classProtein

Functions

x.get_sequence()

returns the sequence as a string of single letter amino acid codes.

x.print_sequence()

prints the sequence as a string of single letter amino acid codes.

x.fill_pseudo_sidechains(type=1)

if type 1, calculate the center of mass of each sidechain and store as each residue's .pseudo_sidechain attribute. If type 0, calculate the bisector of the triangle formed between a query residue's alpha carbon and the two adjacent alpha carbons. Follow the line made by the bisector and the query alpha carbon two angstroms past the carbon. That point gets stored as the residue's .pseudo_sidechain attribute. This is useful for approximating sidechain center of mass when residue type is not important, or when only alpha carbon atoms are available.

x.fill_neighbors_lists(qscore=0.35, dist_thresh=14.0, force_rewrite=0)

This function attempts to extract, for each residue, other residues whose sidechains are unshielded from the query residue's sidechain. The neighboring residues are stored in a list for each residue, called .neighbors. Unshielded residues are useful for describing the chemical environment of a central residue. Unshielded pairs tend to interact in the same functions as one another. Lower qscore values give larger patches (down to about 0.05), and higher values give smaller patches (up to about 2-3). dist_thresh can be used to give a maximum distance another pseudo-sidechain is allowed to be before being unavailable. fill_neighbors_lists creates a file for fast re-loading of the contacts. The file is the standard system.get_filename_by_extension call, with a '.ctc' extension.

x.assign_ss_from_header()

Use the header lines from the pdb file (available in the System object) to assign secondary structure to each residue. The information is stored in each residue's .features dictionary, under the index 'SS'.

x.assign_asa(solvent_radius, point_count, forced_rewrite=0)

calculate the percent solvent accessability for each residue, and store in the residue's .features dictionary, under 'asa' and 'sidechain_asa'.

x.get_core_alpha_carbons(core_cutoff=8, neighbor_thresh=3)

Makes a quick calculation to determine whether a residue is 'core' or not. Depends on .fill_neighbors_lists having been run already. First the function passes through all residues, marking those with > core_cutoff neighbors present in their .neighbors attributes. Then, any marked residue that is neighbors with neighbor_thresh or greater marked residues is marked as core. The core alpha carbons are returned in a list.

x.assign_core_atom_distances(core_cutoff, neighbor_thresh,mindist,maxdist)

Assigns core residues, and builds a futamura hash that lists only these. Each core central atom recieves a list of other core central atoms between mindist and maxdist away.