with open(design) as des_pdb, open("../pdb/%s.pdb" % scaffold) as wt_pdb:
wt = [l.split()[3] for l in wt_pdb if "CA" in l and l.startswith("ATOM")]
d = [l.split()[3] for l in des_pdb if "CA" in l and l.startswith("ATOM")]
diff = zip(wt, d)
m = [(j[0], i, j[1]) for i, j in enumerate(diff) if j[0] != j[1]]
with open("nucleotide/%s.fasta" % scaffold) as fn:
cds = "".join([line.strip() for line in fn])
codons = [cds[i : i + 3] for i in range(0, len(cds), 3)]
l = []
for switch in m:
old, i, new = switch
new1, old1 = (THREE_to_one(new), THREE_to_one(old))
ori = one_to_THREE(aa[codons[i]])
if old == ori:
codons[i] = ecoli_codon[new1].upper()
l += [i]
else:
print "error: mismatch when trying", old, i, new
if l:
e = rc("".join(codons[min(l) - 5 : max(l) + 6]))
e = re.sub(r"([atcg]{15})[atcg]{0,}([atcg]{15})", r"\1,\2", e)
handle = "+".join(["%s%s%s" % (THREE_to_one(s[0]), s[1], THREE_to_one(s[2])) for s in m])
orders += [{"name": handle, "oligos": [{"sequence": ee for ee in e.split(",")}]}]
# transcriptic output format
print json.dumps(
from core.db.amino_acid import one_to_THREE
with open( 'bagel.pdb' ) as wt:
wt = wt.readlines()
with open( 'list.txt' ) as l:
l = l.readlines()
for line in l:
with open( line.strip() + '.pdb' , 'w') as target:
orig, i, new = line[0], line[1:-2], line[-2] #-2 since there's a newline char
for atom in wt:
atom = atom.strip()
atm = atom.split()
if atm[0] == 'ATOM' or atm[0] == 'HETATM':
if atm[5] != i:
print( atom, file = target )
else:
if atm[2] in [ 'N', 'C', 'CA', 'O' ]:
print( atom[:17] + one_to_THREE(new) + atom[20:], file=target )
else:
pass #don't print anything
elif atm[0] == 'REMARK':
print( atom , file=target)
else:
pass