The ihm.representation
Python module¶
Classes for handling representation of the system during modeling.
- class ihm.representation.Segment[source]¶
Base class for part of a
Representation
. SeeAtomicSegment
,ResidueSegment
,MultiResidueSegment
, andFeatureSegment
.
- class ihm.representation.AtomicSegment(asym_unit, rigid, starting_model=None, description=None)[source]¶
Part of the system modeled atomistically, stored in a
Representation
.- Parameters:
asym_unit (
AsymUnit
orAsymUnitRange
) – The asymmetric unit (or part of one) that this segment represents.rigid (bool) – Whether internal coordinates of the segment were fixed during modeling.
starting_model (
StartingModel
) – initial coordinates used for the segment (or None).description (str) – Additional text describing this segment.
- class ihm.representation.ResidueSegment(asym_unit, rigid, primitive, starting_model=None, description=None)[source]¶
Part of the system modeled as a set of residues, stored in a
Representation
.- Parameters:
asym_unit (
AsymUnit
orAsymUnitRange
) – The asymmetric unit (or part of one) that this segment represents.rigid (bool) – Whether internal coordinates of the segment were fixed during modeling.
primitive (str) – The type of object used to represent this segment (sphere/gaussian/other).
starting_model (
StartingModel
) – initial coordinates used for the segment (or None).description (str) – Additional text describing this segment.
- class ihm.representation.MultiResidueSegment(asym_unit, rigid, primitive, starting_model=None, description=None)[source]¶
Part of the system modeled as a single object representing a range of residues, stored in a
Representation
.- Parameters:
asym_unit (
AsymUnit
orAsymUnitRange
) – The asymmetric unit (or part of one) that this segment represents.rigid (bool) – Whether internal coordinates of the segment were fixed during modeling.
primitive (str) – The type of object used to represent this segment (sphere/gaussian/other).
starting_model (
StartingModel
) – initial coordinates used for the segment (or None).description (str) – Additional text describing this segment.
- class ihm.representation.FeatureSegment(asym_unit, rigid, primitive, count, starting_model=None, description=None)[source]¶
Part of the system modeled as a number of geometric features, stored in a
Representation
.- Parameters:
asym_unit (
AsymUnit
orAsymUnitRange
) – The asymmetric unit (or part of one) that this segment represents.rigid (bool) – Whether internal coordinates of the segment were fixed during modeling.
primitive (str) – The type of object used to represent this segment (sphere/gaussian/other).
count (int) – The number of objects used to represent this segment.
starting_model (
StartingModel
) – initial coordinates used for the segment (or None).description (str) – Additional text describing this segment.
- class ihm.representation.Representation(elements=(), name=None, details=None)[source]¶
Part of the system modeled as a set of geometric objects, such as spheres or atoms. This is implemented as a simple list of
Segment
objects.- Parameters:
elements (sequence) – Initial set of segments.
name (str) – A short descriptive name.
details (str) – A longer description of the representation.
Typically a Representation is assigned to a
Model
. See alsoihm.System.orphan_representations
.Multiple representations of the same system are possible (multi-scale).