def __init__(self, parent, cmd):
QtWidgets.QWidget.__init__(self, parent, Qt.Window)
self.setMinimumSize(400, 500)
self.cmd = cmd
self.model = QtGui.QStandardItemModel(self)
self.proxy_model = QtCoreModels.QSortFilterProxyModel(self)
self.proxy_model.setSourceModel(self.model)
self.setWindowTitle('PyMOL Advanced Settings')
layout = QtWidgets.QVBoxLayout(self)
self.setLayout(layout)
self.filter_le = QtWidgets.QLineEdit(self)
layout.addWidget(self.filter_le)
self.filter_le.setPlaceholderText("Filter")
self.filter_le.textChanged.connect(self.proxy_model.setFilterRegExp)
self.populateData()
self.table = QtWidgets.QTableView(self)
self.table.setModel(self.proxy_model)
layout.addWidget(self.table)
self.formatTable()
self.model.itemChanged.connect(self.itemChanged)
def initUI(self):
self.setWindowTitle('PyMod Directory Selection')
self.vertical_layout = QtWidgets.QVBoxLayout()
# Main label.
self.label = QtWidgets.QLabel(
"Select a folder inside which to build the 'PyMod Directory'",
self)
self.vertical_layout.addWidget(self.label)
# Entry and "Browse" button.
self.horizontal_layout = QtWidgets.QHBoxLayout()
self.main_entry = QtWidgets.QLineEdit(self.pymod.home_directory, self)
self.main_entry.setStyleSheet("background-color: white; color: black")
self.horizontal_layout.addWidget(self.main_entry)
self.browse_button = QtWidgets.QPushButton("BROWSE", self)
self.browse_button.clicked.connect(self.pymod_directory_browse_state)
self.horizontal_layout.addWidget(self.browse_button)
self.vertical_layout.addLayout(self.horizontal_layout)
# "Submit" button.
self.submit_button = QtWidgets.QPushButton("SUBMIT", self)
self.submit_button.setFixedWidth(self.submit_button.sizeHint().width())
self.submit_button.clicked.connect(self.on_submit_button_press)
self.vertical_layout.addWidget(self.submit_button)
self.vertical_layout.setAlignment(self.submit_button,
QtCore.Qt.AlignCenter)
# Set the layouts.
self.setLayout(self.vertical_layout)
def create_dialog():
dialog = QtWidgets.QDialog()
dialog.setWindowTitle('Lighting Settings')
sliders = [
"Diffuse Reflection",
('ambient', 0, 1, None),
('reflect', -1, 1, None),
"Direct Light from Front",
('direct (+reflect)', -1, 1, None), # diffuse, coupled with "reflect"
('spec_direct', 0, 1, None),
('spec_direct_power', 0, 100, 1),
"Free placeable directed Lights",
('light_count', 1, 8, 1),
('edit_light', 1, 7, 1),
"Specular Reflection",
('spec_count', -1, 8, 1),
# ('spec_power', -1, 200, 1), # deprecated since v1.5
('shininess', 0, 100, None), # same as spec_power
('spec_reflect', -0.01, 1, None),
('specular', 0, 1, None),
('specular_intensity (=specular)', 0, 1, None), # same as specular
"Ambient Occlusion (Surface only)",
('ambient_occlusion_mode', 0, 2, 1),
('ambient_occlusion_scale', 1.0, 50., None),
('ambient_occlusion_smooth', 1, 20, 1),
"Ray trace only",
('power', 1, 10, None),
('reflect_power', 1, 10, None),
]
layout = QtWidgets.QVBoxLayout(dialog)
button_layout = QtWidgets.QHBoxLayout()
layout.addLayout(button_layout)
layout.setContentsMargins(5, 0, 5, 0)
button_layout.addWidget(
QtWidgets.QLabel("<font color=red>Presets:</font>"))
presets = [
("Default", preset_default),
("Metal", preset_metal),
("Plastic", preset_plastic),
("Rubber", preset_rubber),
("X-Ray", preset_xray),
]
for name, fun in presets:
btn = QtWidgets.QPushButton(name, dialog)
btn.pressed.connect(fun)
btn.setAutoDefault(False)
button_layout.addWidget(btn)
form_layout = QtWidgets.QFormLayout()
form_layout.setContentsMargins(0, 0, 0, 0)
form_layout.setVerticalSpacing(0)
form_layout.setLabelAlignment(Qt.AlignLeft)
layout.addLayout(form_layout)
for i, item in enumerate(sliders, 1):
if isinstance(item, str):
label = QtWidgets.QLabel("<font color=blue>" + item + "</font>")
form_layout.addRow(label)
continue
name, min, max, res = item
if res is None:
res = 0.01 if (max - min < 100) else 0.1
line_edit = QtWidgets.QLineEdit(dialog)
slider = SettingSlider(dialog,
name.split()[0], min, max, res, line_edit)
h_layout = QtWidgets.QHBoxLayout()
h_layout.addWidget(slider, 3)
h_layout.addWidget(line_edit, 1)
