moleculekit.projections.metricsecondarystructure module

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

Bases: 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.

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