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
def show_vertex(self, vertex: Graph.vertex) -> Chimera:
"""
Shows the protein that corresponds to that specific vertex with the
fragment colored in red
:param vertex: A Graph.vertex object. The domain to be shown,
:return: A Chimera object with an internal representation of the fragment
"""
graph = self.graph
domain = graph.vp.domain[vertex]
start = int(round(np.mean(graph.vp.start[vertex])))
end = int(round(np.mean(graph.vp.end[vertex])))
domain_path = get_SCOP_domain(domain)
mol = Chimera(filename=domain_path, validateElements=False)
mol.renumberResidues()
mol.reps.add(sel='protein', style='NewCartoon', color=8)
mol.reps.add(sel=f"protein and resid '{start}' to '{end}'",
style='NewCartoon',
color=1)
mol.view(name=domain)
return mol