def __init__(self, session, tool_name, *, title=None):
ToolInstance.__init__(self, session, tool_name)
from chimerax.ui import MainToolWindow
tw = MainToolWindow(self)
if title is not None:
tw.title = title
self.tool_window = tw
parent = tw.ui_area
from matplotlib import figure
self.figure = f = figure.Figure(dpi=100, figsize=(2, 2))
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as Canvas
self.canvas = c = Canvas(f)
parent.setMinimumHeight(
1
) # Matplotlib gives divide by zero error when plot resized to 0 height.
c.setParent(parent)
from PyQt5.QtWidgets import QHBoxLayout
layout = QHBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(c)
parent.setLayout(layout)
tw.manage(placement="side")
self.axes = axes = f.gca()
self._pan = None # Pan/zoom mouse control
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
# 'display_name' defaults to class name with spaces inserted
# between lower-then-upper-case characters (therefore "Tool UI"
# in this case), so only override if different name desired
self.display_name = "ChimeraX Python Shell"
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
parent = self.tool_window.ui_area
# UI content code
from ipykernel.ipkernel import IPythonKernel
save_ns = IPythonKernel.user_ns
IPythonKernel.user_ns = {'session': session}
from qtconsole.inprocess import QtInProcessKernelManager
kernel_manager = QtInProcessKernelManager()
kernel_manager.start_kernel()
kernel_client = kernel_manager.client()
kernel_client.start_channels()
from qtconsole.rich_jupyter_widget import RichJupyterWidget
self.shell = RichJupyterWidget(parent)
def_banner = self.shell.banner
self.shell.banner = "{}\nCurrent ChimeraX session available as 'session'.\n\n".format(
def_banner)
self.shell.kernel_manager = kernel_manager
self.shell.kernel_client = kernel_client
IPythonKernel.user_ns = save_ns
from PyQt5.QtWidgets import QHBoxLayout
layout = QHBoxLayout()
layout.addWidget(self.shell)
layout.setStretchFactor(self.shell, 1)
parent.setLayout(layout)
self.tool_window.manage(placement=None)
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
from chimerax.ui import MainToolWindow
self.tool_window = tw = MainToolWindow(self)
parent = tw.ui_area
from PyQt5.QtWidgets import QVBoxLayout, QDialogButtonBox
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
parent.setLayout(layout)
from .gui import HBondsGUI
self.gui = HBondsGUI(session, show_model_restrict=False)
layout.addWidget(self.gui)
from PyQt5.QtWidgets import QDialogButtonBox as qbbox
bbox = qbbox(qbbox.Ok | qbbox.Apply | qbbox.Close | qbbox.Help)
bbox.accepted.connect(self.run_hbonds)
bbox.button(qbbox.Apply).clicked.connect(self.run_hbonds)
bbox.accepted.connect(
self.delete) # slots executed in the order they are connected
bbox.rejected.connect(self.delete)
from chimerax.core.commands import run
bbox.helpRequested.connect(
lambda run=run, ses=session: run(ses, "help " + self.help))
layout.addWidget(bbox)
tw.manage(placement=None)
def __init__(self, session):
ToolInstance.__init__(self, session, "Bogus Toolshed-demo Tool")
self.display_name = "Open Models"
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self, size=self.SIZE)
parent = self.tool_window.ui_area
# UI content code
from wx import html2
import wx
self.webview = html2.WebView.New(parent, wx.ID_ANY, size=self.SIZE)
self.webview.Bind(html2.EVT_WEBVIEW_NAVIGATING,
self._on_navigating,
id=self.webview.GetId())
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.webview, 1, wx.EXPAND)
parent.SetSizerAndFit(sizer)
self.tool_window.manage(placement="side")
# Add triggers for model addition/removal
from chimerax.core.models import ADD_MODELS, REMOVE_MODELS
self._handlers = [
session.triggers.add_handler(ADD_MODELS, self._make_page),
session.triggers.add_handler(REMOVE_MODELS, self._make_page)
]
self._make_page()
def delete(self):
ses = self.session
ses.triggers.remove_handler(self._model_display_change_handler)
sm = self._sphere_model
if sm and not sm.deleted:
ses.models.close([sm])
self._sphere_model = None
ToolInstance.delete(self)
def delete(self):
mmh = self._model_move_handler
if mmh:
self.session.triggers.remove_handler(mmh)
self._model_move_handler = None
ToolInstance.delete(self)
def restore_snapshot(cls, session, data):
bp = ButtonPanel(session, data['title'])
ToolInstance.set_state_from_snapshot(bp, session, data["super"])
bp.set_grid_size(data['rows'], data['columns'])
bp.set_fill_order(data['fill_order'])
for r, c, name, command in data['buttons']:
bp.add_button(name, command, row=r, column=c)
return bp
def __init__(self, session, tool_name, models=None, attr_names=None):
""" if 'models' is None, then we are being restored from a session and
set_state_from_snapshot will be called later.
