molsysmt.structure.get_secondary_structure#

molsysmt.structure.get_secondary_structure(molecular_system, selection='all', structure_indices='all', simplified=True, syntax='MolSysMT', engine='MDTraj')[source]#

Secondary structure assignment per residue over one or more structures.

Parameters:

  • molecular_system (molecular system) – Molecular system in any supported MolSysMT format.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • structure_indices (int, list, tuple, or numpy.ndarray, default='all') – Structure indices (0-based) to include or process.

  • simplified (object, default=True) – Argument simplified.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

  • engine (object, default='MDTraj') – Argument engine.

Returns:

Secondary structure code per residue per structure.

Simplified codes (simplified=True):

  • 'H' : Helix (alpha, 3/10, or pi).

  • 'E' : Strand (extended or isolated beta-bridge).

  • 'C' : Coil (turn, bend, or loop).

  • 'NA' : Non-protein residue.

Full DSSP codes (simplified=False):

  • 'H' : Alpha helix.

  • 'G' : 3/10 helix.

  • 'I' : Pi helix.

  • 'E' : Extended strand.

  • 'B' : Isolated beta-bridge.

  • 'T' : Hydrogen-bonded turn.

  • 'S' : Bend.

  • ' ' : Loop or irregular element.

  • 'NA' : Non-protein residue.

Return type:

numpy.ndarray, shape (n_structures, n_groups), dtype ‘U2’

Raises:

NotImplementedMethodError – If an unsupported engine is requested.

Added in version 1.0.0.