def update_results(self, results):
self.atoms = results.atoms
self.cavities_center = results.center_cavities
self.cavities_surface = results.surface_cavities
self.domains = results.domains
self.discretization = Discretization(results.atoms.volume,
results.resolution, True)
self.show_atom_group()
def update_results(self, results):
self.atoms = results.atoms
self.cavities_center = results.center_cavities
self.cavities_surface = results.surface_cavities
self.domains = results.domains
self.discretization = Discretization(results.atoms.volume, results.resolution, True)
self.show_atom_group()
class HTMLWindow(QtWidgets.QWidget):
def __init__(self):
QtWidgets.QWidget.__init__(self)
box = QtWidgets.QVBoxLayout()
self.webview = WebWidget(
css_filepath='gui/tabs/statistics/templates/style.css')
self.atoms = None
self.cavities_center = None
self.cavities_surface = None
self.domains = None
self.discretization = None
self.tree_list = None
self.webview.set_gui_html(None)
self.webview.gui_link_clicked.connect(self.link_clicked)
box.addWidget(self.webview)
self.setLayout(box)
box.setContentsMargins(5, 0, 0, 0)
self.show()
def minimumSizeHint(self):
return QtCore.QSize(150, -1)
def sizeHint(self):
return QtCore.QSize(250, -1)
def link_clicked(self, value):
'''
examines the data of the given link by *data* an calls the specific method to render the new HTML page
:param data: Value of the link clicked in Webview
:return: None
'''
value = value.split("/")
if value[0] == "surface_cavity":
self.show_surface_cavity(int(value[1]) - 1)
elif value[0] == "center_cavity":
self.show_center_cavity(int(value[1]) - 1)
elif value[0] == "domain":
self.show_domain(int(value[1]) - 1)
elif value[0] == "focus":
position = [float(value[1]), float(value[2]), float(value[3])]
self.window().control.visualization.set_focus_on(*position)
self.window().center.gl_widget.update()
self.window().center.combo.setCurrentIndex(0)
self.window().center.gl_stack.setCurrentIndex(0)
elif value[0] == "atom":
self.show_atom(int(value[1]))
elif value[0] == 'hideothers':
parent = self.parent()
while parent.parent():
parent = parent.parent()
main_window = parent
view_tab = main_window.view_dock.view_tab
if value[1] == 'atom':
atom_index = int(value[2]) - 1
view_tab.atom_check.indices = [atom_index]
view_tab.atom_check.selection_checkbox_set_checked(True)
elif value[1] == 'element':
element = core.elements.names[int(value[2])]
visible_atom_indices = []
for i, element_name in enumerate(self.atoms.elements):
if core.elements.names[core.elements.numbers[
element_name.upper()]] == element:
visible_atom_indices.append(i)
view_tab.atom_check.indices = visible_atom_indices
view_tab.atom_check.selection_checkbox_set_checked(True)
elif value[1] == 'domain':
domain_index = int(value[2]) - 1
view_tab.domain_check.indices = [domain_index]
view_tab.domain_check.selection_checkbox_set_checked(True)
elif value[1] == 'surface_cavity':
surface_cavity_index = int(value[2]) - 1
view_tab.surface_cavity_check.indices = [surface_cavity_index]
view_tab.surface_cavity_check.selection_checkbox_set_checked(
True)
elif value[1] == 'center_cavity':
center_cavity_index = int(value[2]) - 1
view_tab.center_cavity_check.indices = [center_cavity_index]
view_tab.center_cavity_check.selection_checkbox_set_checked(
True)
elif value[0] == 'addtovisible':
parent = self.parent()
while parent.parent():
parent = parent.parent()
main_window = parent
view_tab = main_window.view_dock.view_tab
if value[1] == 'atom':
atom_index = int(value[2]) - 1
view_tab.domain_check.add_indices([atom_index])
elif value[1] == 'domain':
domain_index = int(value[2]) - 1
view_tab.domain_check.add_indices([domain_index])
elif value[1] == 'surface_cavity':
surface_cavity_index = int(value[2]) - 1
view_tab.surface_cavity_check.add_indices(
[surface_cavity_index])
elif value[1] == 'center_cavity':
