9.2.3. 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.
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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.
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class
MDAnalysis.core.topologyattrs.
AtomAttr
(values, guessed=False)[source]¶ Base class for atom attributes.
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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.
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class
MDAnalysis.core.topologyattrs.
Atomnames
(values, guessed=False)[source]¶ Name for each atom.
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chi1_selection
(residue)[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
- AtomGroup – 4-atom selection in the correct order. If no CB and/or CG is found
then this method returns
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omega_selection
(residue)[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
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class
MDAnalysis.core.topologyattrs.
Bfactors
(values, guessed=False)[source]¶ Crystallographic B-factors in A**2 for each atom
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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.
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class
MDAnalysis.core.topologyattrs.
ChainIDs
(values, guessed=False)[source]¶ ChainID per atom
Note
This is an attribute of the Atom, not Residue or Segment
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class
MDAnalysis.core.topologyattrs.
Dihedrals
(values, types=None, guessed=False, order=None)[source]¶ A connection between four sequential atoms
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class
MDAnalysis.core.topologyattrs.
Impropers
(values, types=None, guessed=False, order=None)[source]¶ An imaginary dihedral between four atoms
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class
MDAnalysis.core.topologyattrs.
ResidueAttr
(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.
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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.
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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.
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class
MDAnalysis.core.topologyattrs.
SegmentAttr
(values, guessed=False)[source]¶ Base class for segment attributes.
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class
MDAnalysis.core.topologyattrs.
Tempfactors
(values, guessed=False)[source]¶ Tempfactor for atoms
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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
¶ str – the name used for the attribute when attached to a
Topology
object
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singular
¶ str – name for the attribute on a singular object (Atom/Residue/Segment)
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per_object
¶ str – If there is a strict mapping between Component and Attribute
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top
¶ Topology – handle for the Topology object TopologyAttr is associated with
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is_guessed
¶ Bool of if the source of this information is a guess
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