Exemplo n.º 1
0
    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(
Exemplo n.º 2
0
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