def computeContacts(mut, contacts, denominator_cons, denominator_cen, outf):
# for each contact, compute two separated values for wild type and mutant
contacts_keys = [x for x in contacts.keys() if x.split(",")[1].isdigit()]
contacts_keys = sorted(contacts_keys, key=lambda x: int(x.split(",")[1]))
idx = 1
outfh = open(outf, "w")
normal_cmap = args.sdir + "/" + mut.p.lower() + ".clean.cmap"
for con in contacts_keys:
numerator_w = sum([float(x.split()[1]) for x in contacts[con] if x.split()[0] == mut.w])
numerator_m = sum([float(x.split()[1]) for x in contacts[con] if x.split()[0] == mut.m])
if numerator_w == 0:
contactdegree_w = 0
else:
denominator_cen_w = [x for x in denominator_cen if x.split()[0] == PDB.s2t(mut.w)][0].split()[1:]
denominator_con = denominator_cons[con].split()[1:]
denominator_w = 0
for p1, p2 in itertools.product(denominator_cen_w[1:], denominator_con[1:]):
denominator_w += float(p1) * float(p2)
denominator_w *= float(denominator_cen_w[0]) * float(denominator_con[0])
contactdegree_w = numerator_w / denominator_w
if numerator_m == 0:
contactdegree_m = 0
else:
denominator_cen_m = [x for x in denominator_cen if x.split()[0] == PDB.s2t(mut.m)][0].split()[1:]
denominator_con = denominator_cons[con].split()[1:]
denominator_m = 0
for p1, p2 in itertools.product(denominator_cen_m[1:], denominator_con[1:]):
denominator_m += float(p1) * float(p2)
denominator_m *= float(denominator_cen_m[0]) * float(denominator_con[0])
contactdegree_m = numerator_m / denominator_m
contactdegree_w, contactdegree_m = format(contactdegree_w, ".4f"), format(contactdegree_m, ".4f")
# also add normal contact degree between these two position:
normal_cond = Fragment.getConD(normal_cmap, mut.c + "," + str(mut.n), con)
normal_cond = format(normal_cond, ".4f")
outstring = (
"\t".join(
map(
str,
[
idx,
mut.p,
mut.c + "," + str(mut.n),
con,
contactdegree_w,
contactdegree_m,
normal_cond,
denominator_cons[con].split()[0],
],
)
)
+ "\n"
)
idx += 1
outfh.write(outstring)
# there could be some contacts which are not detected by two side chains
normal_cons, normal_conress = Fragment.contactList(normal_cmap, mut.c, mut.n, dcut=0.01)
for k in range(len(normal_cons)):
if normal_cons[k] in contacts_keys: # already indexed contact
continue
else:
normal_cond = Fragment.getConD(normal_cmap, mut.c + "," + str(mut.n), normal_cons[k])
normal_cond = format(normal_cond, ".4f")
outstring = (
"\t".join(
map(
str,
[
idx,
mut.p,
mut.c + "," + str(mut.n),
normal_cons[k],
0.0000,
0.0000,
normal_cond,
normal_conress[k],
],
)
)
+ "\n"
)
idx += 1
outfh.write(outstring)
# it would be also nice to have permanent contact, but they are rare and probably captured by environment
outfh.close()