center_cavity_index = int(value[2]) - 1
view_tab.center_cavity_check.add_indices([center_cavity_index])
elif value[0] == 'showall':
parent = self.parent()
while parent.parent():
parent = parent.parent()
main_window = parent
view_tab = main_window.view_dock.view_tab
if value[1] == 'atoms':
view_tab.atom_check.setChecked(True)
view_tab.atom_check.selection_checkbox_set_checked(False)
if value[1] == 'domains':
view_tab.domain_check.setChecked(True)
view_tab.domain_check.selection_checkbox_set_checked(False)
if value[1] == 'surface_cavities':
view_tab.surface_cavity_check.setChecked(True)
view_tab.surface_cavity_check.selection_checkbox_set_checked(
False)
if value[1] == 'center_cavities':
view_tab.center_cavity_check.setChecked(True)
view_tab.center_cavity_check.selection_checkbox_set_checked(
False)
elif value[0] == 'recalculate':
parent = self.parent()
while parent.parent():
parent = parent.parent()
main_window = parent
file_tab = main_window.file_dock.file_tab
current_filename, current_frame = file_tab.last_shown_filename_with_frame
file_tab.calculate({current_filename: [current_frame]})
def update_results(self, results):
self.atoms = results.atoms
self.cavities_center = results.center_cavities
self.cavities_surface = results.surface_cavities
self.domains = results.domains
self.discretization = Discretization(results.atoms.volume,
results.resolution, True)
self.show_atom_group()
def show_atom_group(self):
atom_number = self.atoms.number
atom_elements = Counter(self.atoms.elements)
self.webview.set_gui_html(
render_html_atom_group(atom_number, atom_elements))
def show_atom(self, index):
if self.tree_list is not None:
self.tree_list.select_atom(index)
#for bond in bonds:
# if index not in self.atoms.bonds[bond]:
# self.atoms.bonds[bond].append(index)
atom_name = self.atoms.elements[
index] # atom name from periodic systen
atom_fullname = core.elements.names[core.elements.numbers[
atom_name.upper()]] # get full atom name
atom_color_rgb = core.elements.colors[core.elements.numbers[
atom_name.upper()]]
atom_positions = self.atoms.positions[index]
atom_number = core.elements.numbers[atom_name.upper()]
covalent_radius = self.atoms.covalence_radii[index]
cutoff_radius = self.atoms.radii[index]
bonds = self.atoms.bonds[index]
#print dir(self.domains[0])
self.webview.set_gui_html(
render_html_atom(index, atom_fullname, atom_positions, atom_number,
covalent_radius, cutoff_radius, atom_color_rgb,
bonds))
def show_center_cavity_group(self):
number = 0
surface_area = 0.0
volumes = 0.0
volume_fraction = 0.0
if self.cavities_center is None:
self.webview.set_gui_html(
render_html_cavity_center_group_unknown())
return
number = self.cavities_center.number
for sf in self.cavities_center.surface_areas:
surface_area += sf
for vl in self.cavities_center.volumes:
volumes += vl
if self.atoms.volume is not None:
volume_fraction = (volumes / self.atoms.volume.volume) * 100
self.webview.set_gui_html(
render_html_cavity_center_group(number, surface_area, volumes,
volume_fraction))
def show_center_cavity(self, index):
if self.tree_list is not None:
self.tree_list.select_center_cavity(index)
attrs = self._create_attr_getter(self.cavities_center, index)
data = {}
data['index'] = index
data['volume_fraction'] = 0.0
cavities = attrs.multicavities
domains = []
for cavity in cavities:
domains.append((cavity + 1,
self.discretization.discrete_to_continuous(
self.domains.centers[cavity])))
data['domains'] = domains
data['surface'] = attrs.surface_areas
data['volume'] = attrs.volumes
data['mass_center'] = attrs.mass_centers
data['squared_gyration_radius'] = attrs.squared_gyration_radii
data['asphericity'] = attrs.asphericities
data['acylindricity'] = attrs.acylindricities
data['anisotropy'] = attrs.anisotropies
data['characteristic_radius'] = attrs.characteristic_radii
data['is_cyclic'] = index in self.cavities_center.cyclic_area_indices
