def _build_table_elements(self, parent):
'''
Create the various elements in the table and add them to the
proper layout.
'''
self.setWindowTitle('Scene Panel')
layout = QtWidgets.QVBoxLayout(self)
self.setLayout(layout)
top_layout = QtWidgets.QGridLayout()
layout.addLayout(top_layout)
mid_layout = QtWidgets.QGridLayout()
layout.addLayout(mid_layout)
low_layout = QtWidgets.QGridLayout()
layout.addLayout(low_layout)
# Top Elements
self.instructionLabel = QtWidgets.QLabel(self)
self.instructionLabel.setText(
'Double click selected thumbnail to \nload into Workspace.')
top_layout.addWidget(self.instructionLabel, 0, 0)
self.addSceneButton = QtWidgets.QPushButton(self)
self.addSceneButton.setText('Add Scene')
top_layout.addWidget(self.addSceneButton, 0, 1)
# Mid Elements
self.sceneTableWidget = QtWidgets.QTableWidget(self)
mid_layout.addWidget(self.sceneTableWidget, 0, 0)
self.sceneTableWidget.viewport().installEventFilter(self)
self.sceneTableWidget.itemChanged.connect(self._item_changed)
self.sceneTableWidget.selectionModel().selectionChanged.connect(
self._selection_changed)
self.sceneTableWidget.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.sceneTableWidget.verticalHeader().setSectionsMovable(True)
# Lower Buttom Elements
self.deleteButton = QtWidgets.QPushButton(self)
self.deleteButton.setText("Delete Scene")
low_layout.addWidget(self.deleteButton, 0, 1)
self.deleteButton.setEnabled(False)
self.updateButton = QtWidgets.QPushButton(self)
self.updateButton.setText("Update Scene")
low_layout.addWidget(self.updateButton, 0, 0)
self.updateButton.setEnabled(False)
def setupUi(self, Dialog):
# Based on auto-generated code from ui file
from pymol.Qt import QtCore, QtWidgets
Dialog.resize(400, 50)
self.gridLayout = QtWidgets.QGridLayout(Dialog)
label = QtWidgets.QLabel("Select loaded object:", Dialog)
self.gridLayout.addWidget(label, 0, 0, 1, 1)
self.select_object_combo_box = QtWidgets.QComboBox(Dialog)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Fixed)
self.select_object_combo_box.setSizePolicy(sizePolicy)
self.select_object_combo_box.setEditable(True)
self.gridLayout.addWidget(self.select_object_combo_box, 0, 1, 1, 1)
label = QtWidgets.QLabel("Select loaded object:", Dialog)
self.gridLayout.addWidget(label, 1, 0, 1, 1)
self.select_object_combo_box2 = QtWidgets.QComboBox(Dialog)
self.select_object_combo_box2.setSizePolicy(sizePolicy)
self.select_object_combo_box2.setEditable(True)
self.gridLayout.addWidget(self.select_object_combo_box2, 1, 1, 1, 1)
self.buttonBox = QtWidgets.QDialogButtonBox(Dialog)
self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel
| QtWidgets.QDialogButtonBox.Ok)
self.gridLayout.addWidget(self.buttonBox, 2, 0, 1, 2)
self.buttonBox.accepted.connect(Dialog.accept)
self.buttonBox.rejected.connect(Dialog.reject)
def initUI(self):
self.loop_selector_frame_layout = QtWidgets.QGridLayout()
self.setLayout(self.loop_selector_frame_layout)
label_text = "Select two residues for a loop"
self.modeling_cluster_loop_selection_label = QtWidgets.QLabel(
label_text)
self.modeling_cluster_loop_selection_label.setStyleSheet(
modeling_options_subsections_style)
self.loop_selector_frame_layout.addWidget(
self.modeling_cluster_loop_selection_label, 0, 0, 1, 3)
def build_protocol_middle_frame(self):
"""
Allow to choose between plotting all amino acids types or only a subset
of them.
"""
# Radioselect.
aa_select_choices = ("Use all amino acids", "Select amino acids types")
aa_select_choices_values = ["all", "single"]
self.aa_select_choices_dict = dict([
(k, v)
for (k, v) in zip(aa_select_choices, aa_select_choices_values)
])
self.aa_select_rds = PyMod_radioselect_qt(
label_text="Select Amino Acids", buttons=aa_select_choices)
self.aa_select_rds.setvalue(aa_select_choices[0])
self.aa_select_rds.buttons_dict[aa_select_choices[0]].clicked.connect(
self.hide_select_single_aa_frame)
self.aa_select_rds.buttons_dict[aa_select_choices[1]].clicked.connect(
self.show_select_single_aa_frame)
self.middle_formlayout.add_widget_to_align(self.aa_select_rds)
# Checkboxes for selecting single amino acids.
self.aa_select_grid_layout = QtWidgets.QGridLayout()
self.aa_select_rds.input.addLayout(self.aa_select_grid_layout)
self.aa_checkbutton = {}
self.aa_freq_dict = {}
self.aa_checkbutton_list = []
for i, aa in enumerate(prot_standard_one_letter):
# Get the number of aa in the sequence.
aa_freq = str(self.protocol.target_sequence.my_sequence).count(aa)
self.aa_freq_dict[aa] = aa_freq
# Build a checkbox for the aa.
checkbox = QtWidgets.QCheckBox(
pmsm.one2three(aa) + " (" + str(aa_freq) + ")")
checkbox.setEnabled(False)
self.aa_select_grid_layout.addWidget(checkbox, int(i % 10),
int(i / 10))
self.aa_checkbutton[aa] = checkbox
self.aa_checkbutton_list.append(checkbox)
self.aa_select_grid_layout.setAlignment(QtCore.Qt.AlignLeft)
self.middle_formlayout.set_input_widgets_width("auto", padding=40)
def __init__(self, *args, **kwargs):
super(PyMod_plot_window_qt, self).__init__(*args, **kwargs)
# Central widget.
self.central_widget = QtWidgets.QWidget()
self.setCentralWidget(self.central_widget)
self.central_widget_layout = QtWidgets.QGridLayout()
self.central_widget.setLayout(self.central_widget_layout)
#------------------------------------------------
# Upper frame (contains the plot and controls). -
#------------------------------------------------
expanding_size_policy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Expanding)
preferred_size_policy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Preferred)
