SwiftStride

This is a Swift adaptation of STRIDE. It is meant to be used with Swift projects as a Package dependency.

For more information about the original implementation, visit the GitHub repo from MDAnalysis.

https://github.com/MDAnalysis/stride

Installation

Add the URL of this repository to your Xcode Project.

https://github.com/chdominguez/stride_swift.git

Import

To use the module import SwiftStride

import SwiftStride

Usage

SwiftStride will return an amino acid array containing the prediction data (secondary structure, angles...) provided a file URL pointing to a PDB file.

let aa = Stride.predict(from: fileURL)

You can apply Stride arguments via the arguments parameter. Please refer to the original repository for documentation about the valid arguments.

let arg = ["-o", "-h"]

let aa = Stride.predict(from: fileURL, arguments: arg)

The output can be printed to the console setting to true the showReport parameter

let aa = Stride.predict(from: fileURL, showReport: true)

The returned array aa is filled with Residue types from which you can extract the predicted information.

public struct Residue {
    // Default values:
    public let type: AminoAcid
    public let structure: SecondaryStructure
    public let phi: Float
    public let psi: Float
    public let area: Float
}

About STRIDE:

STRIDE [1] is a program to recognize secondary structural elements in proteins from their atomic coordinates. It performs the same task as DSSP by Kabsch and Sander [2] but utilizes both hydrogen bond energy and mainchain dihedral angles rather than hydrogen bonds alone. It relies on database-derived recognition parameters with the crystallographers' secondary structure definitions as a standard-of- truth. Please see Frishman and Argos [1] for detailed description of the algorithm.

1. Frishman,D & Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins: structure, function and genetics, 23,
   566-579.

2. Kabsch,W. & Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22: 2577-2637.