Overview

This package uses STRIDE or DSSP to compute secondary structures of proteins from their structure files:

• STRIDE supports reading PDB files.
• DSSP supports reading both PDB and mmCIF files.

Secondary structure classes

The outputs of STRIDE or DSSP follow the convention of secondary strucure codes, which are:

See the DSSP secondary structure classification for further information.

Data structure

The outputs of the secondary structure calculations are vectors of SSData elements, with the following data, for each residue:

• resname::String - residue name
• chain::String - chain identifier
• resnum::Int - residue number
• sscode::String - secondary structure code
• phi::Float64 - phi dihedral angle
• psi::Float64 - psi dihedral angle

For example:

julia> using ProteinSecondaryStructures

julia> pdbfile = ProteinSecondaryStructures.Testing.examples[1].filename;

julia> ss = stride_run(pdbfile);

julia> ss[1]
SSData("MET", "A", 1, "C", 360.0, 150.62)

julia> ss[1].sscode
"C"

julia> ss_name(ss[1].sscode)
"coil"

Reference structure

SSData