper dihedral angle) between four Atom instances.

MDAnalysis treats the improper dihedral angle as the angle between the planes formed by Atoms (1, 2, 3) and (2, 3, 4).

Warning

Definitions of Atom ordering in improper dihedrals can change. Check the definitions here against your software.

New in version 0.9.0.

Changed in version 0.11.0: Renamed to ImproperDihedral (was Improper_Torsion)

Create a topology object

Parameters: ix (numpy array) – indices of the Atoms universe (MDAnalysis.Universe) – type (optional) – Type of the bond guessed (optional) – If the Bond is guessed
improper()[source]

Improper dihedral angle in degrees.

Note

The numerical precision is typically not better than 4 decimals (and is only tested to 3 decimals).

class MDAnalysis.core.topologyobjects.TopologyDict(topologygroup)[source]

A customised dictionary designed for sorting the bonds, angles and dihedrals present in a group of atoms.

Usage:

topologydict = TopologyDict(members)


TopologyDicts are also built lazily from a TopologyGroup.topDict attribute.

The TopologyDict collects all the selected topology type from the atoms and categorises them according to the types of the atoms within. A TopologyGroup containing all of a given bond type can be made by querying with the appropriate key. The keys to the TopologyDict are a tuple of the atom types that the bond represents and can be viewed using the keys() method.

For example, from a system containing pure ethanol

>>> td = u.bonds.topDict
>>> td.keys()
[('C', 'C'),
('C', 'H'),
('O', 'H'),
('C', 'O')]
>>> td['C', 'O']
< TopologyGroup containing 912 bonds >


Note

The key for a bond is taken from the type attribute of the atoms.

Getting and setting types of bonds is done smartly, so a C-C-H angle is considered identical to a H-C-C angle.

Duplicate entries are automatically removed upon creation and combination of different Dicts. This means a bond between atoms 1 and 2 will only ever appear once in a dict despite both atoms 1 and 2 having the bond in their bond attribute.

Two TopologyDict instances can be combined using addition and it will not create any duplicate bonds in the process.

Parameters: members – A list of TopologyObject instances

New in version 0.8.

Changed in version 0.9.0: Changed initialisation to use a list of TopologyObject instances instead of list of atoms; now used from within TopologyGroup instead of accessed from AtomGroup.

keys()[source]

Returns a list of the different types of available bonds

class MDAnalysis.core.topologyobjects.TopologyGroup(bondidx, universe, btype=None, type=None, guessed=None, order=None)[source]

A container for a groups of bonds.

All bonds of a certain types can be retrieved from within the TopologyGroup by querying with a tuple of types:

tg2 = tg.select_bonds([key])


Where key describes the desired bond as a tuple of the involved Atom types, as defined by the .type Atom attribute). A list of available keys can be displayed using the types() method.

Alternatively, all the bonds which are in a given AtomGroup can be extracted using atomgroup_intersection():

tg2 = tg.atomgroup_intersection(ag)


This allows the keyword strict to be given, which forces all members of all bonds to be inside the AtomGroup passed to it.

Finally, a TopologyGroup can be sliced similarly to AtomGroups:

tg2 = tg[5:10]


The bonds(), angles() and dihedrals() methods offer a “shortcut” to the Cython distance calculation functions in MDAnalysis.lib.distances.

TopologyGroups can be combined with TopologyGroups of the same bond type (ie can combine two angle containing TopologyGroups).

New in version 0.8.

Changed in version 0.9.0: Overhauled completely: (1) Added internal TopologyDict accessible by the topDict attribute. (2) selectBonds() allows the topDict to be queried with tuple of types. (3) Added atomgroup_intersection() to allow bonds which are in a given AtomGroup to be retrieved.

Changed in version 0.10.0: Added from_indices() constructor, allowing class to be created from indices. Can now create empty Group. Renamed dump_contents() to to_indices()

Changed in version 0.11.0: Added values method to return the size of each object in this group Deprecated selectBonds method in favour of select_bonds

Changed in version 0.19.0: Empty TopologyGroup now returns correctly shaped empty array via indices property and to_indices()

angles(result=None, pbc=False)[source]

Calculates the angle in radians formed between a bond between atoms 1 and 2 and a bond between atoms 2 & 3

Parameters: result (array_like) – allows a predefined results array to be used, note that this will be overwritten pbc (bool) – apply periodic boundary conditions when calculating angles [False] this is important when connecting vectors between atoms might require minimum image convention angles (ndarray) .. versionchanged :: 0.9.0 – Added pbc option (default False)
atom1

The first atom in each TopologyObject in this Group

atom2

The second atom in each TopologyObject in this Group

atom3

The third atom in each TopologyObject in this Group

atom4

The fourth atom in each TopologyObject in this Group

atomgroup_intersection(ag, **kwargs)[source]

Retrieve all bonds from within this TopologyGroup that are within the AtomGroup which is passed.

