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. See AtomicSegment, ResidueSegment, MultiResidueSegment, and FeatureSegment.

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 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)[source]

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)[source]

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)[source]

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)[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 also ihm.System.orphan_representations.

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