if self.atoms.volume is not None:
data['volume_fraction'] = (data['volume'] /
self.atoms.volume.volume) * 100
self.webview.set_gui_html(render_html_cavity_center(**data))
def show_surface_cavity_group(self):
number = 0
surface_area = 0.0
volumes = 0.0
volume_fraction = 0.0
if self.cavities_surface is None:
self.webview.set_gui_html(
render_html_cavity_surface_group_unknown())
return
number = self.cavities_surface.number
for sf in self.cavities_surface.surface_areas:
surface_area += sf
for vl in self.cavities_surface.volumes:
volumes += vl
if self.atoms.volume is not None:
volume_fraction = (volumes / self.atoms.volume.volume) * 100
self.webview.set_gui_html(
render_html_cavity_surface_group(number, surface_area, volumes,
volume_fraction))
def show_surface_cavity(self, index):
if self.tree_list is not None:
self.tree_list.select_surface_cavity(index)
attrs = self._create_attr_getter(self.cavities_surface, index)
data = {}
data['index'] = index
data['volume_fraction'] = 0.0
cavities = attrs.multicavities
domains = []
for cavity in cavities:
domains.append((cavity + 1,
self.discretization.discrete_to_continuous(
self.domains.centers[cavity])))
data['domains'] = domains
data['surface'] = attrs.surface_areas
data['volume'] = attrs.volumes
data['mass_center'] = attrs.mass_centers
data['squared_gyration_radius'] = attrs.squared_gyration_radii
data['asphericity'] = attrs.asphericities
data['acylindricity'] = attrs.acylindricities
data['anisotropy'] = attrs.anisotropies
data['characteristic_radius'] = attrs.characteristic_radii
data['is_cyclic'] = index in self.cavities_surface.cyclic_area_indices
if self.atoms.volume is not None:
data['volume_fraction'] = (data['volume'] /
self.atoms.volume.volume) * 100
self.webview.set_gui_html(render_html_cavity_surface(**data))
def show_domain_group(self):
number = 0
surface = 0.0
volumes = 0.0
volume_fraction = 0.0
if self.domains is None:
self.webview.set_gui_html(
render_html_cavity_domain_group_unknown())
return
number = self.domains.number
for sf in self.domains.surface_areas:
surface += sf
for vl in self.domains.volumes:
volumes += vl
if self.atoms.volume is not None:
volume_fraction = (volumes / self.atoms.volume.volume) * 100
self.webview.set_gui_html(
render_html_cavity_domain_group(number, surface, volumes,
volume_fraction))
def show_domain(self, index):
if self.tree_list is not None:
self.tree_list.select_domain(index)
attrs = self._create_attr_getter(self.domains, index)
data = {}
data['index'] = index
discrete_center = attrs.centers
data['center'] = self.discretization.discrete_to_continuous(
discrete_center)
data['surface'] = attrs.surface_areas
data['volume'] = attrs.volumes
data['volume_fraction'] = 0.0
data['surface_cavity_index'] = None
data['center_cavity_index'] = None
data['mass_center'] = attrs.mass_centers
data['squared_gyration_radius'] = attrs.squared_gyration_radii
data['asphericity'] = attrs.asphericities
data['acylindricity'] = attrs.acylindricities
data['anisotropy'] = attrs.anisotropies
data['characteristic_radius'] = attrs.characteristic_radii
data['is_cyclic'] = index in self.domains.cyclic_area_indices
if self.atoms.volume is not None:
data['volume_fraction'] = (data['volume'] /
self.atoms.volume.volume) * 100
if self.domains is not None and self.cavities_surface is not None:
for i in range(len(self.cavities_surface.multicavities)):
if index in self.cavities_surface.multicavities[i]:
data['surface_cavity_index'] = i + 1
break
if self.domains is not None and self.cavities_center is not None:
for i in range(len(self.cavities_center.multicavities)):
if index in self.cavities_center.multicavities[i]:
data['center_cavity_index'] = i + 1
break
self.webview.set_gui_html(render_html_cavity_domain(**data))
@staticmethod
def _create_attr_getter(obj, index):
class AttrGetter(object):