form_layout.addRow(name, h_layout)
return dialog
def initUI(self):
#----------------------------
# Left frame (for headers). -
#----------------------------
self.sequence_ID_groupbox = QtWidgets.QGroupBox('SEQUENCE ID')
# self.sequence_ID_groupbox.setStyleSheet("QLabel {font: 14pt COURIER NEW font-weight: bold} ")
id_frame_stylesheet = "QLabel {font: %spt %s; font-weight: %s; color: white}" % (
self.main_window.font_size, self.main_window.font,
self.main_window.font_weight)
self.sequence_ID_groupbox.setStyleSheet(id_frame_stylesheet)
self.id_form_layout = QtWidgets.QFormLayout()
#self.left_scroll
self.left_scroll = QtWidgets.QScrollArea()
self.left_scroll.setHorizontalScrollBarPolicy(
QtCore.Qt.ScrollBarAlwaysOn)
self.left_scroll.setVerticalScrollBarPolicy(
QtCore.Qt.ScrollBarAsNeeded)
self.left_scroll.resize(200, 400)
self.left_scroll.setWidget(
self.sequence_ID_groupbox
) # sequence_ID_groupbox dentro left_scroll area
self.left_scroll.setWidgetResizable(True)
#self.left_frame
self.left_frame = QtWidgets.QFrame(self)
self.left_frame.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.left_frame.resize(200, 400)
self.left_frame.setStyleSheet(self.style)
self.left_frame.setFrameShadow(QtWidgets.QFrame.Sunken)
#self.left_frame_layout
self.left_frame_layout = QtWidgets.QVBoxLayout(self)
self.left_frame_layout.addWidget(self.left_scroll)
self.left_frame.setLayout(
self.left_frame_layout) # left_frame_layout dentro left_frame
#-------------------------------
# Right frame (for sequences). -
#-------------------------------
# This groupbox
self.sequence_SEQ_groupbox = QtWidgets.QGroupBox('SEQUENCES')
seq_frame_stylesheet = "QLabel {font: %spt %s; font-weight: %s; color: white}" % (
self.main_window.font_size, self.main_window.font,
self.main_window.font_weight)
self.sequence_SEQ_groupbox.setStyleSheet(seq_frame_stylesheet)
self.seq_form_layout = QtWidgets.QFormLayout()
#self.right_scroll
self.right_scroll = QtWidgets.QScrollArea()
self.right_scroll.setHorizontalScrollBarPolicy(
QtCore.Qt.ScrollBarAlwaysOn)
self.right_scroll.setVerticalScrollBarPolicy(
QtCore.Qt.ScrollBarAsNeeded)
self.right_scroll.resize(900, 400)
self.right_scroll.setWidget(
self.sequence_SEQ_groupbox
) # sequence_ID_groupbox dentro left_scroll area
self.right_scroll.setWidgetResizable(True)
#self.right_frame
self.right_frame = QtWidgets.QFrame(self)
self.right_frame.setFrameShape(QtWidgets.QFrame.StyledPanel)
self.right_frame.resize(900, 400)
self.right_frame.setStyleSheet(self.style)
self.right_frame.setFrameShadow(QtWidgets.QFrame.Sunken)
#self.right_frame_layout
self.right_frame_layout = QtWidgets.QVBoxLayout(self)
self.right_frame_layout.addWidget(self.right_scroll)
self.right_frame.setLayout(
self.right_frame_layout) # left_frame_layout dentro left_frame
#connect the two Vertical Bars to move them togheter
self.left_scroll.verticalScrollBar().valueChanged.connect(
self.right_scroll.verticalScrollBar().setValue)
self.right_scroll.verticalScrollBar().valueChanged.connect(
self.left_scroll.verticalScrollBar().setValue)
#----------------------------------
# Bottom part of the main window. -
#----------------------------------
self.splitter1 = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
self.splitter1.addWidget(self.left_frame)
self.splitter1.addWidget(self.right_frame)
# creating sequence and position labels
self.label_sequence = QtWidgets.QLabel(self)
self.label_sequence.setText('Sequence:')
self.label_sequence.setStyleSheet(small_font_style)
self.textbox_sequence = QtWidgets.QLineEdit(self)
self.textbox_sequence.setStyleSheet(self.style + "; " +
small_font_style)
self.textbox_sequence.setReadOnly(True)
self.label_position = QtWidgets.QLabel(self)
self.label_position.setText('Position:')
self.label_position.setStyleSheet(small_font_style)
self.textbox_position = QtWidgets.QLineEdit(self)
self.textbox_position.setReadOnly(True)
self.textbox_position.setStyleSheet(self.style + "; " +
small_font_style)
self.textbox_position.setMinimumWidth(
675) # Width of the residues message bar width.
