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
