Code author: Niklaus Johner <niklaus.johner@a3.epfl.ch>
This module contains functions to analyze the secondary structure of proteins It uses DSSP, which has to be installed and in the path for OpenStructure
This function calls DSSP to assign the secondary structure to a protein.
This function calculates the secondary structure of a protein for each frame in a trajectory. Inputs: t : Trajectory prot : EntityView for which the secondary structure will be computed first : First frame to be analyzed last : Last frame to be analyzed stride: Number of frames skipped between two analyzed frames Outputs: ss_list: A list of lists. Each element of ss_list is a list of letters corresponding to the secondary structure of a residue for the different frames of the trajectory.
This function takes a list of lists of secondary structures and plots it. Inputs: ss_list: A list of lists of secondary structures as obtained from AnalyzeSecondaryStructure, see SecStrucColorMap. color_dict: a dicitonary mapping a color given in rgb to each secondary structure type title: The title of the plot labels:the labels shown in the colorbar l,b,r,t:the left, bottom,top and right relative positions for the axes in the plot
This function takes in a list ssl of standard dssp secondary structure letters (G,H,I,E,B,T,C,S) and returns a simplified list where each element is assigned to the broader category of helix, beta or coil (H,E,C). So it basically maps G,H and I to H; E and B to E; T,C and S to C.
This function takes a list of lists of secondary structures as obtained from AnalyzeSecondaryStructure and reassigns each element to the broader categories of Helix, Extended and Coil (see SimplifySecStructure) Inputs: ss_list: A list of lists of secondary structures as obtained from AnalyzeSecondaryStructure, see SecStrucColorMap. Outpu: ss_list: Simplified list of lists of secondary structures
This function assigns the secondary structure to the EntityView prot and then searches for structural elements and returns a list of index pairs corresponding to the begining and end of the secondary structure elements. Inputs: prot: EntityView for which the secondary structure should be analyzed Output: A list of tuples. Each tuple corresponds to a structural element and has three elements: the start index, the end index and a letter indicating the secondary structure of that structural element. For example: [(1,5,’H’),(8,15,’E’)] means that there is a helix spanning prot.residues[1:6] and a beta strand prot.residues[8:16].