# creating an horizontal layout with sequence and position labels
self.text_layout = QtWidgets.QHBoxLayout()
self.text_layout.addWidget(self.label_sequence)
self.text_layout.addWidget(self.textbox_sequence)
self.text_layout.addWidget(self.label_position)
self.text_layout.addWidget(self.textbox_position)
# creating a layout with sequence window and labels
self.grid = QtWidgets.QVBoxLayout()
self.grid.addWidget(self.splitter1)
self.grid.addLayout(self.text_layout)
self.setLayout(self.grid)
def display_paramenter_options(self, parameter):
"""
Used to display a series of widgets to choose the parameter value in PyMod
options window. This is conditioned on the type of input widget of the
'parameter'.
"""
# Label with the name of the parameter.
param_full_name_label = QtWidgets.QLabel(parameter.full_name)
self.middle_formlayout.addWidget(param_full_name_label,
self.row_counter, 0)
# Do not display any input widget.
if parameter.widget_type is None:
pass
# Display any a text entry input.
elif parameter.widget_type == "path_entryfield":
# Entry for the path.
path_entryfield = QtWidgets.QLineEdit(
str(parameter.get_starting_value()))
if parameter.editable:
path_entryfield.setStyleSheet(active_entry_style + "; " +
small_font_style)
else:
path_entryfield.setStyleSheet(inactive_entry_style + "; " +
small_font_style)
path_entryfield.setEnabled(False)
self.middle_formlayout.addWidget(path_entryfield, self.row_counter,
1)
self.tools_params_dict[parameter.parent_tool.name][
parameter.name] = path_entryfield
# Button for browsing the path.
if parameter.editable:
path_browse_button = QtWidgets.QPushButton("Browse")
path_browse_button.setStyleSheet(small_font_style)
if parameter.path_type in ("file", "directory"):
path_browse_button.clicked.connect(
lambda a=None, p=parameter: self.choose_path(p))
else:
raise KeyError("Unknown 'path_type': %s" %
str(parameter.path_type))
self.middle_formlayout.addWidget(path_browse_button,
self.row_counter, 2)
# Button to automatically identifying the path.
if parameter.auto_find:
auto_find_button = QtWidgets.QPushButton("Auto Find")
auto_find_button.setStyleSheet(small_font_style)
self.middle_formlayout.addWidget(auto_find_button,
self.row_counter, 3)
auto_find_button.clicked.connect(
lambda a=None, e=path_entryfield: parameter.
auto_find_command(e))
# Show the status of a parameter.
elif parameter.widget_type == "show_status":
text_to_show, status = parameter.get_status()
status_entryfield = QtWidgets.QLineEdit(text_to_show)
if status:
status_entryfield.setStyleSheet("background-color: %s" %
success_bg_color)
else:
status_entryfield.setStyleSheet("background-color: %s" %
failure_bg_color)
status_entryfield.setEnabled(False)
status_entryfield.setFixedWidth(200)
self.middle_formlayout.addWidget(status_entryfield,
self.row_counter, 1)
else:
raise KeyError("Unkown 'widget_type': %s" % parameter.widget_type)
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()
