def _thread_fun(self, queue, device, show_q):
self.queue = queue
self.show_q = show_q
if self.use_buffer:
self.input_buffer = {}
try:
self.setup_connections()
self.start(device)
if DEBUG:
print(f"{self.name} starting...")
try:
while True:
try:
FPS.update(self.name)
if self.use_buffer:
self.consume_queue_data()
self.run()
except StopNodeException:
break
finally:
self.end(device)
except Exception as e:
traceback.print_exc()
instance = self.getWrapper().canvasRef().pyFlowInstance
threading.Thread(target=stop_pipeline, args=(instance, )).start()
msg = QMessageBox()
msg.setIcon(QMessageBox.Critical)
msg.setText("Error occured during node execution!")
msg.setInformativeText(str(e))
msg.setDetailedText(traceback.format_exc())
msg.setWindowTitle("Node execution error!")
msg.setStandardButtons(QMessageBox.Ok)
msg.exec()
def failed_template_warning(residue):
'''
Warning dialog handling the case where a template is not recognised by
OpenMM when attempting to start a simulation.
'''
from Qt.QtWidgets import QMessageBox, QPushButton
msg = QMessageBox()
msg.setIcon(QMessageBox.Warning)
msgtext = 'Residue {} {} of chain {} (shown) does not match any template'\
+ ' in the molecular dynamics database. It may be missing atoms (have'\
+ ' you added hydrogens?) or be an unusual residue that has not been'\
+ ' parameterised. Choose what you wish to do with it from the options'\
+ ' below.'
msg.setText(msgtext.format(residue.name, residue.number, residue.chain_id))
addh = QPushButton('Add hydrogens and retry')
msg.addButton(addh, QMessageBox.AcceptRole)
exclude = QPushButton('Exclude residue from simulations and retry')
msg.addButton(exclude, QMessageBox.RejectRole)
abort = QPushButton('Abort')
msg.addButton(abort, QMessageBox.NoRole)
msg.exec_()
btn = msg.clickedButton()
# print("Button: {}".format(btn))
if btn == addh:
return "addh"
if btn == exclude:
return "exclude"
return "abort"
def generic_warning(message):
from Qt.QtWidgets import QMessageBox
msg = QMessageBox()
msg.setIcon(QMessageBox.Warning)
msg.setText(message)
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
def show_info_dialog(self, msg, title='Info'):
"""
Shows a info dialog
:param msg: str, message to show with the dialog
:param title: str, title of the dialog
"""
dialog = QMessageBox()
dialog.setIcon(QMessageBox.Information)
dialog.setWindowTitle(title)
dialog.setText(msg)
dialog.exec_()
def libadd_ring(self):
"""add ring to library or open it in a new model"""
selection = self.session.seqcrow_ordered_selection_manager.selection
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
rescol = ResidueCollection(selection[0].structure)
walk_atoms = rescol.find(
[AtomSpec(atom.atomspec) for atom in selection])
if len(walk_atoms) < 1:
raise RuntimeError("no walk direction could be determined")
ring_name = self.ring_name.text()
ring = Ring(rescol, name=ring_name, end=walk_atoms)
ring.comment = "E:%s" % ",".join(
[str(rescol.atoms.index(atom) + 1) for atom in walk_atoms])
if len(ring_name) == 0:
chimerax_ring = ResidueCollection(ring).get_chimera(self.session)
chimerax_ring.name = "ring preview"
self.session.models.add([chimerax_ring])
bild_obj = show_walk_highlight(ring, chimerax_ring,
[0.9, 0.4, 0.3, 0.9], self.session)
self.session.models.add(bild_obj, parent=chimerax_ring)
else:
check_aaronlib_dir()
filename = os.path.join(AARONLIB, "Rings", ring_name + ".xyz")
if os.path.exists(filename):
exists_warning = QMessageBox()
exists_warning.setIcon(QMessageBox.Warning)
exists_warning.setText(
"%s already exists.\nWould you like to overwrite?" %
filename)
exists_warning.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
rv = exists_warning.exec_()
if rv == QMessageBox.Yes:
ring.write(outfile=filename)
self.tool_window.status("%s added to ring library" %
ring_name)
else:
self.tool_window.status(
"%s has not been added to ring library" % ring_name)
else:
ring.write(outfile=filename)
self.tool_window.status("%s added to ring library" % ring_name)
class PopUpWarning(Error):
"""
display a popup error box with a custom message
"""
def __init__(self, _msg):
self.msg_box = QMessageBox()
self.msg_box.setWindowFlags(self.msg_box.windowFlags()
| QtCore.Qt.WindowStaysOnTopHint)
self.msg_box.setWindowTitle("Warning")
self.msg_box.setIcon(QMessageBox.Warning)
self.msg_box.setStandardButtons(QMessageBox.Ok)
self.msg_box.setText(_msg)
self.msg_box.exec_()
class SidNotValid(Error):
"""
Raised when the file can't be open
"""
def __init__(self):
self.msg_box = QMessageBox()
self.msg_box.setWindowFlags(self.msg_box.windowFlags()
| QtCore.Qt.WindowStaysOnTopHint)
self.msg_box.setWindowTitle("Error")
self.msg_box.setIcon(QMessageBox.Warning)
self.msg_box.setStandardButtons(QMessageBox.Ok)
self.msg_box.setText("Sid not valid")
self.msg_box.exec_()
class NoSelectionError(Error):
"""
Raised when the user don't select a file needed
"""
def __init__(self):
self.msg_box = QMessageBox()
self.msg_box.setWindowFlags(self.msg_box.windowFlags()
| QtCore.Qt.WindowStaysOnTopHint)
self.msg_box.setWindowTitle("Error")
self.msg_box.setIcon(QMessageBox.Critical)
self.msg_box.setStandardButtons(QMessageBox.Ok)
self.msg_box.setText("Select a file !")