Parameters: ag (AtomGroup) – The :class:~MDAnalysis.core.groups.AtomGroup to intersect with. strict (bool) – Only retrieve bonds which are completely contained within the AtomGroup. [False]

New in version 0.9.0.

bonds(pbc=False, result=None)[source]

Calculates the distance between all bonds in this TopologyGroup

Keywords: pbc apply periodic boundary conditions when calculating distance [False] result allows a predefined results array to be used, note that this will be overwritten

Uses cython implementation

dihedrals(result=None, pbc=False)[source]

Calculate the dihedral angle in radians for this topology group.

Defined as the angle between a plane formed by atoms 1, 2 and 3 and a plane formed by atoms 2, 3 and 4.

Parameters: result (array_like) – allows a predefined results array to be used, note that this will be overwritten pbc (bool) – apply periodic boundary conditions when calculating angles [False] this is important when connecting vectors between atoms might require minimum image convention angles (ndarray) .. versionchanged:: 0.9.0 – Added pbc option (default False)
dump_contents()

Return a data structure with atom indices describing the bonds.

This format should be identical to the original contents of the entries in universe._topology. Note that because bonds are sorted as they are initialised, the order that atoms are defined in each entry might be reversed.

Returns: indices (tuple) – A tuple of tuples which define the contents of this TopologyGroup in terms of the atom numbers. (0 based index within u.atoms) .. versionadded:: 0.9.0 .. versionchanged:: 0.10.0 – Renamed from “dump_contents” to “to_indices”
indices

all bond indices

to_indices
function that just returns indices
selectBonds(selection)

Retrieves a selection from this topology group based on types.

select_bonds(selection)[source]

Retrieves a selection from this topology group based on types.

to_indices()[source]

Return a data structure with atom indices describing the bonds.

This format should be identical to the original contents of the entries in universe._topology. Note that because bonds are sorted as they are initialised, the order that atoms are defined in each entry might be reversed.

Returns: indices (tuple) – A tuple of tuples which define the contents of this TopologyGroup in terms of the atom numbers. (0 based index within u.atoms) .. versionadded:: 0.9.0 .. versionchanged:: 0.10.0 – Renamed from “dump_contents” to “to_indices”
topDict

Returns the TopologyDict for this topology group.

This is used for the select_bonds method when fetching a certain type of bond.

This is a cached property so will be generated the first time it is accessed.

types()[source]

Return a list of the bond types in this TopologyGroup

universe

The Universe that we belong to

values(**kwargs)[source]

Return the size of each object in this Group

Keywords: pbc apply periodic boundary conditions when calculating distance [False] result allows a predefined results array to be used, note that this will be overwritten

New in version 0.11.0.

class MDAnalysis.core.topologyobjects.TopologyObject(ix, universe, type=None, guessed=False, order=None)[source]

Base class for all Topology items.

Defines the behaviour by which Bonds/Angles/etc in MDAnalysis should behave.

New in version 0.9.0.

Changed in version 0.10.0: All TopologyObject now keep track of if they were guessed or not via the is_guessed managed property.

New in version 0.11.0: Added the value method to return the size of the object

Create a topology object

Parameters: ix (numpy array) – indices of the Atoms universe (MDAnalysis.Universe) – type (optional) – Type of the bond guessed (optional) – If the Bond is guessed
atoms

Atoms within this Bond

indices

Tuple of indices describing this object

New in version 0.10.0.

type

Type of the bond as a tuple

Note

When comparing types, it is important to consider the reverse of the type too, i.e.:

a.type == b.type or a.type == b.type[::-1]

class MDAnalysis.core.topologyobjects.UreyBradley(ix, universe, type=None, guessed=False, order=None)[source]

A Urey-Bradley angle between two Atom instances. Two UreyBradley instances can be compared with the == and != operators. A UreyBradley angle is equal to another if the same atom numbers are involved.

New in version 1.0.0.

Create a topology object

Parameters: ix (numpy array) – indices of the Atoms universe (MDAnalysis.Universe) – type (optional) – Type of the bond guessed (optional) – If the Bond is guessed
distance(pbc=True)[source]

Distance between the atoms.

partner(Atom)[source]
Returns: the other Atom in this interaction
value(pbc=True)

Distance between the atoms.