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def renum_pdb_str(pdb_str, Ls=None, renum=True, offset=1): | |
from string import ascii_uppercase, ascii_lowercase | |
assert len(Ls) == 2 | |
Ls = [int(i) for i in Ls] | |
alphabet_list = list(ascii_uppercase+ascii_lowercase) | |
if Ls is not None: | |
L_init = 0 | |
new_chain = {} | |
for L,c in zip(Ls, alphabet_list): | |
new_chain.update({i:c for i in range(L_init,L_init+L)}) | |
L_init += L | |
n,num,pdb_out = 0,offset,[] | |
resnum_ = None | |
chain_ = None | |
new_chain_ = new_chain[0] | |
for line in pdb_str.split("\n"): | |
if line[:4] == "ATOM": | |
chain = line[21:22] | |
resnum = int(line[22:22+5]) | |
if resnum_ is None: resnum_ = resnum | |
if chain_ is None: chain_ = chain | |
if resnum != resnum_ or chain != chain_: | |
num += (resnum - resnum_) | |
n += 1 | |
resnum_,chain_ = resnum,chain | |
if Ls is not None: | |
if new_chain[n] != new_chain_: | |
num = offset | |
new_chain_ = new_chain[n] | |
N = num if renum else resnum | |
if Ls is None: pdb_out.append("%s%4i%s" % (line[:22],N,line[26:])) | |
else: pdb_out.append("%s%s%4i%s" % (line[:21],new_chain[n],N,line[26:])) | |
pdb_str = "\n".join(pdb_out) | |
return pdb_str |
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