# The upper frame contains three frames: info, plot and controls frames.
# The infor and controls frames will be displayed only if the 'use_controls'
# argument is set to 'True' when calling the 'build_plotting_area' method.
self.upper_frame = QtWidgets.QFrame()
self.upper_frame.setStyleSheet("background-color: #646464")
self.upper_frame_layout = QtWidgets.QGridLayout()
self.upper_frame.setLayout(self.upper_frame_layout)
self.upper_frame.setSizePolicy(expanding_size_policy)
self.central_widget_layout.addWidget(self.upper_frame, 0, 0)
# Info frame, it contains the messagebar of the plot.
self.info_frame = QtWidgets.QFrame()
self.info_frame_layout = QtWidgets.QHBoxLayout()
self.info_frame.setLayout(self.info_frame_layout)
self.info_frame.setSizePolicy(preferred_size_policy)
self.info_label = QtWidgets.QLabel("")
self.info_frame_layout.addWidget(self.info_label)
# Plot frame.
self.plot_frame = QtWidgets.QFrame()
# self.plot_frame.setStyleSheet("background-color: red")
self.plot_frame_layout = QtWidgets.QGridLayout()
self.plot_frame.setLayout(self.plot_frame_layout)
self.plot_frame.setSizePolicy(expanding_size_policy)
self.build_plot_widget()
# Controls frame.
self.controls_frame = QtWidgets.QWidget()
self.controls_frame.setStyleSheet("background-color: #747474")
self.controls_frame_layout = QtWidgets.QGridLayout()
self.controls_frame.setLayout(self.controls_frame_layout)
self.controls_frame_layout.setAlignment(QtCore.Qt.AlignLeft | QtCore.Qt.AlignTop)
self.controls_scrollarea = QtWidgets.QScrollArea()
self.controls_scrollarea.setWidgetResizable(True)
self.controls_scrollarea.setWidget(self.controls_frame)
self.labels_title = QtWidgets.QLabel("Plots list")
# Middle splitter.
self.middle_splitter = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
self.middle_splitter.setSizePolicy(expanding_size_policy)
#---------------------------------------
# Lower frame (contains some options). -
#---------------------------------------
self.lower_frame = QtWidgets.QFrame()
self.lower_frame_layout = QtWidgets.QGridLayout()
self.lower_frame.setLayout(self.lower_frame_layout)
self.central_widget_layout.addWidget(self.lower_frame, 1, 0)
# View buttons.
self.view_label = QtWidgets.QLabel("View:")
self.lower_frame_layout.addWidget(self.view_label, 0, 0)
self.home_view_button = QtWidgets.QPushButton("Fit to data")
self.home_view_button.clicked.connect(self.on_home_button_click)
self.lower_frame_layout.addWidget(self.home_view_button, 0, 1)
# On click behaviour. The buttons will be shown later, in the
# 'build_plotting_area' metohd.
self.interact_buttons_group = QtWidgets.QButtonGroup()
self.on_click_label = QtWidgets.QLabel("Interact on click:")
self.interact_button = QtWidgets.QPushButton("Yes")
self.interact_button.setCheckable(True)
self.interact_buttons_group.addButton(self.interact_button)
self.interact_button.clicked.connect(self.on_interact_button_click)
self.no_interaction_button = QtWidgets.QPushButton("No")
self.no_interaction_button.setCheckable(True)
self.no_interaction_button.setChecked(True)
self.interact_buttons_group.addButton(self.no_interaction_button)
self.no_interaction_button.clicked.connect(self.on_no_interaction_button_click)
# Show/hide all buttons. They will be shown later, in the 'build_plotting_area'
# method.
self.show_label = QtWidgets.QLabel("Show:")
self.show_all_button = QtWidgets.QPushButton("All")
self.show_all_button.clicked.connect(self.show_all_command)
self.hide_all_button = QtWidgets.QPushButton("None")
self.hide_all_button.clicked.connect(self.hide_all_command)
self.lower_frame_layout.setAlignment(QtCore.Qt.AlignLeft)
#---------------------
# Build a main menu. -
#---------------------
self.save_to_csv_action = QtWidgets.QAction('Save to CSV', self)
self.save_to_csv_action.triggered.connect(lambda a=None: self.save_to_csv_event())
self.save_to_png_action = QtWidgets.QAction('Save to PNG', self)
self.save_to_png_action.triggered.connect(lambda a=None: self.save_to_png_event())
self.main_menubar = self.menuBar()
self.file_menu = self.main_menubar.addMenu('File')
def initialize_map(self,
pymod,
data_array,
pymod_elements,
ref_residues,
ref_selectors,
title=None,
pixel_size=5,
feature_type="contact",
threshold=8.0,
interaction_center="ca"):
# Sets the attributes.
self.data_array = data_array
self.pixel_size = pixel_size
self.feature_type = feature_type
self.threshold = threshold
self.interaction_center = interaction_center
if self.feature_type in ("contact", "distance"):
self.pymod_elements = pymod_elements
self.pymod_element = self.pymod_elements[0]
else:
self.pymod_elements = pymod_elements
# Get the PyMod residues for each residue having an interaction center and the PyMOL selectors
# for each residue.
self.ref_residues = ref_residues
self.ref_selectors = ref_selectors
# Assign the methods to get the labels.
if self.feature_type == "contact":
self.get_value_label = self._get_value_label_contact
elif self.feature_type == "distance":
self.get_value_label = self._get_value_label_distance
elif self.feature_type == "distances_difference":
self.get_value_label = self._get_value_label_distance_diff
elif self.feature_type == "distances_mean":
self.get_value_label = self._get_value_label_distance_mean
elif self.feature_type == "distances_std":
self.get_value_label = self._get_value_label_distance_std
else:
raise KeyError(self.feature_type)
# Set the canvas size.
min_size = 150
h = self.pixel_size * len(self.data_array)
win_size = min((910, h))
win_size = max((min_size, win_size))
if title:
self.setWindowTitle(title)
# Set some appearance parameters.
self.controls_padding = 4
if self.feature_type in ("contact", "distance"):
self.controls_font = "helvetica 11 bold"
else:
self.controls_font = "helvetica 10 bold"
self.controls_config = {
"fg": "black",
"font": self.controls_font,
"padx": self.controls_padding,
"pady": self.controls_padding
}
self.labels_pack_config = {
"side": "left",
"pady": (0, 5),
"padx": (5, 0)
}
self.buttons_pack_config = {
"side": "left",
"pady": (0, 5),
"padx": (1, 0)
}
# Frame of the window containing a row for some control buttons, a row for
# the plot and a row for a messagebar.
self.plot_frame = QtWidgets.QWidget()
self.plot_frame_layout = QtWidgets.QGridLayout()
self.plot_frame.setLayout(self.plot_frame_layout)
self.setCentralWidget(self.plot_frame)
