def fastaToCNSThreeLetter(seqRecord,width=10): seqStr = seqRecord.seq.tostring() L = len(seqStr) outSeq = [PP.one_to_three(i) for i in seqStr] numbered = zip(outSeq,count(0)) groups = [[j[0] for j in i[1]] for i in groupby(numbered,lambda x:x[1]/width)] joined = '\n'.join([' '.join(one_group) for one_group in groups]) + '\n' return joined
def GetList(protein, mincount, measure_cutoffs, thresh=9.0, loss=True):
"""Get list with SSP positions, AA in three letter code.
If loss==False, use complement for gain predictions. """
pos = GetNetworkExtremes(protein, mincount, measure_cutoffs, thresh=thresh)
if not loss:
total_pos = functional_data[protein].columns
complement = [i for i in total_pos if i not in pos]
pos = complement
positions = map(lambda x: pp.one_to_three(x[0]) + x[1:], pos)
return list(positions)
def write_pdb_tleap(output_filepath, sequence, phi, psi):
leapfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
leapfile.write('source leaprc.ff14SB\n')
sequence = ' '.join([Polypeptide.one_to_three(aa) for aa in sequence])
leapfile.write('system = sequence {' + sequence + '}\n')
for i in range(len(phi)):
leapfile.write((
'impose system {%s} '
'{{"N" "CA" "C" "N" %s} '
'{"C" "N" "CA" "C" %s}}\n') % (
i + 1,
phi[i],
psi[i],
)
)
leapfile.write('savepdb system ' + output_filepath)
leapfile.write('\nquit\n')
leapfile.close()
subprocess.check_call(['tleap', '-f', leapfile.name])
os.remove(leapfile.name)
