def crete_bonds_list(self):
b = self.read_psf()
list_of_bonds = []
atom_list = self.create_atom_list()
for i in range(len(b)):
if len(b[i]) % 2 == 0:
for j in range(len(b[i])):
if j == 0:
atom_1 = Tools.find_atom(b[i][j], atom_list)
atom_2 = Tools.find_atom(b[i][j + 1], atom_list)
if atom_1 is not None and atom_2 is not None:
bond = Bond(atom_1, atom_2).create_bond()
list_of_bonds.append(bond)
else:
if ((j * 2) + 1) < len(b[i]):
atom_1 = Tools.find_atom(b[i][j * 2], atom_list)
atom_2 = Tools.find_atom(b[i][(j * 2) + 1],
atom_list)
if atom_1 is not None and atom_2 is not None:
bond = Bond(atom_1, atom_2).create_bond()
list_of_bonds.append(bond)
else:
logging.info('The number of bonds is odd')
break
return list_of_bonds
def read_psf(self):
can_print = False
b = []
try:
psf_file = open(self.psf_filename, 'r')
for line in psf_file:
if "bonds\n" in line:
can_print = True
elif "angles" in line:
can_print = False
if can_print:
b.append(line.split(' '))
psf_file.close()
b.pop(0)
bond_list = [[] for i in range(len(b))]
for i in range(len(b)):
for j in range(len(b[i])):
if b[i][j] == '':
logging.info('Space found, line passed...')
else:
bond_list[i].append(str.rstrip(b[i][j]))
return bond_list
except FileNotFoundError as error:
logging.error(error.strerror)
def create_commands_list(self, frames):
comands_frames = []
completed = 0
self.option.progress.setRange(0, len(frames))
for frame in frames:
commands_list = []
completed += 1
self.option.progress.setValue(completed)
for key, value in frame.colors_command_list.items():
if value:
if len(value) >= 96:
logging.info(
'To much atoms to color, list mast be truncated')
truncated_command_list = self.truncate_command(
key, value)
for command in truncated_command_list:
commands_list.append(command)
else:
color_command = ColorCommand(key, value)
color_command.create_color_command()
commands_list.append(color_command)
command_frame = CommandFrame(frame.number, commands_list)
comands_frames.append(command_frame)
return comands_frames
def truncate_command(key, value):
truncated_command_list = []
while value:
logging.info('Truncate in progress...')
atoms = value[0:95]
del value[0:95]
color_command = ColorCommand(key, atoms)
color_command.create_color_command()
truncated_command_list.append(color_command)
return truncated_command_list
def create_frames_list(self, residue):
frames = []
completed = 0
self.option.progress.setRange(0, self.p1.cmd.count_frames() + 1)
for i in range((self.p1.cmd.count_frames()) + 1):
completed += 1
self.option.progress.setValue(completed)
self.p1.cmd.frame(i)
logging.info('Processing frame number ' + str(i) + '...')
bonds = []
index = 0
for bond in residue:
d0 = residue[index].distance
atom_1_coords = self.p1.cmd.get_atom_coords('id ' +
bond.atom_1.number)
atom_2_coords = self.p1.cmd.get_atom_coords('id ' +
bond.atom_2.number)
di = Tools.calculate_distance(
atom_1_coords[0], atom_1_coords[1], atom_1_coords[2],
atom_2_coords[0], atom_2_coords[1], atom_2_coords[2])
atom_1 = Atom(bond.atom_1.number, bond.atom_1.element,
bond.atom_1.residue, atom_1_coords[0],
atom_1_coords[1], atom_1_coords[2])
atom_2 = Atom(bond.atom_2.number, bond.atom_2.element,
bond.atom_2.residue, atom_2_coords[0],
atom_2_coords[1], atom_2_coords[2])
delta_d_percent = Tools.distance_percent_change(d0, di)
color = Color(delta_d_percent, self.config)
new_bond = Bond(atom_1.create_atom(), atom_2.create_atom(),
color.return_color())
bonds.append(new_bond.create_bond())
index += 1
colors_command_list = Frames.create_color_list(bonds)
frame = Frame(i, bonds, colors_command_list)
frames.append(frame.create_frame())
return frames
def read_pdb(self):
try:
pdb_file = open(self.pdb_filename, 'r')
a = []
for line in pdb_file:
if "ATOM" in line:
if 'TIP3W' in line:
logging.info('Water was reached, scanning completed.')
break
else:
a.append(line.split(' '))
pdb_file.close()
logging.info('File ' + self.pdb_filename + 'closed.')
atom_list = [[] for i in range(len(a))]
for i in range(len(a)):
for j in range(len(a[i])):
if a[i][j] == '':
logging.info('Space found, line passed...')
else:
atom_list[i].append(a[i][j])
return atom_list
except FileNotFoundError as error:
logging.error(error.strerror)
def run_option(self):
if self.file_pdb and self.file_psf and self.file_dcd:
input_files = InputFiles(self.file_pdb, self.file_psf)
bonds = input_files.crete_bonds_list()
select_residue = SelectAtomGroup(bonds)
if str(self.combo_box_option) == 'Backbone':
selected_atoms = select_residue.backbone()
elif str(self.combo_box_option) == 'All':
selected_atoms = select_residue.all_atoms()
else:
QMessageBox.information(self, 'ADIST',
'Something gone wrong !')
self.p1 = pymol2.PyMOL()
self.p1.start()
self.p1.cmd.util.performance(100)
self.p1.cmd.set('defer_builds_mode', 10)
self.p1.cmd.load(self.file_pdb, 'loaded_protein')
self.p1.cmd.load_traj(self.file_dcd, 'loaded_protein')
self.p1.cmd.remove('solvent')
self.frames_list = self.create_frames_list(selected_atoms)
self.p1.stop()
if self.option.file_check.isChecked():
if self.frames_list:
Tools.export_to_file(self.frames_list)
QMessageBox.information(self, 'ADIST', 'CSV file created!')
logging.info('CSV file created!')
if self.option.chart_check.isChecked():
if self.frames_list:
atom_1 = self.option.atom_1_input.text()
atom_2 = self.option.atom_2_input.text()
if atom_1.isdigit() and atom_2.isdigit():
Tools.plot(self.frames_list, atom_1, atom_2)
QMessageBox.information(self, 'ADIST', 'Plot created!')
logging.info('Plot created!')
if self.option.ten_colors_check.isChecked():
if self.frames_list:
self.comand_frames = self.create_commands_list(
self.frames_list)
with open("frames.file", "wb") as f:
pickle.dump(self.comand_frames, f,
pickle.HIGHEST_PROTOCOL)
f.close()
if os.path.isfile('frames.file'):
logging.info('File dropped')
QMessageBox.information(
self, 'ADIST',
'Done,Hit CapsLock to watch result in PyMOL')
subprocess.call([
'python', 'ten_colors.py', self.file_pdb,
self.file_dcd, 'frames.file'
])
else:
QMessageBox.critical(self, 'Error', 'File not found!')
logging.error('File not found')
else:
QMessageBox.critical(self, 'Error', 'None file selected!')
logging.error('None file selected')