def calc_dist_matrix(chimera: Chimera = None, filename: str = None, selection: str = 'residue', type='contacts', plot=False): """ Returns a matrix of C-alpha distances for a given pdb :param chimera: A Chimera object with n residues. :param filename: path to a pdb file :param selection: How to compute the distance. 'residue' (the closest two :param type: between contacts (contact map when distances are below 8 armstrongs) or distances atoms between two residues) or 'alpha' distance of the alpha carbons. :param plot: whether to plot the distance matrix. Default is False :return: matrix. np.array. An n by n distance matrix. """ if chimera and filename: raise ValueError("Only a Chimera object or the path to a pdb file must be specified") if not chimera and not filename: raise ValueError("At least a Chimera object or the path to a pdb file must be specified") if filename: chimera = Chimera(filename=filename) if selection == 'residue': metr = MetricSelfDistance("protein", groupsel="residue", metric="distances", pbc=False) mapping = metr.getMapping(chimera) a = metr.project(chimera) matrix, _, _ = contactVecToMatrix(a[0], mapping.atomIndexes) elif selection == 'alpha': metr = MetricSelfDistance("protein and name CA", metric="distances", pbc=False) a = metr.project(chimera) mapping = metr.getMapping(chimera) matrix, _, _ = contactVecToMatrix(a, mapping.atomIndexes) else: raise ValueError("Specify a selection type: 'residue' or 'atom'") if type == "contacts": matrix = matrix < 8 elif type != "contacts" and type != "distances": raise ValueError("Please select contact type between 'contacts' or distances") if plot: fig = plt.figure(figsize=(12, 12)) ax = fig.add_subplot(111) cmap = 'binary' cax = ax.imshow(matrix, cmap=matplotlib.cm.get_cmap(cmap), interpolation='nearest', origin="lower") if type == 'distances': cmap = 'gist_rainbow' cax = ax.imshow(matrix, cmap=matplotlib.cm.get_cmap(cmap), interpolation='nearest', origin="lower") cbar = fig.colorbar(cax, cmap=matplotlib.cm.get_cmap(cmap)) plt.xlabel('xlabel', fontsize=24) plt.ylabel('ylabel', fontsize=24) plt.xticks(fontsize=22) plt.yticks(fontsize=22) plt.xlabel("Residue index") plt.ylabel("Residue index") return matrix
def calc_contact_order(chimera: Chimera = None, filename: str = None, diss_cutoff: int = 8): """ The contact order of a protein is a measure of the locality of the inter-amino acid contacts in the native folded state. It is computed as the average seqeuence distance between residues that form contacts below a threshold in the folded protein divided by the total length of the protein" :param chimera: A Chimera object with n residues. :param filename: path to a pdb file :param diss_cutoff: The maximum distance in Armstrong between two residues to be in contact, default 8 Angstroms :return: the contact order (%) """ if chimera and filename: raise ValueError("Only a Chimera object or the path to a pdb file must be specified") if not chimera and not filename: raise ValueError("At least a Chimera object or the path to a pdb file must be specified") if filename: chimera = Chimera(filename=filename) chimera.renumberResidues() metr = MetricSelfDistance("protein and noh", groupsel="residue", metric="contacts", threshold=diss_cutoff, pbc=False) a = metr.project(chimera) mapping = metr.getMapping(chimera) matrix, _, _ = contactVecToMatrix(a[0], mapping.atomIndexes) triang = np.triu(matrix) idx1, idx2 = np.where(triang) total_contacts = len(idx1) total_residues = chimera.numResidues summation = np.sum(idx2 - idx1) co = 1 / (total_contacts * total_residues) * summation print(f"Contact order is {co*100} %") return co * 100