10.2.3. Topology attribute objects — MDAnalysis.core.topologyattrs

Common TopologyAttr instances that are used by most topology parsers.

TopologyAttrs are used to contain attributes such as atom names or resids. These are usually read by the TopologyParser.

class MDAnalysis.core.topologyattrs.AltLocs(values, guessed=False)[source]

AltLocs for each atom

dtype

alias of builtins.object

class MDAnalysis.core.topologyattrs.Angles(values, types=None, guessed=False, order=None)[source]

Angles between three atoms

Initialise with a list of 3 long tuples E.g., [(0, 1, 2), (1, 2, 3), (2, 3, 4)]

These indices refer to the atom indices.

class MDAnalysis.core.topologyattrs.AtomAttr(values, guessed=False)[source]

Base class for atom attributes.

get_atoms(ag)[source]

Get atom attributes for a given AtomGroup

get_residues(rg)[source]

By default, the values for each atom present in the set of residues are returned in a single array. This behavior can be overriden in child attributes.

get_segments(sg)[source]

By default, the values for each atom present in the set of residues are returned in a single array. This behavior can be overriden in child attributes.

set_atoms(ag, values)[source]

Set atom attributes for a given AtomGroup

set_residues(rg, values)[source]

Set residue attributes for a given ResidueGroup

set_segments(sg, values)[source]

Set segmentattributes for a given SegmentGroup

class MDAnalysis.core.topologyattrs.Atomids(values, guessed=False)[source]

ID for each atom.

dtype

alias of builtins.int

class MDAnalysis.core.topologyattrs.Atomindices[source]

Globally unique indices for each atom in the group.

If the group is an AtomGroup, then this gives the index for each atom in the group. This is the unambiguous identifier for each atom in the topology, and it is not alterable.

If the group is a ResidueGroup or SegmentGroup, then this gives the indices of each atom represented in the group in a 1-D array, in the order of the elements in that group.

get_atoms(ag)[source]

Get atom attributes for a given AtomGroup

get_residues(rg)[source]

Get residue attributes for a given ResidueGroup

get_segments(sg)[source]

Get segment attributes for a given SegmentGroup

set_atoms(ag, values)[source]

Set atom attributes for a given AtomGroup

class MDAnalysis.core.topologyattrs.Atomnames(values, guessed=False)[source]

Name for each atom.

chi1_selection()[source]

AtomGroup corresponding to the chi1 sidechain dihedral N-CA-CB-CG.

Returns

  • AtomGroup – 4-atom selection in the correct order. If no CB and/or CG is found then this method returns None.

  • .. versionadded:: 0.7.5

dtype

alias of builtins.object

omega_selection()[source]

AtomGroup corresponding to the omega protein backbone dihedral CA-C-N’-CA’.

omega describes the -C-N- peptide bond. Typically, it is trans (180 degrees) although cis-bonds (0 degrees) are also occasionally observed (especially near Proline).

Returns

4-atom selection in the correct order. If no C’ found in the previous residue (by resid) then this method returns None.

Return type

AtomGroup

phi_selection()[source]

AtomGroup corresponding to the phi protein backbone dihedral C’-N-CA-C.

Returns

4-atom selection in the correct order. If no C’ found in the previous residue (by resid) then this method returns None.

Return type

AtomGroup

psi_selection()[source]

AtomGroup corresponding to the psi protein backbone dihedral N-CA-C-N’.

Returns

4-atom selection in the correct order. If no N’ found in the following residue (by resid) then this method returns None.

Return type

AtomGroup

class MDAnalysis.core.topologyattrs.Atomtypes(values, guessed=False)[source]

Type for each atom

dtype

alias of builtins.object

class MDAnalysis.core.topologyattrs.Bfactors(values, guessed=False)[source]

Crystallographic B-factors in A**2 for each atom

dtype

alias of builtins.float

class MDAnalysis.core.topologyattrs.Bonds(values, types=None, guessed=False, order=None)[source]

Bonds between two atoms

Must be initialised by a list of zero based tuples. These indices refer to the atom indices. E.g., ` [(0, 1), (1, 2), (2, 3)]`

Also adds the bonded_atoms, fragment and fragments attributes.

bonded_atoms()[source]

An AtomGroup of all Atoms bonded to this Atom.

fragindex()[source]

The index (ID) of the fragment this Atom is part of.

Note

This property is only accessible if the underlying topology contains bond information.