self.msg_box.exec_()
class Error(Exception):
"""
Basic exeption class
"""
def __init__(self, msg):
self.msg_box = QMessageBox()
self.msg_box.setWindowFlags(self.msg_box.windowFlags()
| QtCore.Qt.WindowStaysOnTopHint)
self.msg_box.setWindowTitle("Error")
self.msg_box.setIcon(QMessageBox.Critical)
self.msg_box.setStandardButtons(QMessageBox.Ok)
self.msg_box.setText(msg)
self.msg_box.exec_()
def choice_warning(message):
'''
Pop up a warning dialog box with the given message, and return True
if the user wants to go ahead.
'''
from Qt.QtWidgets import QMessageBox
msg = QMessageBox()
msg.setIcon(QMessageBox.Warning)
msg.setText(message)
msg.setStandardButtons(QMessageBox.Ok | QMessageBox.Cancel)
reply = msg.exec_()
if reply == QMessageBox.Ok:
return True
return False
def show_warning_dialog(self, msg, detail=None):
"""
Shows a warning dialog
:param msg: str, message to show with the dialog
:param detail: str, detail information to show (optional)
"""
dialog = QMessageBox()
dialog.setIcon(QMessageBox.Warning)
dialog.setWindowTitle('Warning')
dialog.setText(msg)
if detail:
dialog.setDetailedText(detail)
dialog.exec_()
def show_confirm_dialog(self, msg, title='Title'):
"""
Shows a yes/no confirmation dialog
:param msg: str, message to show with the dialog
:param title: str, title of the dialog
:return: bool, Whether the user has pressed yes(True) or No(False)
"""
dialog = QMessageBox()
dialog.setIcon(QMessageBox.Question)
result = dialog.question(self.parent_window, title, msg,
QMessageBox.Yes, QMessageBox.No)
if result == QMessageBox.Yes:
return True
return False
def _fun(self, device):
try:
self.setup_connections()
self.run(device)
except Exception as e:
traceback.print_exc()
self._terminate()
msg = QMessageBox()
msg.setIcon(QMessageBox.Critical)
msg.setText("Error occured during node execution!")
msg.setInformativeText(str(e))
msg.setDetailedText(traceback.format_exc())
msg.setWindowTitle("Node execution error!")
msg.setStandardButtons(QMessageBox.Ok)
msg.exec()
def libadd_substituent(self):
"""add ligand to library or open it in a new model"""
selection = selected_atoms(self.session)
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
residues = []
for atom in selection:
if atom.residue not in residues:
residues.append(atom.residue)
rescol = ResidueCollection(selection[0].structure,
convert_residues=residues)
substituent_atoms = [
atom for atom in rescol.atoms if atom.chix_atom in selection
]
start = None
avoid = None
for atom in substituent_atoms:
for atom2 in atom.connected:
if atom2 not in substituent_atoms:
if start is None:
start = atom
avoid = atom2
else:
raise RuntimeError(
"substituent must only have one connection to the molecule"
)
if start is None:
raise RuntimeError(
"substituent is not connected to a larger molecule")
substituent_atoms.remove(start)
substituent_atoms.insert(0, start)
sub_name = self.sub_name.text()
confs = self.sub_confs.value()
angle = self.sub_angle.value()
comment = "CF:%i,%i" % (confs, angle)
if len(sub_name) == 0:
sub = Substituent(substituent_atoms,
name="test",
conf_num=confs,
conf_angle=angle)
else:
sub = Substituent(substituent_atoms,
name=sub_name,
conf_num=confs,
conf_angle=angle)
sub.comment = comment
#align substituent bond to x axis
sub.coord_shift(-avoid.coords)
x_axis = np.array([1., 0., 0.])
