def get_orig_seq(res_path, orig_pdb_path, renum_pdb_path):
print "Extracting residue position from " + res_path + "..."
res_lines = filelines2list(res_path)
residues = [int(line.strip()) for line in res_lines]
orig = get_pdb_info(orig_pdb_path)
renum = get_pdb_info(renum_pdb_path)
to_print = set()
for residue in residues:
renum_aa = renum[residue - 1]
for orig_aa in orig:
if renum_aa == orig_aa:
to_print.add(orig_aa)
to_print_tuples = list()
for res in to_print:
try:
to_print_tuples.append((res.chainID, int(res.position), res.string_name, res.char_name))
except:
to_print_tuples.append((res.chainID, res.position, res.string_name, res.char_name))
to_print_tuples.sort()
for t in to_print_tuples:
print t[2] + " " + t[0] + " " + str(t[1])
for t in to_print_tuples:
sys.stdout.write(t[3])
print ""
def create_res(pdb_orig_path, pdb_renum_path, out_res_path, positions):
orig = get_pdb_info(pdb_orig_path)
renum = get_pdb_info(pdb_renum_path)
# Adding all ligand residues we're interesting in mutating to this set()
# and converting them to residues in new_res
res = set()
new_res = set()
for position in positions:
if isinstance(position, tuple):
(chain, start, end) = position
i = 0
while not (orig[i].chainID == chain and orig[i].position == start):
i += 1
while not (orig[i].chainID == chain and orig[i].position == end):
res.add(orig[i])
i += 1
res.add(orig[i])
elif len(position) == 1:
inchain = False
for residue in orig:
if residue.chainID == position:
inchain = True
res.add(residue)
else:
if inchain:
break
else:
for residue in orig:
if residue.chainID == position[0] and residue.position == position[1:]:
res.add(residue)
break
for residue in res:
i = 0
for r in renum:
if (
r.atom_dict["CA"].coordinates == residue.atom_dict["CA"].coordinates
and r.int_name == residue.int_name
and r.chainID == residue.chainID
):
new_res.add(r)
break
out = open(out_res_path, "w")
positions = [int(residue.position) for residue in new_res]
positions.sort()
for position in positions:
out.write(str(position) + "\n")
out.close()
def renumber(start_res_num, start_atom_num, chains, in_pdb, out_pdb):
RN = start_res_num
AN = start_atom_num
residues = get_pdb_info(in_pdb)
new_residues = list()
# Putting non-mutating chains first
for residue in residues:
if residue.chainID in chains:
continue
residue.position = str(RN)
for atom in residue.atoms:
atom.num = AN
AN += 1
RN += 1
new_residues.append(residue)
# Put mutating chains second
for residue in residues:
if residue.chainID not in chains:
continue
residue.position = str(RN)
for atom in residue.atoms:
atom.num = AN
AN += 1
RN += 1
new_residues.append(residue)
print_pdb(new_residues, out_pdb)