# Control frame.
self.controls_frame = QtWidgets.QWidget()
self.controls_frame_layout = QtWidgets.QGridLayout()
self.controls_frame.setLayout(self.controls_frame_layout)
self.plot_frame_layout.addWidget(self.controls_frame)
self.delete_distances_button = QtWidgets.QPushButton(
"Delete all distances in PyMOL")
self.delete_distances_button.setEnabled(False)
self.delete_distances_button.clicked.connect(
lambda a=None: self.clear_plot())
self.controls_frame_layout.addWidget(self.delete_distances_button, 0,
0)
self.scale_factor = 0
self.scale_down_button = QtWidgets.QPushButton("Zoom out")
try:
self.scale_down_button.setIcon(QtGui.QIcon.fromTheme("go-down"))
except:
pass
self.scale_down_button.clicked.connect(
lambda a=None: self.scale_plot_down())
self.controls_frame_layout.addWidget(self.scale_down_button, 0, 1)
self.scale_up_button = QtWidgets.QPushButton("Zoom in")
try:
self.scale_up_button.setIcon(QtGui.QIcon.fromTheme("go-up"))
except:
pass
self.scale_up_button.clicked.connect(
lambda a=None: self.scale_plot_up())
self.controls_frame_layout.addWidget(self.scale_up_button, 0, 2)
self.controls_frame_layout.setAlignment(QtCore.Qt.AlignLeft)
# Frame containing the plot (with a scrollbar).
self.canvas_plot_frame = QtWidgets.QWidget()
self.canvas_plot_frame.setStyleSheet("background-color: white")
self.canvas_plot_frame_layout = QtWidgets.QGridLayout()
self.canvas_plot_frame.setLayout(self.canvas_plot_frame_layout)
self.canvas_plot_scrollarea = QtWidgets.QScrollArea()
self.canvas_plot_scrollarea.setWidgetResizable(True)
self.canvas_plot_scrollarea.setWidget(self.canvas_plot_frame)
self.plot_frame_layout.addWidget(self.canvas_plot_scrollarea)
# Builds the scene where to draw the contact map.
self.canvas_plot_scene = QtWidgets.QGraphicsScene()
# Builds the graphics view containing the scene above.
self.canvas_plot_view = Contact_map_graphics_view(
self.canvas_plot_scene)
self.canvas_plot_frame_layout.addWidget(self.canvas_plot_view)
# A bottom frame fo the window, containing some buttons to interact with the graph.
self.message_frame = QtWidgets.QFrame()
self.message_frame_layout = QtWidgets.QHBoxLayout()
self.message_frame.setLayout(self.message_frame_layout)
self.plot_frame_layout.addWidget(self.message_frame)
# Label to show which residue/position pair is currently being hovered by the mouse pointer.
if self.feature_type in ("contact", "distance"):
view_label_text = "Couple:"
else:
view_label_text = "Alignment positions:"
self.view_label = QtWidgets.QLabel(view_label_text)
# self.view_label.setStyleSheet(self.controls_config)
self.message_frame_layout.addWidget(self.view_label)
# Actually draws the contact map.
self.draw_map()
def initialize_plot(self, pymod, target_element, residues_tags, plot_title,
aa_list):
self.pymod = pymod
self.target_element = target_element
self.residues_tags = residues_tags
self.plot_title = plot_title
self.setWindowTitle("%s Ramachandran Plot" %
self.target_element.my_header)
self.aa_list = aa_list
# Frame of the window containing a row for some control buttons, a row for
# the plot and a row for a messagebar.
self.plot_frame = QtWidgets.QWidget()
self.plot_frame_layout = QtWidgets.QGridLayout()
self.plot_frame.setLayout(self.plot_frame_layout)
self.setCentralWidget(self.plot_frame)
# Control frame.
self.controls_frame = QtWidgets.QWidget()
self.controls_frame_layout = QtWidgets.QGridLayout()
self.controls_frame.setLayout(self.controls_frame_layout)
self.plot_frame_layout.addWidget(self.controls_frame, 0, 0)
self.scale_factor = 0
self.scale_down_button = QtWidgets.QPushButton("Zoom out")
try:
self.scale_down_button.setIcon(QtGui.QIcon.fromTheme("go-down"))
except:
pass
self.scale_down_button.clicked.connect(
lambda a=None: self.scale_plot_down())
self.controls_frame_layout.addWidget(self.scale_down_button, 0, 0)
self.scale_up_button = QtWidgets.QPushButton("Zoom in")
try:
self.scale_up_button.setIcon(QtGui.QIcon.fromTheme("go-up"))
except:
pass
self.scale_up_button.clicked.connect(
lambda a=None: self.scale_plot_up())
self.controls_frame_layout.addWidget(self.scale_up_button, 0, 1)
self.controls_frame_layout.setAlignment(QtCore.Qt.AlignLeft)
# Frame containing the plot (with a scrollbar).
self.canvas_plot_frame = QtWidgets.QWidget()
self.canvas_plot_frame.setStyleSheet("background-color: white")
self.canvas_plot_frame_layout = QtWidgets.QGridLayout()
self.canvas_plot_frame.setLayout(self.canvas_plot_frame_layout)
self.canvas_plot_scrollarea = QtWidgets.QScrollArea()
self.canvas_plot_scrollarea.setWidgetResizable(True)
self.canvas_plot_scrollarea.setWidget(self.canvas_plot_frame)
self.plot_frame_layout.addWidget(self.canvas_plot_scrollarea, 1, 0)
self.default_pen = QtGui.QPen(QtGui.QColor(0, 0, 0, 255), 1)
self.default_brush = QtGui.QBrush(QtGui.QColor(0, 0, 0, 230))
self.highlight_brush = QtGui.QBrush(QtGui.QColor(255, 0, 255))
self.highlight_region_brush = QtGui.QBrush(QtGui.QColor(0, 255, 255))
# Builds the scene where to draw the Ramachandran plot.
self.canvas_plot_scene = QtWidgets.QGraphicsScene()
# Builds the graphics view containing the scene above.
self.canvas_plot_view = QtWidgets.QGraphicsView(self.canvas_plot_scene)
self.canvas_plot_frame_layout.addWidget(self.canvas_plot_view)
# A bottom frame fo the window, containing some buttons to interact with the graph.
self.message_frame = QtWidgets.QFrame()
self.message_frame_layout = QtWidgets.QFormLayout()
self.message_frame.setLayout(self.message_frame_layout)
self.plot_frame_layout.addWidget(self.message_frame, 1, 1)
# Label to show which residue/position pair is currently being hovered by the mouse pointer.
self.view_label_prefix = "Showing: "
self.default_message = "Hover dots to color residues of the same type" # Hover over title.
