def sequence_maker(length,
pdb_folder=os.getcwd() + '/pdb',
outputname='allpeps.txt'):
outputname = str(len) + outputname
sequences = {}
total = len(os.listdir(pdb_folder))
count = 0
for i in os.listdir(pdb_folder):
count += 1
print(str(count) + ' out of ' + str(total) +
' completed, Unique Found: ' + str(len(sequences.keys())),
end='\r')
file = pd.parsePDB(pdb_folder + '/' + i)
if file is None:
os.remove(pdb_folder + '/' + i)
continue
seq = pp.find_seq(file)[0]
info = m.pep_parser(seq, length)
for mot in info:
if mot != 'full':
for pep in info[mot]:
if pep not in sequences:
sequences[pep] = 1
else:
sequences[pep] += 1
print('Saving Sequences')
with open(outputname, 'w+') as g:
g.write('Sequence,Amount Found \n')
for i in sequences:
g.write(i + ',' + str(sequences[i]) + '\n')
def make_structure(pdb_loc, length, maxValues, temp_value):
# pdb = pdb_loc.split('/')[-1]
seperate_pdb(
pdb_loc,
temp_value) # seperates pdb files by block, see above function
completed = []
# for every seperated file
for i in os.listdir(d + "/temp_pdb/" + str(temp_value)):
try:
# gets atom data
pdb_parsed = pd.parsePDB(d + "/temp_pdb/" + str(temp_value) +
"/" + i)
except:
continue
if pdb_parsed == None:
continue
seq, elements = find_seq(pdb_parsed)
for i in elements:
if i not in ELEMENT_INDEX:
return []
# gets all the motifs from the peptides
info = m.pep_parser(
seq['full'], length
) # sends a sequence array and the given length to the pep parser
# if not os.path.exists(d + '/made_adj/' + pdb.replace('.pdb','')):
# os.mkdir(d + '/made_adj/' + pdb.replace('.pdb',''))
for motif in info:
if motif == 'full':
continue
for pep in info[motif]:
completed.append(main_calc(pep, seq, maxValues,
pdb_parsed))
return completed
def make_structure(pdb1, length, maxValues):
global seq, file, seq_to_pdb, pdb, mV
mV = maxValues
pdb = pdb1
cleaning.cleanATOM(d + '\\pdb\\' + pdb,
out_file=d + '\\cleaned\\' + pdb,
ext='.pdb')
file = pd.parsePDB(d + '\\cleaned\\' + pdb)
seq, seq_to_pdb, pdb_to_seq = find_seq(file)
info = m.pep_parser(seq, length)
peps = []
if not os.path.exists(d + '\\made_adj\\' + pdb.replace('.pdb', '')):
os.mkdir(d + '\\made_adj\\' + pdb.replace('.pdb', ''))
completed = []
for motif in info:
if motif == 'full':
continue
for pep in info[motif]:
peps.append(pep)
completed.append(main_calc(pep))
return completed
d = os.getcwd()
file = eg.fileopenbox(msg='Where is the file?')
peps = {}
full_string = ''
with open(file, 'r') as g:
string = g.read()
while string:
full_string += string
string = g.read()
full_string.replace(' ', ' ')
full_string = full_string.split('>')
for i in range(len(full_string)):
full_string[i] = full_string[i].replace('\n', ' ').replace('>',
'').split(' ')
if len(full_string[i]) > 1:
peps[full_string[i][0]] = full_string[i][-2]
count = 0
for i in peps:
count += 1
with open('pep_titles.txt', 'w+') as f:
f.write(i + ' ')
print('Current Peptide: ' + i + " (" + str(count) + "/" + str(len(peps)) +
")")
if not os.path.isdir(d + '\\found_peps\\' + i):
os.mkdir(d + '\\found_peps\\' + i)
found_peps = m.pep_parser(peps[i], 12)
with open(d + '\\found_peps\\' + i + '\\peps.pickle', 'wb') as f:
pickle.dump(found_peps, f, pickle.HIGHEST_PROTOCOL)