n = np.linalg.norm(start.coords)
vb = start.coords / n
d = np.linalg.norm(vb - x_axis)
theta = np.arccos((d**2 - 2) / -2)
vx = np.cross(vb, x_axis)
sub.rotate(vx, theta)
add = False
if len(sub_name) == 0:
chimerax_sub = ResidueCollection(sub).get_chimera(self.session)
chimerax_sub.name = "substituent preview"
self.session.models.add([chimerax_sub])
bild_obj = ghost_connection_highlight(
sub, [0.60784, 0.145098, 0.70196, 0.5], self.session)
self.session.models.add(bild_obj, parent=chimerax_sub)
else:
check_aaronlib_dir()
filename = os.path.join(AARONLIB, "Subs", sub_name + ".xyz")
if os.path.exists(filename):
exists_warning = QMessageBox()
exists_warning.setIcon(QMessageBox.Warning)
exists_warning.setText(
"%s already exists.\nWould you like to overwrite?" %
filename)
exists_warning.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
rv = exists_warning.exec_()
if rv == QMessageBox.Yes:
add = True
else:
self.tool_window.status(
"%s has not been added to substituent library" %
sub_name)
else:
add = True
if add:
sub.write(outfile=filename)
self.tool_window.status("%s added to substituent library" %
sub_name)
register_selectors(self.session.logger, sub_name)
if self.session.ui.is_gui:
if (sub_name not in ELEMENTS and sub_name[0].isalpha()
and (len(sub_name) > 1
and not any(not (c.isalnum() or c in "+-")
for c in sub_name[1:]))):
add_submenu = self.session.ui.main_window.add_select_submenu
add_selector = self.session.ui.main_window.add_menu_selector
substituent_menu = add_submenu(['Che&mistry'],
'Substituents')
add_selector(substituent_menu, sub_name, sub_name)
def libadd_ligand(self):
"""add ligand to library or open it in a new model"""
selection = selected_atoms(self.session)
if not selection.single_structure:
raise RuntimeError("selected atoms must be on the same model")
rescol = ResidueCollection(selection[0].structure)
ligand_atoms = [
atom for atom in rescol.atoms if atom.chix_atom in selection
]
key_chix_atoms = [
atom for atom in self.key_atomspec if not atom.deleted
]
if len(key_chix_atoms) < 1:
key_atoms = set([])
for atom in ligand_atoms:
for atom2 in atom.connected:
if atom2 not in ligand_atoms:
key_atoms.add(atom)
else:
key_atoms = rescol.find(
[AtomSpec(atom.atomspec) for atom in key_chix_atoms])
if len(key_atoms) < 1:
raise RuntimeError("no key atoms could be determined")
lig_name = self.ligand_name.text()
ligand = Component(ligand_atoms, name=lig_name, key_atoms=key_atoms)
ligand.comment = "K:%s" % ",".join(
[str(ligand.atoms.index(atom) + 1) for atom in key_atoms])
if len(lig_name) == 0:
chimerax_ligand = ResidueCollection(ligand).get_chimera(
self.session)
chimerax_ligand.name = "ligand preview"
self.session.models.add([chimerax_ligand])
bild_obj = key_atom_highlight(ligand, [0.2, 0.5, 0.8, 0.5],
self.session)
self.session.models.add(bild_obj, parent=chimerax_ligand)
else:
check_aaronlib_dir()
filename = os.path.join(AARONLIB, "Ligands", lig_name + ".xyz")
if os.path.exists(filename):
exists_warning = QMessageBox()
exists_warning.setIcon(QMessageBox.Warning)
exists_warning.setText(
"%s already exists.\nWould you like to overwrite?" %
filename)
exists_warning.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
rv = exists_warning.exec_()
if rv == QMessageBox.Yes:
ligand.write(outfile=filename)
self.tool_window.status("%s added to ligand library" %
lig_name)
else:
self.tool_window.status(
"%s has not been added to ligand library" % lig_name)
else:
ligand.write(outfile=filename)
self.tool_window.status("%s added to ligand library" %
lig_name)