def __init__(self, obj, index):
self._obj = obj
self._index = index
def __getattr__(self, attr):
value = getattr(self._obj, attr)
is_numpy_array = isinstance(value, np.ndarray)
if ((is_numpy_array and len(value.shape) > 0)
or (not is_numpy_array and len(value) > 0)):
return value[self._index]
else:
return None
return AttrGetter(obj, index)
class HTMLWindow(QtWidgets.QWidget):
def __init__(self):
QtWidgets.QWidget.__init__(self)
box = QtWidgets.QVBoxLayout()
self.webview = WebWidget(css_filepath='gui/tabs/statistics/templates/style.css')
self.atoms = None
self.cavities_center = None
self.cavities_surface = None
self.domains = None
self.discretization = None
self.tree_list = None
self.webview.set_gui_html(None)
self.webview.gui_link_clicked.connect(self.link_clicked)
box.addWidget(self.webview)
self.setLayout(box)
box.setContentsMargins(5, 0, 0, 0)
self.show()
def minimumSizeHint(self):
return QtCore.QSize(150, -1)
def sizeHint(self):
return QtCore.QSize(250, -1)
def link_clicked(self, value):
'''
examines the data of the given link by *data* an calls the specific method to render the new HTML page
:param data: Value of the link clicked in Webview
:return: None
'''
value = value.split("/")
if value[0] == "surface_cavity":
self.show_surface_cavity(int(value[1])-1)
elif value[0] == "center_cavity":
self.show_center_cavity(int(value[1])-1)
elif value[0] == "domain":
self.show_domain(int(value[1])-1)
elif value[0] == "focus":
position = [float(value[1]),float(value[2]),float(value[3])]
self.window().control.visualization.set_focus_on(*position)
self.window().center.gl_widget.update()
self.window().center.combo.setCurrentIndex(0)
self.window().center.gl_stack.setCurrentIndex(0)
elif value[0] == "atom":
self.show_atom(int(value[1]))
elif value[0] == 'hideothers':
parent = self.parent()
while parent.parent():
parent = parent.parent()
main_window = parent
view_tab = main_window.view_dock.view_tab
if value[1] == 'atom':
atom_index = int(value[2])-1
view_tab.atom_check.indices = [atom_index]
view_tab.atom_check.selection_checkbox_set_checked(True)
elif value[1] == 'element':
element = core.elements.names[int(value[2])]
visible_atom_indices = []
for i, element_name in enumerate(self.atoms.elements):
if core.elements.names[core.elements.numbers[element_name.upper()]] == element:
visible_atom_indices.append(i)
view_tab.atom_check.indices = visible_atom_indices
view_tab.atom_check.selection_checkbox_set_checked(True)
elif value[1] == 'domain':
domain_index = int(value[2])-1
view_tab.domain_check.indices = [domain_index]
view_tab.domain_check.selection_checkbox_set_checked(True)
elif value[1] == 'surface_cavity':
surface_cavity_index = int(value[2])-1
view_tab.surface_cavity_check.indices = [surface_cavity_index]
view_tab.surface_cavity_check.selection_checkbox_set_checked(True)
elif value[1] == 'center_cavity':
center_cavity_index = int(value[2])-1
view_tab.center_cavity_check.indices = [center_cavity_index]
view_tab.center_cavity_check.selection_checkbox_set_checked(True)
elif value[0] == 'addtovisible':
parent = self.parent()
while parent.parent():
parent = parent.parent()
main_window = parent
view_tab = main_window.view_dock.view_tab
if value[1] == 'atom':
atom_index = int(value[2])-1
view_tab.domain_check.add_indices([atom_index])
elif value[1] == 'domain':
domain_index = int(value[2])-1
view_tab.domain_check.add_indices([domain_index])
elif value[1] == 'surface_cavity':
surface_cavity_index = int(value[2])-1
view_tab.surface_cavity_check.add_indices([surface_cavity_index])
elif value[1] == 'center_cavity':
center_cavity_index = int(value[2])-1
view_tab.center_cavity_check.add_indices([center_cavity_index])
elif value[0] == 'showall':
parent = self.parent()
while parent.parent():
parent = parent.parent()
main_window = parent
view_tab = main_window.view_dock.view_tab
if value[1] == 'atoms':