New in version 0.20.0.

fragindices()[source]

The fragment indices of all Atoms in this AtomGroup.

A numpy.ndarray with shape=(n_atoms,) and dtype=numpy.int64.

Note

This property is only accessible if the underlying topology contains bond information.

New in version 0.20.0.

fragment()[source]

An AtomGroup representing the fragment this Atom is part of.

A fragment is a group of atoms which are interconnected by Bonds, i.e., there exists a path along one or more Bonds between any pair of Atoms within a fragment. Thus, a fragment typically corresponds to a molecule.

Note

This property is only accessible if the underlying topology contains bond information.

New in version 0.9.0.

fragments()[source]

Read-only tuple of fragments.

Contains all fragments that any Atom in this AtomGroup is part of.

A fragment is a group of atoms which are interconnected by Bonds, i.e., there exists a path along one or more Bonds between any pair of Atoms within a fragment. Thus, a fragment typically corresponds to a molecule.

Note

  • This property is only accessible if the underlying topology contains bond information.

  • The contents of the fragments may extend beyond the contents of this AtomGroup.

New in version 0.9.0.

n_fragments()[source]

The number of unique fragments the Atoms of this AtomGroup are part of.

Note

This property is only accessible if the underlying topology contains bond information.

New in version 0.20.0.

class MDAnalysis.core.topologyattrs.ChainIDs(values, guessed=False)[source]

ChainID per atom

Note

This is an attribute of the Atom, not Residue or Segment

dtype

alias of builtins.object

class MDAnalysis.core.topologyattrs.Charges(values, guessed=False)[source]
dtype

alias of builtins.float

get_residues(rg)[source]

By default, the values for each atom present in the set of residues are returned in a single array. This behavior can be overriden in child attributes.

get_segments(sg)[source]

By default, the values for each atom present in the set of residues are returned in a single array. This behavior can be overriden in child attributes.

total_charge(compound='group')[source]

Total charge of (compounds of) the group.

Computes the total charge of Atoms in the group. Total charges per Residue, Segment, molecule, or fragment can be obtained by setting the compound parameter accordingly.

Parameters

compound ({'group', 'segments', 'residues', 'molecules', 'fragments'}, optional) – If ‘group’, the total charge of all atoms in the group will be returned as a single value. Otherwise, the total charges per Segment, Residue, molecule, or fragment will be returned as a 1d array. Note that, in any case, only the charges of Atoms belonging to the group will be taken into account.

Returns

Total charge of (compounds of) the group. If compound was set to 'group', the output will be a single value. Otherwise, the output will be a 1d array of shape (n,) where n is the number of compounds.

Return type

float or numpy.ndarray

Changed in version 0.20.0: Added compound parameter

class MDAnalysis.core.topologyattrs.Dihedrals(values, types=None, guessed=False, order=None)[source]

A connection between four sequential atoms

class MDAnalysis.core.topologyattrs.Elements(values, guessed=False)[source]

Element for each atom

dtype

alias of builtins.object

class MDAnalysis.core.topologyattrs.ICodes(values, guessed=False)[source]

Insertion code for Atoms

dtype

alias of builtins.object

class MDAnalysis.core.topologyattrs.Impropers(values, types=None, guessed=False, order=None)[source]

An imaginary dihedral between four atoms

class MDAnalysis.core.topologyattrs.Masses(values, guessed=False)[source]
align_principal_axis(axis, vector)[source]

Align principal axis with index axis with vector.

Parameters

  • axis ({0, 1, 2}) – Index of the principal axis (0, 1, or 2), as produced by principal_axes().

  • vector (array_like) – Vector to align principal axis with.

Notes

To align the long axis of a channel (the first principal axis, i.e. axis = 0) with the z-axis:

u.atoms.align_principal_axis(0, [0,0,1])
u.atoms.write("aligned.pdb")
asphericity(pbc=None, unwrap=None, compound='group')[source]

Asphericity.

See [Dima2004b] for background information.

Parameters

  • pbc (bool, optional) – If True, move all atoms within the primary unit cell before calculation. If None use value defined in MDAnalysis.core.flags[‘use_pbc’]

  • unwrap (bool, optional) – If True, compounds will be unwrapped before computing their centers.

  • compound ({'group', 'segments', 'residues', 'molecules', 'fragments'}, optional) – Which type of component to keep together during unwrapping.

Note

The MDAnalysis.core.flags flag use_pbc when set to True allows the pbc flag to be used by default.

