The ihm.representation Python module

Classes for handling representation of the system during modeling.

class ihm.representation.Segment

Base class for part of a Representation. See AtomicSegment, ResidueSegment, MultiResidueSegment, and FeatureSegment.

class ihm.representation.AtomicSegment(asym_unit, rigid, starting_model=None, description=None)

Part of the system modeled atomistically, stored in a Representation.

Parameters:

• asym_unit (AsymUnit or AsymUnitRange) – 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)

Part of the system modeled as a set of residues, stored in a Representation.

Parameters:

• asym_unit (AsymUnit or AsymUnitRange) – 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)

Part of the system modeled as a single object representing a range of residues, stored in a Representation.

Parameters:

• asym_unit (AsymUnit or AsymUnitRange) – 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)

Part of the system modeled as a number of geometric features, stored in a Representation.

Parameters:

• asym_unit (AsymUnit or AsymUnitRange) – 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)

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 also ihm.System.orphan_representations.

Multiple representations of the same system are possible (multi-scale).