self.message_label = QtWidgets.QLabel(self.default_message)
self.message_label.setStyleSheet(small_font_style)
self.message_frame_layout.addRow(self.message_label)
# Actually draws the plot.
self.draw_plot()
# Shows some data about the type of residues and their dihedral angles.
self.regions_labels_dict = {}
tot_regular_res = float(self.residues_count["T"])
label_params = [
("F", "Residues in the most favoured regions",
"residues in most favoured regions", True, True),
("A", "Residues in additional allowed regions",
"residues in additional allowed regions", True, True),
("G", "Residues in generously allowed regions",
"residues in generously allowed regions", True, True),
("D", "Residues in disallowed regions",
"residues in disallowed regions", True, True),
("T", "Non-gly and non-pro residues (circles)",
"non-glycine and non-proline residues", True, True),
("end_res", "End-residues", "end residues", False, False),
("gly", "Gly residues (triangles)", "glycine residues", True,
False),
("pro", "Pro residues (squares)", "proline residues", True, False),
("total", "Total number of residues", "all residues", True, False)
]
for region, label, message, active, use_ratio in label_params:
region_label = Ramachandran_plot_info_labels(
label, message, region, active, self)
region_label.setStyleSheet(small_font_style)
if use_ratio:
text = "%s (%s%%)" % (self.residues_count[region],
round(
self.residues_count[region] /
tot_regular_res * 100, 1))
else:
text = str(self.residues_count[region])
region_label_count = QtWidgets.QLabel(text)
region_label_count.setStyleSheet(small_font_style)
self.message_frame_layout.addRow(region_label, region_label_count)
self.regions_labels_dict[region] = {
"info": region_label,
"data": region_label_count
}
def __init__(self, parent, protocol):
super(Similarity_searches_results_window_qt, self).__init__(parent)
self.protocol = protocol
#########################
# Configure the window. #
#########################
self.setWindowTitle(self._get_window_title())
# Sets the central widget.
self.central_widget = QtWidgets.QWidget()
self.setCentralWidget(self.central_widget)
# The window has a main vbox layout.
self.main_vbox = QtWidgets.QVBoxLayout()
################
# Upper frame. #
################
title_text = self._get_upper_frame_title()
self.upper_frame_title = QtWidgets.QLabel(title_text)
self.main_vbox.addWidget(self.upper_frame_title)
#################
# Middle frame. #
#################
# Scroll area which contains the widgets, set as the centralWidget.
self.middle_scroll = QtWidgets.QScrollArea()
self.main_vbox.addWidget(self.middle_scroll)
# Widget that contains the collection of Vertical Box.
self.middle_widget = QtWidgets.QWidget()
# Scroll area properties.
self.middle_scroll.setWidgetResizable(True)
self.middle_scroll.setWidget(self.middle_widget)
# QFormLayout in the middle frame.
self.middle_formlayout = QtWidgets.QFormLayout()
self.middle_widget.setLayout(self.middle_formlayout)
#-----------------
# Buttons frame. -
#-----------------
# Set the frame and its layout.
self.buttons_frame = QtWidgets.QFrame()
self.middle_formlayout.addRow(self.buttons_frame)
self.buttons_hbox = QtWidgets.QHBoxLayout()
self.buttons_frame.setLayout(self.buttons_hbox)
# Build the control buttons.
self.blast_select_all_button = QtWidgets.QPushButton(text="Select All")
self.blast_select_all_button.clicked.connect(self.blast_select_all)
self.blast_select_none_button = QtWidgets.QPushButton(text="Select None")
self.blast_select_none_button.clicked.connect(self.blast_select_none)
self.blast_select_n_button = QtWidgets.QPushButton(text="Select Top:")
self.blast_select_n_button.clicked.connect(self.blast_select_n)
for button in [self.blast_select_all_button, self.blast_select_none_button, self.blast_select_n_button]:
self.buttons_hbox.addWidget(button)
# Build the line-edit for selecting only top entries.
self.blast_select_n_enf = PyMod_entryfield_qt(label_text="", value="10",
validate={'validator': 'integer',
'min': 1, 'max': 5000})
self.blast_select_n_enf.entry.setFixedWidth(70)
self.buttons_hbox.addWidget(self.blast_select_n_enf.entry)
# Align to the left all these widgets.
self.buttons_hbox.setAlignment(QtCore.Qt.AlignLeft)
for button in [self.blast_select_all_button, self.blast_select_none_button, self.blast_select_n_button]:
button.setFixedWidth(button.sizeHint().width()+30)
#-----------------
# Results frame. -
#-----------------
# Set the frame and its layout.
self.results_frame = QtWidgets.QFrame()
self.middle_formlayout.addRow(self.results_frame)
self.results_grid = QtWidgets.QGridLayout()
self.results_frame.setLayout(self.results_grid)
# Calls a method which actually displays the similarity searches results.
self.display_blast_hits()
# Align the gridded widgets to the left.
self.results_grid.setAlignment(QtCore.Qt.AlignLeft)
self.results_grid.setHorizontalSpacing(30)
#################
# Bottom frame. #
#################
self.main_button = QtWidgets.QPushButton("Submit")
self.main_button.clicked.connect(lambda a=None: self.protocol.blast_results_state())
self.main_vbox.addWidget(self.main_button)
self.main_button.setFixedWidth(self.main_button.sizeHint().width())
# Sets the main vertical layout.
self.central_widget.setLayout(self.main_vbox)
self.main_vbox.setAlignment(self.main_button, QtCore.Qt.AlignCenter)
def __init__(
self,
parent,
title="New PyMod Window",
upper_frame_title="New PyMod Window Sub-title",
submit_command=None,
submit_button_text="Submit",
with_scroll=True,
# geometry=None
):
super(PyMod_tool_window_qt, self).__init__(parent)
#------------------------
# Configure the window. -
#------------------------
# Command executed when pressing on the main button of the window.
self.submit_command = submit_command
# Configure the window.
self.setWindowTitle(title)
# if geometry is not None:
# self.setGeometry(*geometry)
# Sets the central widget.
self.central_widget = QtWidgets.QWidget()
self.setCentralWidget(self.central_widget)
# The window has a main vbox layout.
self.main_vbox = QtWidgets.QVBoxLayout()
#---------------
# Upper frame. -
#---------------
self.upper_frame_title = QtWidgets.QLabel(upper_frame_title)
self.main_vbox.addWidget(self.upper_frame_title)
#----------------
# Middle frame. -
#----------------
# Widget that contains the collection of Vertical Box.
self.middle_widget = QtWidgets.QWidget()
# The Vertical Box that contains other widgets to be displayed in the window.
self.middle_vbox = QtWidgets.QVBoxLayout()
self.middle_widget.setLayout(self.middle_vbox)
# Scroll area which contains the widgets, set as the centralWidget.
self.middle_scroll = QtWidgets.QScrollArea()