view_tab.atom_check.setChecked(True)
view_tab.atom_check.selection_checkbox_set_checked(False)
if value[1] == 'domains':
view_tab.domain_check.setChecked(True)
view_tab.domain_check.selection_checkbox_set_checked(False)
if value[1] == 'surface_cavities':
view_tab.surface_cavity_check.setChecked(True)
view_tab.surface_cavity_check.selection_checkbox_set_checked(False)
if value[1] == 'center_cavities':
view_tab.center_cavity_check.setChecked(True)
view_tab.center_cavity_check.selection_checkbox_set_checked(False)
elif value[0] == 'recalculate':
parent = self.parent()
while parent.parent():
parent = parent.parent()
main_window = parent
file_tab = main_window.file_dock.file_tab
current_filename, current_frame = file_tab.last_shown_filename_with_frame
file_tab.calculate({current_filename: [current_frame]})
def update_results(self, results):
self.atoms = results.atoms
self.cavities_center = results.center_cavities
self.cavities_surface = results.surface_cavities
self.domains = results.domains
self.discretization = Discretization(results.atoms.volume, results.resolution, True)
self.show_atom_group()
def show_atom_group(self):
atom_number = self.atoms.number
atom_elements = Counter(self.atoms.elements)
self.webview.set_gui_html(render_html_atom_group(atom_number, atom_elements))
def show_atom(self, index):
if self.tree_list is not None:
self.tree_list.select_atom(index)
#for bond in bonds:
# if index not in self.atoms.bonds[bond]:
# self.atoms.bonds[bond].append(index)
atom_name = self.atoms.elements[index] # atom name from periodic systen
atom_fullname = core.elements.names[core.elements.numbers[atom_name.upper()]] # get full atom name
atom_color_rgb = core.elements.colors[core.elements.numbers[atom_name.upper()]]
atom_positions = self.atoms.positions[index]
atom_number = core.elements.numbers[atom_name.upper()]
covalent_radius = self.atoms.covalence_radii[index]
cutoff_radius = self.atoms.radii[index]
bonds = self.atoms.bonds[index]
#print dir(self.domains[0])
self.webview.set_gui_html(render_html_atom(index, atom_fullname, atom_positions, atom_number, covalent_radius, cutoff_radius, atom_color_rgb, bonds))
def show_center_cavity_group(self):
number = 0
surface_area = 0.0
volumes = 0.0
volume_fraction = 0.0
if self.cavities_center is None:
self.webview.set_gui_html(render_html_cavity_center_group_unknown())
return
number = self.cavities_center.number
for sf in self.cavities_center.surface_areas:
surface_area += sf
for vl in self.cavities_center.volumes:
volumes += vl
if self.atoms.volume is not None:
volume_fraction = (volumes/self.atoms.volume.volume)*100
self.webview.set_gui_html(render_html_cavity_center_group(number, surface_area, volumes, volume_fraction))
def show_center_cavity(self, index):
if self.tree_list is not None:
self.tree_list.select_center_cavity(index)
attrs = self._create_attr_getter(self.cavities_center, index)
data = {}
data['index'] = index
data['volume_fraction'] = 0.0
cavities = attrs.multicavities
domains = []
for cavity in cavities:
domains.append((cavity+1, self.discretization.discrete_to_continuous(self.domains.centers[cavity])))
data['domains'] = domains
data['surface'] = attrs.surface_areas
data['volume'] = attrs.volumes
data['mass_center'] = attrs.mass_centers
data['squared_gyration_radius'] = attrs.squared_gyration_radii
data['asphericity'] = attrs.asphericities
data['acylindricity'] = attrs.acylindricities
data['anisotropy'] = attrs.anisotropies
data['characteristic_radius'] = attrs.characteristic_radii
data['is_cyclic'] = index in self.cavities_center.cyclic_area_indices
if self.atoms.volume is not None:
data['volume_fraction'] = (data['volume']/self.atoms.volume.volume)*100
self.webview.set_gui_html(render_html_cavity_center(**data))
def show_surface_cavity_group(self):
number = 0
surface_area = 0.0
volumes = 0.0
volume_fraction = 0.0
