def parseVerbose(vf, mut):
# parse the verbose file
vfh = open(vf)
contacts = {}
cons_aa = {}
con = None
rotamerpairs = []
for vfh_l in vfh:
if vfh_l.startswith("crwdnes"):
break
# looking for contacts involving the central residue
if vfh_l.startswith("contact"):
if con != None:
# first, dump the last contact
if len(rotamerpairs) > 0:
contacts[con] = rotamerpairs
con = None
rotamerpairs = []
items = vfh_l.strip().split()
if mut.c + "," + str(mut.n) in items:
cenfirst = 0
if items[1] == mut.c + "," + str(mut.n):
cenfirst = 1
contmp, con_aa = items[1 + cenfirst], items[4 + cenfirst]
# only look at contact in the same chain
if not contmp.startswith(mut.c):
continue
else:
con = contmp
cons_aa[con] = con_aa
elif con != None: # reading rotamer pairs under the potential contacts
items = vfh_l.strip().split()
if items[0 + cenfirst * 3] == con_aa:
if items[3 - cenfirst * 3] == PDB.s2t(mut.w):
rotamerpairs.append(mut.w + " " + vfh_l.strip().split()[-1])
if items[3 - cenfirst * 3] == PDB.s2t(mut.m):
rotamerpairs.append(mut.m + " " + vfh_l.strip().split()[-1])
# the last one can be left
if len(rotamerpairs) > 0:
contacts[con] = rotamerpairs
# now go back to the beginning of file and read the denominator
# first look at the denominator of the central residue
vfh.seek(0)
denominator_cen = []
cen = False
for vfh_l in vfh:
if vfh_l.startswith("end of rotamer filtering"):
break
if vfh_l.startswith("position"):
if cen == True:
break
if vfh_l.strip().split()[-1] == mut.c + "," + str(mut.n):
cen = True
elif vfh_l.startswith(PDB.s2t(mut.w)) or vfh_l.startswith(PDB.s2t(mut.m)):
if cen == True:
info = (
vfh_l.strip().split(":")[0]
+ " "
+ " ".join([x.strip().split()[1] for x in vfh_l.strip().split(":")[1].split(";")[:-1]])
)
denominator_cen.append(info)
vfh.seek(0)
denominator_cons = {}
con = None
for vfh_l in vfh:
if vfh_l.startswith("end of rotamer filtering"):
break
if vfh_l.startswith("position"):
if vfh_l.strip().split()[-1] in contacts:
con = vfh_l.strip().split()[-1]
elif con != None:
if vfh_l.startswith(cons_aa[con]):
info = (
vfh_l.strip().split(":")[0]
+ " "
+ " ".join([x.strip().split()[1] for x in vfh_l.strip().split(":")[1].split(";")[:-1]])
)
denominator_cons[con] = info
con = None
return contacts, denominator_cons, denominator_cen
# start and end residue for the peptide chain
pepstart = p.numResidues() + 1
pepend = pepstart + pepchain.numResidues() -1
# add peptide backbone from template to receptor
rec = p + pepchain.copy()
writePDB('_start.pdb', rec)
if args.flip:
# flip the structure
os.system('perl -w '+ SELFBIN + '/flipPeptideChirality.pl _start.pdb _startf.pdb 0')
# mutate the chirality of the residues on the domain
domainseq = []
for dres in p.iterResidues():
dresname = PDB.s2t(PDB.t2s(dres.getResname()))
if dresname != 'GLY':
domainseq.append('D'+ dresname)
else:
domainseq.append(dresname)
pdz.normalMut('_startf.pdb', range(1, pepstart), domainseq, '_startf1.pdb')
# mutate the residue on peptide
pepseq = []
for pres in args.pseq:
if len(pres) == 4: # if should be a D-residue, make the name to be a L-residue (since the domain has been flipped)
pepseq.append(pres[1:])
if len(pres) == 3:
if pres != 'GLY':
pepseq.append('D' + pres)
else:
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()