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 get_save_permission(message,
file_path=None,
title='Permission',
parent=None):
"""
Shows a save path message box
:param message: str, message to show to the user
:param file_path: str, path you want to save
:param title: str, title of the window
:param parent: QWidget
:return: bool
"""
message_box = QMessageBox()
message_box.setWindowTitle(title)
flags = message_box.windowFlags(
) ^ Qt.WindowContextHelpButtonHint | Qt.WindowStaysOnTopHint
if file_path:
path_message = 'Path: {}'.format(file_path)
message_box.setInformativeText(path_message)
message_box.setWindowFlags(flags)
save = message_box.addButton('Save', QMessageBox.YesRole)
no_save = message_box.addButton('Do not save', QMessageBox.NoRole)
cancel = message_box.addButton('Cancel', QMessageBox.RejectRole)
message_box.exec_()
if message_box.clickedButton() == save:
return True
elif message_box.clickedButton() == no_save:
return False
elif message_box.clickedButton() == cancel:
return None
return None
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 handleAbout(self):
"""
Displays the About dialog
"""
about_box = QMessageBox()
about_box.setText(__doc__)
about_box.exec_()
def help_about(self):
"""About Hypnotoad"""
about_text = __doc__.strip()
about_text += f"\nVersion : {__version__}"
about_box = QMessageBox(self)
about_box.setText(about_text)
about_box.exec_()
def handleAbout(self):
"""
Displays the About dialog
"""
about_box = QMessageBox()
version_text = f"PyXPad version {version}\n\n"
about_box.setText(version_text + __doc__.strip())
about_box.exec_()
def accept(self, *args, **kwargs):
selected_file, selected_dir, selected_file_name = self.get_result()
if not os.path.isdir(selected_file):
if os.path.exists(selected_file):
super(BaseOpenFileDialog, self).accept()
else:
message_box = QMessageBox()
message_box.setWindowTitle('Confirme file selection')
message_box.setText(
'File "{0}" does not exists!'.format(selected_file))
message_box.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_()
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 save(self):
if not config.HAVE_PYEVTK:
msg = QMessageBox(QMessageBox.Critical, 'Error', 'VTK output disabled. Pleas install pyvtk.')
msg.exec_()
return
filename = QFileDialog.getSaveFileName(self, 'Save as vtk file')[0]
base_name = filename.split('.vtu')[0].split('.vtk')[0].split('.pvd')[0]
if base_name:
if len(self.U) == 1:
write_vtk(self.grid, NumpyVectorSpace.make_array(self.U[0]), base_name, codim=self.codim)
else:
for i, u in enumerate(self.U):
write_vtk(self.grid, NumpyVectorSpace.make_array(u), f'{base_name}-{i}',
codim=self.codim)
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 info_message(message, parent=None):
"""
Shows a warning message
:param message: str
:param parent: QWidget
"""
parent = None
message_box = QMessageBox(parent)
flags = message_box.windowFlags(
) ^ Qt.WindowContextHelpButtonHint | Qt.WindowStaysOnTopHint
message_box.setWindowFlags(flags)
message_box.setText(message)
message_box.exec_()
def save(self):
if not config.HAVE_PYVTK:
msg = QMessageBox(QMessageBox.Critical, 'Error', 'VTK output disabled. Pleas install pyvtk.')
msg.exec_()
return
filename = QFileDialog.getSaveFileName(self, 'Save as vtk file')[0]
base_name = filename.split('.vtu')[0].split('.vtk')[0].split('.pvd')[0]
if base_name:
if len(self.U) == 1:
write_vtk(self.grid, NumpyVectorSpace.make_array(self.U[0]), base_name, codim=self.codim)
else:
for i, u in enumerate(self.U):
write_vtk(self.grid, NumpyVectorSpace.make_array(u), '{}-{}'.format(base_name, i),
codim=self.codim)
def setPassword(self):
newPassword = self.let_password.text()
if not newPassword:
msgBox = QMessageBox()
msgBox.setText(u'请输入密码！')
msgBox.exec_()
return 0
colUser = userdb[self.username]
# 从数据库提取密码
for x in colUser.find({"_id": "Password"}, {"Password": 1}):
if "Password" in x:
DBpassword = x["Password"]
oldD = {"Password": DBpassword}
newD = {"$set": {"Password": newPassword}}
x = colUser.update_many(oldD, newD)
def get_permission(message=None, cancel=True, title='Permission', parent=None):
"""
Shows a permission message box
:param message: str, message to show to the user
:param cancel: bool, Whether the user can cancel the operation or not
:param title: str, title of the window
:param parent: QWidget
:return: bool
"""
message_box = QMessageBox()
message_box.setWindowTitle(title)
flags = message_box.windowFlags(
) ^ Qt.WindowContextHelpButtonHint | Qt.WindowStaysOnTopHint
if message:
message_box.setText(message)
if cancel:
message_box.setStandardButtons(QMessageBox.Yes | QMessageBox.No
| QMessageBox.Cancel)
else:
message_box.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
message_box.setWindowFlags(flags)
result = message_box.exec_()
if result == QMessageBox.Yes:
return True
elif result == QMessageBox.No:
return False
elif result == QMessageBox.Cancel:
return None
return None
def on_featurePermissionRequested(self, securityOrigin, feature):
if feature != QWebEnginePage.Geolocation:
return
mgsbox = QMessageBox(self)
mgsbox.setAttribute(Qt.WA_DeleteOnClose)
mgsbox.setText(
self.tr("{} wants to know your location".format(securityOrigin.host()))
)
mgsbox.setInformativeText(
self.tr("Do you want to send your current location to this website?")