References

Dima2004b

Dima, R. I., & Thirumalai, D. (2004). Asymmetry in the shapes of folded and denatured states of proteins. J Phys Chem B, 108(21), 6564-6570. doi:10.1021/jp037128y

New in version 0.7.7.

Changed in version 0.8: Added pbc keyword

Changed in version 0.20.0: Added unwrap and compound parameter

center_of_mass(pbc=None, compound='group', unwrap=False)[source]

Center of mass of (compounds of) the group.

Computes the center of mass of Atoms in the group. Centers of mass per Residue, Segment, molecule, or fragment can be obtained by setting the compound parameter accordingly. If the masses of a compound sum up to zero, the center of mass coordinates of that compound will be nan (not a number).

Parameters

  • pbc (bool, optional) – If True and compound is 'group', move all atoms to the primary unit cell before calculation. If True and compound is 'segments' or 'residues', the centers of mass of each compound will be calculated without moving any atoms to keep the compounds intact. Instead, the resulting center-of-mass position vectors will be moved to the primary unit cell after calculation.

  • compound ({'group', 'segments', 'residues', 'molecules', 'fragments'}, optional) – If 'group', the center of mass of all atoms in the group will be returned as a single position vector. Otherwise, the centers of mass of each Segment, Residue, molecule, or fragment will be returned as an array of position vectors, i.e. a 2d array. Note that, in any case, only the positions of Atoms belonging to the group will be taken into account.

  • unwrap (bool, optional) – If True, compounds will be unwrapped before computing their centers.

Returns

center – Position vector(s) of the center(s) of mass of the group. If compound was set to 'group', the output will be a single position vector. If compound was set to 'segments' or 'residues', the output will be a 2d coordinate array of shape (n, 3) where n is the number of compounds.

Return type

numpy.ndarray

Note

  • This method can only be accessed if the underlying topology has information about atomic masses.

  • The MDAnalysis.core.flags flag use_pbc when set to True allows the pbc flag to be used by default.

Changed in version 0.8: Added pbc parameter

Changed in version 0.19.0: Added compound parameter

Changed in version 0.20.0: Added 'molecules' and 'fragments' compounds

Changed in version 0.20.0: Added unwrap parameter

dtype

alias of numpy.float64

get_residues(rg)[source]

By default, the values for each atom present in the set of residues are returned in a single array. This behavior can be overriden in child attributes.

get_segments(sg)[source]

By default, the values for each atom present in the set of residues are returned in a single array. This behavior can be overriden in child attributes.

moment_of_inertia(**kwargs)[source]

Tensor moment of inertia relative to center of mass as 3x3 numpy array.

Parameters

pbc (bool, optional) – If True, move all atoms within the primary unit cell before calculation. [False]

Note

The MDAnalysis.core.flags flag use_pbc when set to True allows the pbc flag to be used by default.

Changed in version 0.8: Added pbc keyword

Changed in version 0.20.0: Added unwrap parameter

principal_axes(pbc=None)[source]

Calculate the principal axes from the moment of inertia.

e1,e2,e3 = AtomGroup.principal_axes()

The eigenvectors are sorted by eigenvalue, i.e. the first one corresponds to the highest eigenvalue and is thus the first principal axes.

Parameters

pbc (bool, optional) – If True, move all atoms within the primary unit cell before calculation. If None use value defined in setup flags.

Returns

axis_vectors – 3 x 3 array with v[0] as first, v[1] as second, and v[2] as third eigenvector.

Return type

array

Note

The MDAnalysis.core.flags flag use_pbc when set to True allows the pbc flag to be used by default.

Changed in version 0.8: Added pbc keyword

radius_of_gyration(**kwargs)[source]

Radius of gyration.

Parameters

pbc (bool, optional) – If True, move all atoms within the primary unit cell before calculation. [False]

Note

The MDAnalysis.core.flags flag use_pbc when set to True allows the pbc flag to be used by default.

Changed in version 0.8: Added pbc keyword

shape_parameter(**kwargs)[source]

Shape parameter.

See [Dima2004a] for background information.

Parameters

pbc (bool, optional) – If True, move all atoms within the primary unit cell before calculation. [False]

Note

The MDAnalysis.core.flags flag use_pbc when set to True allows the pbc flag to be used by default.

References

Dima2004a

Dima, R. I., & Thirumalai, D. (2004). Asymmetry in the shapes of folded and denatured states of proteins. J Phys Chem B, 108(21), 6564-6570. doi:10.1021/jp037128y

New in version 0.7.7.