if self.cavities_surface is None:
self.webview.set_gui_html(render_html_cavity_surface_group_unknown())
return
number = self.cavities_surface.number
for sf in self.cavities_surface.surface_areas:
surface_area += sf
for vl in self.cavities_surface.volumes:
volumes += vl
if self.atoms.volume is not None:
volume_fraction = (volumes/self.atoms.volume.volume)*100
self.webview.set_gui_html(render_html_cavity_surface_group(number, surface_area, volumes, volume_fraction))
def show_surface_cavity(self, index):
if self.tree_list is not None:
self.tree_list.select_surface_cavity(index)
attrs = self._create_attr_getter(self.cavities_surface, index)
data = {}
data['index'] = index
data['volume_fraction'] = 0.0
cavities = attrs.multicavities
domains = []
for cavity in cavities:
domains.append((cavity+1, self.discretization.discrete_to_continuous(self.domains.centers[cavity])))
data['domains'] = domains
data['surface'] = attrs.surface_areas
data['volume'] = attrs.volumes
data['mass_center'] = attrs.mass_centers
data['squared_gyration_radius'] = attrs.squared_gyration_radii
data['asphericity'] = attrs.asphericities
data['acylindricity'] = attrs.acylindricities
data['anisotropy'] = attrs.anisotropies
data['characteristic_radius'] = attrs.characteristic_radii
data['is_cyclic'] = index in self.cavities_surface.cyclic_area_indices
if self.atoms.volume is not None:
data['volume_fraction'] = (data['volume']/self.atoms.volume.volume)*100
self.webview.set_gui_html(render_html_cavity_surface(**data))
def show_domain_group(self):
number = 0
surface = 0.0
volumes = 0.0
volume_fraction = 0.0
if self.domains is None:
self.webview.set_gui_html(render_html_cavity_domain_group_unknown())
return
number = self.domains.number
for sf in self.domains.surface_areas:
surface += sf
for vl in self.domains.volumes:
volumes += vl
if self.atoms.volume is not None:
volume_fraction = (volumes/self.atoms.volume.volume)*100
self.webview.set_gui_html(render_html_cavity_domain_group(number, surface, volumes, volume_fraction))
def show_domain(self, index):
if self.tree_list is not None:
self.tree_list.select_domain(index)
attrs = self._create_attr_getter(self.domains, index)
data = {}
data['index'] = index
discrete_center = attrs.centers
data['center'] = self.discretization.discrete_to_continuous(discrete_center)
data['surface'] = attrs.surface_areas
data['volume'] = attrs.volumes
data['volume_fraction'] = 0.0
data['surface_cavity_index'] = None
data['center_cavity_index'] = None
data['mass_center'] = attrs.mass_centers
data['squared_gyration_radius'] = attrs.squared_gyration_radii
data['asphericity'] = attrs.asphericities
data['acylindricity'] = attrs.acylindricities
data['anisotropy'] = attrs.anisotropies
data['characteristic_radius'] = attrs.characteristic_radii
data['is_cyclic'] = index in self.domains.cyclic_area_indices
if self.atoms.volume is not None:
data['volume_fraction'] = (data['volume']/self.atoms.volume.volume)*100
if self.domains is not None and self.cavities_surface is not None:
for i in range(len(self.cavities_surface.multicavities)):
if index in self.cavities_surface.multicavities[i]:
data['surface_cavity_index'] = i+1
break
if self.domains is not None and self.cavities_center is not None:
for i in range(len(self.cavities_center.multicavities)):
if index in self.cavities_center.multicavities[i]:
data['center_cavity_index'] = i+1
break
self.webview.set_gui_html(render_html_cavity_domain(**data))
@staticmethod
def _create_attr_getter(obj, index):
class AttrGetter(object):
def __init__(self, obj, index):
self._obj = obj
self._index = index
def __getattr__(self, attr):
value = getattr(self._obj, attr)
is_numpy_array = isinstance(value, np.ndarray)
if ((is_numpy_array and len(value.shape) > 0) or
(not is_numpy_array and len(value) > 0)):
return value[self._index]
else:
return None
return AttrGetter(obj, index)