)
mgsbox.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
mgsbox.setDefaultButton(QMessageBox.Yes)
page = self.m_view.page()
if mgsbox.exec_() == QMessageBox.Yes:
page.setFeaturePermission(
securityOrigin, feature, QWebEnginePage.PermissionGrantedByUser
)
else:
page.setFeaturePermission(
securityOrigin, feature, QWebEnginePage.PermissionDeniedByUser
)
def _ask_user_subset_override(self, instance):
from Qt.QtWidgets import QMessageBox
title = "Subset \"{}\" already exist".format(instance["subset"])
text = ("Instance with subset name \"{}\" already exists."
"\n\nDo you want to override existing?").format(
instance["subset"])
dialog = QMessageBox()
dialog.setWindowTitle(title)
dialog.setText(text)
dialog.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
dialog.setDefaultButton(QMessageBox.Yes)
dialog.exec_()
if dialog.result() == QMessageBox.Yes:
return True
return False
def create_new_directory(self):
name, ok = QInputDialog.getText(self, 'New directory name', 'Name:',
QLineEdit.Normal, 'New Directory')
if ok and name:
path = os.path.join(self.directory, name)
if os.path.exists(path):
msg_box = QMessageBox(self)
msg_box.setWindowTitle('Error')
msg_box.setText('Directory already exists')
msg_box.exec_()
else:
try:
os.makedirs(path)
self.update_view()
except os.error as e:
msg_box = QMessageBox(self)
msg_box.setWindowTitle('Error')
msg_box.setText('Cannot create directory')
msg_box.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)
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 accept(self, *args, **kwargs):
selected_file, selected_dir, selected_filename = self.get_result()
if not os.path.isdir(selected_file):
if os.path.exists(selected_file):
message_box = QMessageBox()
message_box.setWindowTitle('Confirm File Selection')
message_box.setText(
'File "%s" exists.\nDo you want to overwrite it?' %
selected_file)
message_box.setStandardButtons(QMessageBox.Yes
| QMessageBox.No)
message_box.setDefaultButton(QMessageBox.No)
rv = message_box.exec_()
if rv == QMessageBox.Yes and not os.path.isdir(selected_file):
super(BaseSaveFileDialog, self).accept()
else:
super(BaseSaveFileDialog, self).accept()
def save():
"""
Saves current scene in current Maya file
:return: bool, Whether the scene was saved or not
"""
file_check_state = maya.cmds.file(query=True, modified=True)
if file_check_state:
msg_box = QMessageBox()
msg_box.setText('The Maya scene has been modified')
msg_box.setInformativeText('Do you want to save your changes?')
msg_box.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
msg_box.setDefaultButton(QMessageBox.Yes)
res = msg_box.exec_()
if res == QMessageBox.Yes:
maya.cmds.SaveScene()
return True
return False
def save(file_path=None):
"""
Saves current scene in current Max file
:return: bool, Whether the scene was saved or not
"""
file_path = file_path or ''
file_check_state = rt.getSaveRequired()
if file_check_state:
msg_box = QMessageBox()
msg_box.setText('The 3ds Max scene has been modified')
msg_box.setInformativeText('Do you want to save your changes?')
msg_box.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
msg_box.setDefaultButton(QMessageBox.Yes)
res = msg_box.exec_()
if res == QMessageBox.Yes:
file_path = file_path or directory.save_file_dialog('Save File', filters='*.max')
if not file_path:
return
rt.saveMaxFile(file_path)
return True
return False
def save(force=False):
"""
Saves current scene in current Max file
:return: bool, Whether the scene was saved or not
"""
file_check_state = MaxPlus.FileManager.IsSaveRequired()
if file_check_state:
if file_check_state:
if force:
MaxPlus.FileManager.Save()
return True
else:
msg_box = QMessageBox()
msg_box.setText('The 3ds Max scene has been modified')
msg_box.setInformativeText('Do you want to save your changes?')
msg_box.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
msg_box.setDefaultButton(QMessageBox.Yes)
res = msg_box.exec_()
if res == QMessageBox.Yes:
MaxPlus.FileManager.Save()
return True
return False
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 msgbox(message, detail=None):
msgbox = QMessageBox()
msgbox.setText(message)
if detail:
msgbox.setDetailedText(detail)
return msgbox.exec_()
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)