Changed in version 0.8: Added pbc keyword

total_mass(compound='group')[source]

Total mass of (compounds of) the group.

Computes the total mass of Atoms in the group. Total masses per Residue, Segment, molecule, or fragment can be obtained by setting the compound parameter accordingly.

Parameters

compound ({'group', 'segments', 'residues', 'molecules', 'fragments'}, optional) – If 'group', the total mass of all atoms in the group will be returned as a single value. Otherwise, the total masses per Segment, Residue, molecule, or fragment will be returned as a 1d array. Note that, in any case, only the masses of Atoms belonging to the group will be taken into account.

Returns

Total mass of (compounds of) the group. If compound was set to 'group', the output will be a single value. Otherwise, the output will be a 1d array of shape (n,) where n is the number of compounds.

Return type

float or numpy.ndarray

Changed in version 0.20.0: Added compound parameter

class MDAnalysis.core.topologyattrs.Molnums(values, guessed=False)[source]

Name of the molecule type

Two molecules that share a molecule type share a common template topology.

dtype

alias of numpy.int64

class MDAnalysis.core.topologyattrs.Moltypes(values, guessed=False)[source]

Name of the molecule type

Two molecules that share a molecule type share a common template topology.

dtype

alias of builtins.object

class MDAnalysis.core.topologyattrs.Occupancies(values, guessed=False)[source]
dtype

alias of builtins.float

class MDAnalysis.core.topologyattrs.Radii(values, guessed=False)[source]

Radii for each atom

dtype

alias of builtins.float

class MDAnalysis.core.topologyattrs.RecordTypes(values, guessed=False)[source]

For PDB-like formats, indicates if ATOM or HETATM

Defaults to ‘ATOM’

Changed in version 0.20.0: Now stores array of dtype object rather than boolean mapping

dtype

alias of builtins.object

class MDAnalysis.core.topologyattrs.Resids(values, guessed=False)[source]

Residue ID

dtype

alias of builtins.int

class MDAnalysis.core.topologyattrs.ResidueAttr(values, guessed=False)[source]
get_atoms(ag)[source]

Get atom attributes for a given AtomGroup

get_residues(rg)[source]

Get residue attributes for a given ResidueGroup

get_segments(sg)[source]

By default, the values for each residue present in the set of segments are returned in a single array. This behavior can be overriden in child attributes.

set_atoms(ag, values)[source]

Set atom attributes for a given AtomGroup

set_residues(rg, values)[source]

Set residue attributes for a given ResidueGroup

set_segments(sg, values)[source]

Set segmentattributes for a given SegmentGroup

class MDAnalysis.core.topologyattrs.Resindices[source]

Globally unique resindices for each residue in the group.

If the group is an AtomGroup, then this gives the resindex for each atom in the group. This unambiguously determines each atom’s residue membership. Resetting these values changes the residue membership of the atoms.

If the group is a ResidueGroup or SegmentGroup, then this gives the resindices of each residue represented in the group in a 1-D array, in the order of the elements in that group.

get_atoms(ag)[source]

Get atom attributes for a given AtomGroup

get_residues(rg)[source]

Get residue attributes for a given ResidueGroup

get_segments(sg)[source]

Get segment attributes for a given SegmentGroup

set_residues(rg, values)[source]

Set residue attributes for a given ResidueGroup

class MDAnalysis.core.topologyattrs.Resnames(values, guessed=False)[source]
dtype

alias of builtins.object

sequence(**kwargs)[source]

Returns the amino acid sequence.

The format of the sequence is selected with the keyword format:

format

description

‘SeqRecord’

Bio.SeqRecord.SeqRecord (default)

‘Seq’

Bio.Seq.Seq

‘string’

string

The sequence is returned by default (keyword format = 'SeqRecord') as a Bio.SeqRecord.SeqRecord instance, which can then be further processed. In this case, all keyword arguments (such as the id string or the name or the description) are directly passed to Bio.SeqRecord.SeqRecord.

If the keyword format is set to 'Seq', all kwargs are ignored and a Bio.Seq.Seq instance is returned. The difference to the record is that the record also contains metadata and can be directly used as an input for other functions in Bio.

If the keyword format is set to 'string', all kwargs are ignored and a Python string is returned.

