def pdbContact(pdb,all=False):
"""
Generate array of all atom-atom distances in a pdb file. Defaults to only
look at CA atoms
"""
pdb = other.getPolymerAtoms(pdb)
pdb = other.removeRotamers(pdb)
# Remove non-CA atoms
if not all:
pdb = [l for l in pdb if l[13:15] == "CA"]
coord = [[float(l[30+8*i:38+8*i]) for i in range(3)] for l in pdb]
dist = geometry.calcDistances(coord)
return dist
def pdbSeq(pdb,use_atoms=False):
"""
Parse the SEQRES entries in a pdb file. If this fails, use the ATOM
entries. Return dictionary of sequences keyed to chain and type of
sequence used.
"""
# Try using SEQRES
seq = [l for l in pdb if l[0:6] == "SEQRES"]
if len(seq) != 0 and not use_atoms:
seq_type = "SEQRES"
chain_dict = dict([(l[11],[]) for l in seq])
for c in chain_dict.keys():
chain_seq = [l[19:70].split() for l in seq if l[11] == c]
for x in chain_seq:
chain_dict[c].extend(x)
# Otherwise, use ATOM
else:
# Check to see if there are multiple models. If there are, only look
# at the first model.
models = [i for i, l in enumerate(pdb) if l.startswith("MODEL")]
if len(models) > 1:
pdb = pdb[models[0]:models[1]]
seq_type = "ATOM "
atoms = other.getPolymerAtoms(pdb)
#atoms = other.removeRotamers(atoms)
atoms = [l for l in atoms if l[13:15] == "CA"]
atoms = other.removeRotamers(atoms)#this second call removes alternate residues, which may not be interleaved. Actually, the first call could be removed.
chain_dict = dict([(l[21],[]) for l in atoms])
for c in chain_dict.keys():
chain_dict[c] = [l[17:20] for l in atoms if l[21] == c]
return chain_dict, seq_type