def clean_all(pdb_input, pdb_output):
print(pdb_input, pdb_output)
total = len(os.listdir(pdb_input))
count = 0
for i in os.listdir(pdb_input):
cleaning.cleanATOM(pdb_input + '/' + i,
out_file=pdb_output + '/' + i,
ext='.pdb')
count += 1
print(str(count) + ' out of ' + str(total) + ' completed',
end='\r')
def find_max(length):
global seq, file, seq_to_pdb, pdb_to_seq
seq = 'W' * length
out = Bio.PDB.PDBIO()
i = pb.make_structure(seq, [180] * len(seq), [180] * len(seq))
out.set_structure(i)
out.save("ignore.pdb")
cleaning.cleanATOM("ignore.pdb", out_file=d + "\\ignore", ext='.pdb')
file = pd.parsePDB("ignore.pdb")
seq, seq_to_pdb, pdb_to_seq = find_seq(file)
final = main_calc(seq)
atom_length = len(final['primary'])
eucl_length = final['secondary'].max()
return atom_length, eucl_length
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
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 27 17:26:55 2019
@author: jtfl2
"""
import cleaning
import os
d = os.getcwd()
for i in os.listdir(d + '/pdb'):
cleaning.cleanATOM(d + '/pdb/' + i, out_file= d + '/cleaned/' + i, ext = '.pdb')
def cleanPDB():
d = os.getcwd()
filepath = easygui.fileopenbox('Choose a file', filetypes=["*.pdb"])
if filepath is not None:
cleaning.cleanATOM(filepath)