Example: Write FASTA file

Use Bio.SeqIO.write(), which takes sequence records:

import Bio.SeqIO

# get the sequence record of a protein component of a Universe
protein = u.select_atoms("protein")
record = protein.sequence(id="myseq1", name="myprotein")

Bio.SeqIO.write(record, "single.fasta", "fasta")

A FASTA file with multiple entries can be written with

Bio.SeqIO.write([record1, record2, ...], "multi.fasta", "fasta")
Parameters

  • format (string, optional) –

    • "string": return sequence as a string of 1-letter codes

    • "Seq": return a Bio.Seq.Seq instance

    • "SeqRecord": return a Bio.SeqRecord.SeqRecord instance

    Default is "SeqRecord"

  • id (optional) – Sequence ID for SeqRecord (should be different for different sequences)

  • name (optional) – Name of the protein.

  • description (optional) – Short description of the sequence.

  • kwargs (optional) – Any other keyword arguments that are understood by class:Bio.SeqRecord.SeqRecord.

Raises

  • ValueError –

  • 1-letter IUPAC protein amino acid code; make sure to only –

  • select protein residues. –

  • TypeError –

New in version 0.9.0.

class MDAnalysis.core.topologyattrs.Resnums(values, guessed=False)[source]
dtype

alias of builtins.int

class MDAnalysis.core.topologyattrs.Segids(values, guessed=False)[source]
dtype

alias of builtins.object

class MDAnalysis.core.topologyattrs.Segindices[source]

Globally unique segindices for each segment in the group.

If the group is an AtomGroup, then this gives the segindex for each atom in the group. This unambiguously determines each atom’s segment membership. It is not possible to set these, since membership in a segment is an attribute of each atom’s residue.

If the group is a ResidueGroup or SegmentGroup, then this gives the segindices of each segment represented in the group in a 1-D array, in the order of the elements in that group.

get_atoms(ag)[source]

Get atom attributes for a given AtomGroup

get_residues(rg)[source]

Get residue attributes for a given ResidueGroup

get_segments(sg)[source]

Get segment attributes for a given SegmentGroup

set_segments(sg, values)[source]

Set segmentattributes for a given SegmentGroup

class MDAnalysis.core.topologyattrs.SegmentAttr(values, guessed=False)[source]

Base class for segment attributes.

get_atoms(ag)[source]

Get atom attributes for a given AtomGroup

get_residues(rg)[source]

Get residue attributes for a given ResidueGroup

get_segments(sg)[source]

Get segment attributes for a given SegmentGroup

set_atoms(ag, values)[source]

Set atom attributes for a given AtomGroup

set_residues(rg, values)[source]

Set residue attributes for a given ResidueGroup

set_segments(sg, values)[source]

Set segmentattributes for a given SegmentGroup

class MDAnalysis.core.topologyattrs.Tempfactors(values, guessed=False)[source]

Tempfactor for atoms

dtype

alias of builtins.float

class MDAnalysis.core.topologyattrs.TopologyAttr(values, guessed=False)[source]

Base class for Topology attributes.

Note

This class is intended to be subclassed, and mostly amounts to a skeleton. The methods here should be present in all TopologyAttr child classes, but by default they raise appropriate exceptions.

attrname

the name used for the attribute when attached to a Topology object

Type

str

singular

name for the attribute on a singular object (Atom/Residue/Segment)

Type

str

per_object

If there is a strict mapping between Component and Attribute

Type

str

dtype

Type to coerce this attribute to be. For string use ‘object’

Type

int/float/object

top

handle for the Topology object TopologyAttr is associated with

Type

Topology

copy()[source]

Return a deepcopy of this attribute

classmethod from_blank(n_atoms=None, n_residues=None, n_segments=None, values=None)[source]

Create a blank version of this TopologyAttribute

Parameters

  • n_atoms (int, optional) – Size of the TopologyAttribute atoms

  • n_residues (int, optional) – Size of the TopologyAttribute residues

  • n_segments (int, optional) – Size of the TopologyAttribute segments

  • values (optional) – Initial values for the TopologyAttribute

get_atoms(ag)[source]

Get atom attributes for a given AtomGroup

get_residues(rg)[source]

Get residue attributes for a given ResidueGroup

get_segments(sg)[source]

Get segment attributes for a given SegmentGroup

property is_guessed

Bool of if the source of this information is a guess

set_atoms(ag, values)[source]

Set atom attributes for a given AtomGroup

set_residues(rg, values)[source]

Set residue attributes for a given ResidueGroup

set_segments(sg, values)[source]

Set segmentattributes for a given SegmentGroup