# Scroll area properties.
# self.middle_scroll.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)
# self.middle_scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
self.middle_scroll.setWidgetResizable(True)
self.middle_scroll.setWidget(self.middle_widget)
# QFormLayout in the middle frame.
if self.middle_layout_type == "qform":
self.middle_formlayout = PyMod_QFormLayout()
self.middle_vbox.addLayout(self.middle_formlayout)
elif self.middle_layout_type == "qgrid":
self.middle_formlayout = QtWidgets.QGridLayout()
self.middle_vbox.addLayout(self.middle_formlayout)
else:
raise KeyError("Unknown 'middle_layout_type': %s" %
middle_layout_type)
self.add_middle_frame_widgets()
self.main_vbox.addWidget(self.middle_scroll)
#----------------
# Bottom frame. -
#----------------
self.submit_command = submit_command
if self.submit_command is not None:
self.main_button = QtWidgets.QPushButton(submit_button_text)
self.main_button.clicked.connect(
lambda a=None: self.submit_command())
self.main_vbox.addWidget(self.main_button)
self.main_button.setFixedWidth(self.main_button.sizeHint().width())
# Sets the main vertical layout.
self.central_widget.setLayout(self.main_vbox)
self.main_vbox.setAlignment(self.main_button, QtCore.Qt.AlignCenter)
def __init__(self, parent=None, app=None):
super(_BuilderPanel, self).__init__(parent)
self.setWindowTitle("Builder")
self.setObjectName("builder")
self.cmd = app.pymol.cmd
self.layout = QtWidgets.QVBoxLayout()
self.setLayout(self.layout)
self.buttons_layout = QtWidgets.QVBoxLayout()
self.tabs = QtWidgets.QTabWidget(self)
self.layout.setContentsMargins(5, 5, 5, 5);
self.layout.setSpacing(5);
self.layout.addWidget(self.tabs)
self.layout.addLayout(self.buttons_layout)
self.layout.addStretch()
self.fragments_layout = QtWidgets.QGridLayout()
self.fragments_layout.setContentsMargins(5, 5, 5, 5);
self.fragments_layout.setSpacing(5);
self.fragments_tab = QtWidgets.QWidget()
self.fragments_tab.setLayout(self.fragments_layout)
self.protein_layout = QtWidgets.QGridLayout()
self.protein_layout.setContentsMargins(5, 5, 5, 5);
self.protein_layout.setSpacing(5);
self.protein_tab = QtWidgets.QWidget()
self.protein_tab.setLayout(self.protein_layout)
self.tabs.addTab(self.fragments_tab, "Chemical")
self.tabs.addTab(self.protein_tab, "Protein")
self.getIcons()
buttons = [
[ ("H", "Hydrogen", lambda: self.replace("H", 1, 1, "Hydrogen")),
("C", "Carbon", lambda: self.replace("C", 4, 4, "Carbon")),
("N", "Nitrogen", lambda: self.replace("N", 4, 3, "Nitrogen")),
("O", "Oxygen", lambda: self.replace("O", 4, 2, "Oxygen")),
("P", "Phosphorus", lambda: self.replace("P",4,3, "Phosphorous")),
("S", "Sulfur", lambda: self.replace("S",2,2, "Sulfur")),
("F", "Fluorine", lambda: self.replace("F",1,1, "Fluorine")),
("Cl", "Chlorrine", lambda: self.replace("Cl",1,1, "Chlorine")),
("Br", "Bromine", lambda: self.replace("Br",1,1, "Bromine")),
("I", "Iodine", lambda: self.replace("I",1,1, "Iodine")),
("-CF3", "Trifluoromethane", lambda: self.replace("trifluoromethane",4,0, "trifluoro")),
("-OMe", "Methanol", lambda: self.replace("methanol",5,0, "methoxy")),
],
[ ("CH4", "Methyl", lambda: self.grow("methane",1,0,"methyl")),
("C=C", "Ethylene", lambda: self.grow("ethylene",4,0,"vinyl")),
("C#C", "Acetylene", lambda: self.grow("acetylene",2,0,"alkynl")),
("C#N", "Cyanide", lambda: self.grow("cyanide",2,0,"cyano")),
("C=O", "Aldehyde", lambda: self.grow("formaldehyde",2,0,"carbonyl",)),
("C=OO", "Formic Acid", lambda: self.grow("formic",4,0,"carboxyl")),
("C=ON", "C->N amide", lambda: self.grow("formamide",5,0,"C->N amide")),
("NC=O", "N->C amide", lambda: self.grow("formamide",3,1,"N->C amide")),
("S=O2", "Sulfone", lambda: self.grow("sulfone",3,1,"sulfonyl")),
("P=O3", "Phosphite", lambda: self.grow("phosphite",4,0,"phosphoryl")),
("N=O2", "Nitro", lambda: self.grow("nitro",3,0,"nitro")),
],
[
("#cyc3", "Cyclopropane", lambda: self.grow("cyclopropane",4,0,"cyclopropyl")),
("#cyc4", "Cyclobutane", lambda: self.grow("cyclobutane",4,0,"cyclobutyl")),
("#cyc5", "Cyclopentane", lambda: self.grow("cyclopentane",5,0,"cyclopentyl")),
("#cyc6", "Cyclohexane", lambda: self.grow("cyclohexane",7,0,"cyclohexyl")),
("#cyc7", "Cycloheptane", lambda: self.grow("cycloheptane",8,0,"cycloheptyl")),
("#aro5", "Cyclopentadiene", lambda: self.grow("cyclopentadiene",5,0,"cyclopentadienyl")),
("#aro6", "Benzene", lambda: self.grow("benzene",6,0,"phenyl")),
("#aro65", "Indane", lambda: self.grow("indane",12,0,"indanyl")),
("#aro66", "Napthylene", lambda: self.grow("napthylene",13,0,"napthyl")),
("#aro67", "Benzocycloheptane", lambda: self.grow("benzocycloheptane",13,0, "benzocycloheptyl")),
]
]
self.btn_icons = {}
requestsize = QtCore.QSize(48, 48)
for row, btn_row in enumerate(buttons):
for col, bb in enumerate(btn_row):
btn_label, btn_tooltip, btn_command = bb
btn = makeFragmentButton()
if btn_label.startswith('#'):
icons = self.icons[btn_label[1:]]
btn.setIcon(icons[0])
btn.setIconSize(icons[1].actualSize(requestsize))
self.btn_icons[btn] = icons
else:
btn.setText(btn_label)
btn.setToolTip(btn_tooltip)
btn.clicked.connect(btn_command)
self.fragments_layout.addWidget(btn, row, col)
buttons = [
[ 'Ace', 'Ala', 'Arg', 'Asn', 'Asp', 'Cys', 'Gln', 'Glu', 'Gly', 'His', 'Ile', 'Leu' ],
[ 'Lys', 'Met', 'Phe', 'Pro', 'Ser', 'Thr', 'Trp', 'Tyr', 'Val', 'NMe', 'NHH' ]
]
for row, btn_row in enumerate(buttons):
for col, btn_label in enumerate(btn_row):
btn = makeFragmentButton()
btn.setText(btn_label)
btn.setToolTip("Build %s residue" % btn_label)
res = btn_label.lower()
slot = lambda val=None, s=self,r=res: s.attach(r)
btn.clicked.connect(slot)
self.protein_layout.addWidget(btn, row, col)
lab = QtWidgets.QLabel('Secondary Structure:')
lab_cols = 3
self.ss_cbox = QtWidgets.QComboBox()
self.ss_cbox.addItem("Alpha Helix")
self.ss_cbox.addItem("Beta Sheet (Anti-Parallel)")
self.ss_cbox.addItem("Beta Sheet (Parallel)")
self.protein_layout.addWidget(lab, 2, 0, 1, lab_cols)
self.protein_layout.addWidget(self.ss_cbox, 2, lab_cols, 1, 4)
self.ss_cbox.currentIndexChanged[int].connect(self.ssIndexChanged)
buttons = [
[
( "@Atoms:", None, None),
( "Fix H", "Fix hydrogens on picked atoms", self.fixH),
( "Add H", "Add hydrogens to entire molecule", self.addH),
( "Invert", "Invert stereochemistry around pk1 (pk2 and pk3 will remain fixed)", self.invert),
( "Delete", "Remove atoms", self.removeAtom),
( "Clear", "Delete everything", self.clear),
( "@ Charge:", None, None),
( " +1 ", "Positive Charge", lambda: self.setCharge(1,"+1")),
( " 0 ", "Neutral Charge", lambda: self.setCharge(0,"neutral")),
( " -1 ", "Negative Charge", lambda: self.setCharge(-1,"-1")),
],
[
( "@Bonds:", None, None),
( "Create", "Create bond between pk1 and pk2", self.createBond),
( "Delete", "Delete bond between pk1 and pk2", self.deleteBond),
( "Cycle", "Cycle bond valence", self.cycleBond),
( " | ", "Create single bond", lambda: self.setOrder("1", "single")),
( " || ", "Create double bond", lambda: self.setOrder("2", "double")),
( " ||| ", "Create triple bond", lambda: self.setOrder("3", "triple")),
( "Arom", "Create aromatic bond", lambda: self.setOrder("4", "aromatic")),
( "@ Model:", None, None),
( "Clean", "Cleanup structure", self.clean),
( "Sculpt", "Molecular sculpting", self.sculpt),
( "Fix", "Fix atom positions", self.fix),
( "Rest", "Restrain atom positions", self.rest),
],
[
( "$El-stat", "Electrostatics term for 'Clean' action", "clean_electro_mode"),
( "@ ", None, None),
( "$Bumps", "Show VDW contacts during sculpting", "sculpt_vdw_vis_mode"),
( "@ ", None, None),
( "#Undo Enabled", "", "suspend_undo"),
( "Undo", "Undo last change", self.undo),
( "Redo", "Redo last change", self.redo),
]
]
for row, btn_row in enumerate(buttons):
btn_row_layout = QtWidgets.QHBoxLayout()
self.buttons_layout.addLayout(btn_row_layout)
for col, bb in enumerate(btn_row):
btn_label, btn_tooltip, btn_command = bb
if btn_label[0] == '@':
btn = QtWidgets.QLabel(btn_label[1:])
elif btn_label[0] in ('#', '$'):
btn = QtWidgets.QCheckBox(btn_label[1:])
setting = btn_command
value = self.cmd.get_setting_int(setting)
if btn_label[0] == '$':
btn.setChecked(bool(value))
@btn.toggled.connect
def _(checked, n=setting):
self.cmd.set(n, checked, quiet=0)
else:
btn.setChecked(not value)
@btn.toggled.connect
def _(checked, n=setting):
self.cmd.set(n, not checked, quiet=0)
else:
btn = makeFragmentButton()
btn.setText(btn_label)
btn.clicked.connect(btn_command)
if btn_tooltip:
btn.setToolTip(btn_tooltip)
btn_row_layout.addWidget(btn)
btn_row_layout.addStretch()
def __init__(self, parent, protocol):
super(Hmmscan_results_window_qt, self).__init__(parent)
self.protocol = protocol
self.query_len = len(
self.protocol.query_element.my_sequence.replace('-', ''))
#########################
# Configure the window. #
#########################
self.setWindowTitle("HMMSCAN Results")
# Sets the central widget.
self.central_widget = QtWidgets.QWidget()
self.setCentralWidget(self.central_widget)
# The window has a main vbox layout.
self.main_vbox = QtWidgets.QVBoxLayout()
# Parameters used to draw the 'QGraphicsView' widgets for showing domains.
self.preferred_size_policy = QtWidgets.QSizePolicy(
QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
self.view_bg_color = "transparent"
self.full_seq_pen = QtGui.QPen(QtGui.QColor(0, 0, 0, 0), 2)
self.full_seq_color = "#7f7f7f"
qcolor = QtGui.QColor(0, 0, 0)
qcolor.setNamedColor(self.full_seq_color)
self.full_seq_brush = QtGui.QBrush(qcolor)
self.font_qcolor = QtGui.QColor(220, 220, 220, 255)
self.font_size = 7
################
# Upper frame. #
################
self.upper_frame = QtWidgets.QFrame()
self.upper_frame_layout = QtWidgets.QGridLayout()
self.upper_frame.setLayout(self.upper_frame_layout)
self.main_vbox.addWidget(self.upper_frame)
if 'query_descr' in self.protocol.parsed_res[
0] and self.protocol.parsed_res[0]['query_descr']:
labelseq = self.protocol.query_element.my_header # + '\n' + querydescr
else:
try:
if len(self.protocol.query_element.description) > 79:
labelseq = self.protocol.query_element.description[:78] + '...'
