Stride Tools

This module defines functions for executing STRIDE program and parsing its output.

execSTRIDE(pdb, outputname=None, outputdir=None)[source]

Execute STRIDE program for given pdb. pdb can be an identifier or a PDB file path. If pdb is a compressed file, it will be decompressed using Python gzip library. When no outputname is given, output name will be pdb.stride. .stride extension will be appended automatically to outputname. If outputdir is given, STRIDE output and uncompressed PDB file will be written into this folder. Upon successful execution of stride pdb > out command, output filename is returned.

For more information on STRIDE see If you benefited from STRIDE, please consider citing [DF95].

[DF95]Frishman D, Argos P. Knowledge-Based Protein Secondary Structure Assignment. Proteins 1995 23:566-579.
parseSTRIDE(stride, ag)[source]

Parse STRIDE output from file stride into AtomGroup instance ag. STRIDE output file must be in the new format used from July 1995 and onwards. When stride file is parsed, following attributes are added to ag:

  • stride_resnum: STRIDE’s sequential residue number, starting at the first residue actually in the data set.
  • stride_phi, stride_psi: peptide backbone torsion angles phi and psi
  • stride_area: residue solvent accessible area

Perform STRIDE calculations and parse results. STRIDE data is returned in an AtomGroup instance. See also execSTRIDE() and parseSTRIDE().