htmd.projections.metricsecondarystructure module

class htmd.projections.metricsecondarystructure.MetricSecondaryStructure(sel='protein', simplified=True, integer=True)

Bases: htmd.projections.projection.Projection

Calculates the secondary structure of the protein. DSSP implementation and documentation taken from MDtraj.

Parameters:
  • sel (str) – Atom selection string for the protein. See more here
  • simplified (bool) – Uses the simplified 3-letter code
  • integer (bool) – Use integers instead of letter codes.

Notes

The simplified DSSP codes are:
  • ‘C’ : Coil. Either of the ‘T’, ‘S’ or ‘ ‘ codes. Integer code: 0
  • ‘E’ : Strand. Either of the ‘E’, or ‘B’ codes. Integer code: 1
  • ‘H’ : Helix. Either of the ‘H’, ‘G’, or ‘I’ codes. Integer code: 2
The full DSSP assignment codes are:
  • ‘H’ : Alpha helix. Integer code: 3
  • ‘B’ : Residue in isolated beta-bridge. Integer code: 4
  • ‘E’ : Extended strand, participates in beta ladder. Integer code: 5
  • ‘G’ : 3-helix (3/10 helix). Integer code: 6
  • ‘I’ : 5 helix (pi helix). Integer code: 7
  • ‘T’ : hydrogen bonded turn. Integer code: 8
  • ‘S’ : bend. Integer code: 9
  • ‘ ‘ : Loops and irregular elements. Integer code: 10

A special ‘NA’ code will be assigned to each ‘residue’ in the topology which isn’t actually a protein residue (does not contain atoms with the names ‘CA’, ‘N’, ‘C’, ‘O’), such as water molecules that are listed as ‘residue’s in the topology.

Returns:metr – Returns a MetricData object containing the metrics calculated
Return type:MetricData object
copy()

Produces a deep copy of the object

getMapping(mol)

Returns the description of each projected dimension.

Parameters:mol (Molecule object) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.
Returns:map – A DataFrame containing the descriptions of each dimension
Return type:DataFrame object
project(mol)

Project molecule.

Parameters:mol (Molecule) – A Molecule object to project.
Returns:data – An array containing the projected data.
Return type:np.ndarray