else:
labelseq = self.protocol.query_element.description
except TypeError:
labelseq = self.protocol.query_element.my_header
self.upper_frame_title = QtWidgets.QLabel(
"HMMSCAN search results for " + labelseq)
self.upper_frame_layout.addWidget(self.upper_frame_title)
#-------------------------
# Domain graphics frame. -
#-------------------------
# Builds the scene where to draw the domain representations.
self.canvas_plot_scene = QtWidgets.QGraphicsScene()
self.canvas_plot_view = QtWidgets.QGraphicsView(self.canvas_plot_scene)
self.canvas_plot_view.setFixedHeight(120)
self.canvas_plot_view.setSizePolicy(self.preferred_size_policy)
self.canvas_plot_view.setStyleSheet("background: %s" %
self.view_bg_color)
self.upper_frame_layout.addWidget(self.canvas_plot_view)
# Draw a rectangle with the full sequence.
self.x_init = 10
y_init = 95 # 95
self.domain_y_init = y_init - 7
self.full_seq_rect_w = 800
full_seq_rect_h = 10
self.canvas_plot_scene.addRect(self.x_init, y_init,
self.full_seq_rect_w, full_seq_rect_h,
self.full_seq_pen, self.full_seq_brush)
# Draw the labels for the N- and C-terminal residues.
text_offset_y = 15
text_offset_x = 10
text_n = self.canvas_plot_scene.addText("1")
text_n.setPos(self.x_init - text_offset_x, y_init + text_offset_y)
text_n.setDefaultTextColor(self.font_qcolor)
text_n.setFont(QtGui.QFont(text_n.font().family(), self.font_size))
c_label = str(self.query_len)
text_c = self.canvas_plot_scene.addText(c_label)
text_offset_x_add = 5
if len(c_label) > 2:
text_offset_x_add = 10
text_c.setPos(
self.x_init + self.full_seq_rect_w - text_offset_x -
text_offset_x_add, y_init + text_offset_y)
text_c.setDefaultTextColor(self.font_qcolor)
text_c.setFont(QtGui.QFont(text_c.font().family(), self.font_size))
#################
# Middle frame. #
#################
# Scroll area which contains the widgets, set as the centralWidget.
self.middle_scroll = QtWidgets.QScrollArea()
self.main_vbox.addWidget(self.middle_scroll)
# Widget that contains the collection of Vertical Box.
self.middle_widget = QtWidgets.QWidget()
# Scroll area properties.
self.middle_scroll.setWidgetResizable(True)
self.middle_scroll.setWidget(self.middle_widget)
# QFormLayout in the middle frame.
self.middle_formlayout = QtWidgets.QFormLayout()
self.middle_widget.setLayout(self.middle_formlayout)
#-----------------
# Results frame. -
#-----------------
# Set the frame and its layout.
self.results_frame = QtWidgets.QFrame()
self.middle_formlayout.addRow(self.results_frame)
self.results_grid = QtWidgets.QGridLayout()
self.results_frame.setLayout(self.results_grid)
# Calls a method which actually displays the similarity searches results.
self.display_hmmscan_hits()
# Align the gridded widgets to the left.
self.results_grid.setAlignment(QtCore.Qt.AlignLeft)
self.results_grid.setHorizontalSpacing(30)
#################
# Bottom frame. #
#################
self.main_button = QtWidgets.QPushButton("Submit")
self.main_button.clicked.connect(
lambda a=None: self.protocol.hmmer_results_state())
self.main_vbox.addWidget(self.main_button)
self.main_button.setFixedWidth(self.main_button.sizeHint().width())
# Sets the main vertical layout.
self.central_widget.setLayout(self.main_vbox)
self.main_vbox.setAlignment(self.main_button, QtCore.Qt.AlignCenter)
def build_panel_elements(self, parent):
'''
Responsible for creating all panel elements in order and adding them to the layout.
'''
self.create_new_form = parent.load_form("create_shortcut", None)
self.help_form = parent.load_form("help_shortcut", None)
self.confirm_change = parent.load_form("change_confirm", None)
self.model = QtGui.QStandardItemModel(self)
self.proxy_model = QtCoreModels.QSortFilterProxyModel(self)
self.proxy_model.setSourceModel(self.model)
self.proxy_model.setFilterCaseSensitivity(Qt.CaseInsensitive)
self.proxy_model.setFilterKeyColumn(-1)
self.setWindowTitle('Keyboard Shortcut Menu')
layout = QtWidgets.QVBoxLayout(self)
self.setLayout(layout)
# Create layout for filter bar and refresh button
top_layout = QtWidgets.QGridLayout()
layout.addLayout(top_layout)
# Filter
self.filter_le = QtWidgets.QLineEdit(self)
top_layout.addWidget(self.filter_le)
self.filter_le.setPlaceholderText("Filter")
self.filter_le.textChanged.connect(self.proxy_model.setFilterRegExp)
self.refresh_button = QtWidgets.QPushButton(self)
self.refresh_button.resize(26, 26)
top_layout.addWidget(self.refresh_button, 0, 1)
# themed icons only available by default on X11
if self.refresh_button.icon().isNull():
self.refresh_button.setIcon(QtGui.QIcon(
os.path.expandvars('$PYMOL_DATA/pmg_qt/icons/refresh.svg')))
self.refresh_button.setToolTip(
"Refresh the table to reflect any external changes")
self.refresh_button.clicked.connect(self.refresh_populate)
# Table
self.table = QtWidgets.QTableView(self)
self.table.setModel(self.proxy_model)
layout.addWidget(self.table)
self.intial_populate()
self.formatTable()
# Add layout for buttons
button_layout = QtWidgets.QGridLayout()
layout.addLayout(button_layout)
# Buttons
self.create_new_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.create_new_button, 0, 0)
self.create_new_button.setText("Create New")
self.create_new_button.setToolTip(
"Add a key binding that does not currently appear on the table")
self.create_new_button.clicked.connect(
lambda: self.create_new_form._dialog.show())
self.delete_selected_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.delete_selected_button, 0, 1)
self.delete_selected_button.setText("Delete Selected")
self.delete_selected_button.setToolTip(
"Unbind selected key bindings and remove any that have been created")
self.delete_selected_button.clicked.connect(self.delete_selected)
self.delete_selected_button.setEnabled(False)
self.reset_selected_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.reset_selected_button, 0, 2)
self.reset_selected_button.setText("Reset Selected")
self.reset_selected_button.setToolTip(
"Restore selected key bindings to their default values")
self.reset_selected_button.clicked.connect(self.reset_selected)
self.reset_selected_button.setEnabled(False)
self.reset_all_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.reset_all_button, 0, 3)
self.reset_all_button.setText("Reset All")
self.reset_all_button.setToolTip(
"Restore all key bindings to their default values and remove any that have been created")
self.reset_all_button.clicked.connect(self.reset_all_default)
self.save_button = QtWidgets.QPushButton(self)
button_layout.addWidget(self.save_button, 0, 4)
self.save_button.setText("Save")
self.save_button.setToolTip(
"Save the current key bindings to be loaded automatically when opening PyMOL")
self.save_button.clicked.connect(self.shortcut_manager.save_shortcuts)
# Ensuring that confirmed key and binding remain in scope
self.confirm_new_key = ''
self.confirm_new_binding = ''
# Connect create new and confirm menus
self.create_new_shortcut_menu_connect()
self.confirm_menu_connect()
self.model.itemChanged.connect(self.itemChanged)
def __init__(self, parent=None):
super(SurfStampFrame, self).__init__(parent)
self.layout = QtWidgets.QVBoxLayout()
self.setLayout(self.layout)
glayout1 = QtWidgets.QGridLayout()
self.label_message = QtWidgets.QLabel(self)
self.label_message.setText("SurfStamp PyMOL plugin")
self.layout.addWidget(self.label_message)
self.combo_model = QtWidgets.QComboBox()
self.combo_model.addItems([])
self.layout.addWidget(self.combo_model)
self.label_reso = QtWidgets.QLabel(self)
self.label_reso.setText("Surface Resolution")
glayout1.addWidget(self.label_reso, 1, 0)
self.spin_reso = QtWidgets.QDoubleSpinBox(self)
self.spin_reso.setRange(0.1, 1.0)
self.spin_reso.setSingleStep(0.05)
self.spin_reso.setValue(0.7)
glayout1.addWidget(self.spin_reso, 1, 1)
self.label_imagesize = QtWidgets.QLabel(self)
self.label_imagesize.setText("Image Size")
glayout1.addWidget(self.label_imagesize, 2, 0)
self.spin_imagesize = QtWidgets.QSpinBox(self)
self.spin_imagesize.setRange(1000, 10000)
#PILLOW？は 13000 くらいが Max っぽい
self.spin_imagesize.setSingleStep(100)
self.spin_imagesize.setValue(4000)
glayout1.addWidget(self.spin_imagesize, 2, 1)
self.label_fontsize = QtWidgets.QLabel(self)
self.label_fontsize.setText("Font Size")
glayout1.addWidget(self.label_fontsize, 3, 0)
self.spin_fontsize = QtWidgets.QSpinBox(self)
self.spin_fontsize.setRange(3, 100)
self.spin_fontsize.setSingleStep(1)
self.spin_fontsize.setValue(20)
glayout1.addWidget(self.spin_fontsize, 3, 1)
glayout2 = QtWidgets.QGridLayout()
self.check_outline = QtWidgets.QCheckBox('Outline')
self.check_outline.setChecked(True)
glayout2.addWidget(self.check_outline, 0, 0)
self.check_nowater = QtWidgets.QCheckBox('Remove Waters')
self.check_nowater.setChecked(True)
glayout2.addWidget(self.check_nowater, 0, 1)
self.check_colorall = QtWidgets.QCheckBox('Color All')
self.check_colorall.setChecked(False)
glayout2.addWidget(self.check_colorall, 1, 0)
self.check_tile = QtWidgets.QCheckBox('Repeating Tile')
self.check_tile.clicked.connect(self.checkTileOn)
self.check_tile.setChecked(False)
glayout2.addWidget(self.check_tile, 1, 1)
self.check_oneletter = QtWidgets.QCheckBox('One Letter')
glayout2.addWidget(self.check_oneletter, 2, 0)
self.check_nochainname = QtWidgets.QCheckBox('No Chain Name')
glayout2.addWidget(self.check_nochainname, 2, 1)
self.check_ignore_occupancy = QtWidgets.QCheckBox('Ignore Occupancy')
glayout2.addWidget(self.check_ignore_occupancy, 3, 0)
self.check_cartoon = QtWidgets.QCheckBox('Cartoon')
self.check_cartoon.clicked.connect(self.checkCartoonOn)
glayout2.addWidget(self.check_cartoon, 3, 1)
self.check_mmcif = QtWidgets.QCheckBox('Use MMCIF')
glayout2.addWidget(self.check_mmcif, 4, 0)
self.check_builtin = QtWidgets.QCheckBox('Built-in Surface Generator')
glayout2.addWidget(self.check_builtin, 4, 1)
self.check_builtin.clicked.connect(self.checkBuiltinOn)
#MMCIF は AUTH が不完全だ！
#self.check_label = QtWidgets.QCheckBox('ID Label');
#self.layout.addWidget(self.check_label);
# Text field for output file
glayout4 = QtWidgets.QVBoxLayout()
self.label_outprefix = QtWidgets.QLabel(
'Output Prefix (Prefix+<something> will be overwritten.)')
glayout4.addWidget(self.label_outprefix)
glayout4b = QtWidgets.QGridLayout()
self.text_outprefix = QtWidgets.QLineEdit(self)
self.text_outprefix.setReadOnly(True)
glayout4b.addWidget(self.text_outprefix, 0, 0)
self.button_outprefix = QtWidgets.QPushButton(self)
self.button_outprefix.setText("Save As")
self.button_outprefix.clicked.connect(self.getFile)
self.text_outprefix.setStyleSheet("background-color: lightgray;")
glayout4b.addWidget(self.button_outprefix, 0, 1)
glayout4.addLayout(glayout4b)
glayout3 = QtWidgets.QGridLayout()
self.button_ok = QtWidgets.QPushButton('Create')
self.button_ok.clicked.connect(self.runSurfStamp)
glayout3.addWidget(self.button_ok, 0, 0)
self.button_close = QtWidgets.QPushButton('Close')
self.button_close.clicked.connect(self.hide)
glayout3.addWidget(self.button_close, 0, 1)
self.layout.addLayout(glayout1)
self.layout.addLayout(glayout2)
self.layout.addLayout(glayout4)
self.layout.addLayout(glayout3)
screengeom = QtWidgets.qApp.desktop().screenGeometry()
wwidth = 300
hheight = 200
self.setGeometry(screengeom.width() / 2 - wwidth / 2,
screengeom.height() / 2 - hheight / 2, wwidth,
hheight)
self.setWindowTitle('SurfStamp')
self.checkTileOn()
self.checkBuiltinOn()
self.checkCartoonOn()
self.show()