"""
ToolInstance.__init__(self, session, tool_name)
if models is None:
return
self._finalize_init(session, models, attr_names)
def __init__(self, session, tool_name, alignment=None):
""" if 'alignment' is None, then we are being restored from a session and
_finalize_init will be called later.
"""
ToolInstance.__init__(self, session, tool_name)
if alignment is None:
return
self._finalize_init(alignment)
def delete(self):
self.region_browser.destroy()
self.seq_canvas.destroy()
self.alignment.detach_viewer(self)
for seq in self.alignment.seqs:
seq.triggers.remove_handler(self._seq_rename_handlers[seq])
from chimerax.atomic import get_triggers
get_triggers().remove_handler(self._atomic_changes_handler)
ToolInstance.delete(self)
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
# FIXME: display_name' defaults to class name with spaces inserted
# between lower-then-upper-case characters (therefore "Tool UI"
# in this case), so only override if different name desired
self.display_name = "custom name for running tool"
from chimerax.core.ui.gui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.tool_window.manage(placement="side")
parent = self.tool_window.ui_area
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self, close_destroys=False)
parent = self.tool_window.ui_area
from chimerax.ui.file_history import FileHistory
fh = FileHistory(session, parent, size_hint=(575, 200))
self.tool_window.manage(placement="side")
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
self._icon_size = 40
self._icons_per_row = 13
self.tool_window = None
from .shortcuts import keyboard_shortcuts
self.keyboard_shortcuts = keyboard_shortcuts(session)
parent = session.ui.main_window
self.buttons = self.create_toolbar(parent)
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
self.mouse_modes = mm = session.ui.mouse_modes
self.button_to_bind = 'right'
self._icon_size = 40
self._icons_per_row = 13
self.tool_window = None
self.modes = ordered_modes(mm.modes, mode_order)
parent = session.ui.main_window
self.buttons = self.create_toolbar(parent)
def __init__(self, session, tool_name):
self._requested_halt = False
self._model_move_handler = None
self._last_relative_position = None
self.max_steps = 2000
self.ijk_step_size_min = 0.01
self.ijk_step_size_max = 0.5
self._last_status_time = 0
self._status_interval = 0.5 # seconds
ToolInstance.__init__(self, session, tool_name)
from chimerax.ui import MainToolWindow
tw = MainToolWindow(self)
self.tool_window = tw
parent = tw.ui_area
from PyQt5.QtWidgets import QVBoxLayout, QLabel
layout = QVBoxLayout(parent)
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
parent.setLayout(layout)
# Make menus to choose molecule and map for fitting
mf = self._create_mol_map_menu(parent)
layout.addWidget(mf)
# Report correlation
from chimerax.ui.widgets import EntriesRow
cr = EntriesRow(
parent, 'Correlation', 0.0, 'Average map value', 0.0,
('Update',
lambda *args, self=self: self._update_metric_values(log=True)))
self._corr_label, self._ave_label = cl, al = cr.values
cl.value = al.value = None # Make fields blank
# Options panel
options = self._create_options_gui(parent)
layout.addWidget(options)
# Fit, Undo, Redo buttons
bf = self._create_action_buttons(parent)
layout.addWidget(bf)
# Status line
self._status_label = sl = QLabel(parent)
layout.addWidget(sl)
layout.addStretch(1) # Extra space at end
tw.manage(placement="side")
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
parent = self.tool_window.ui_area
# UI content code
from PyQt5.QtCore import Qt
from PyQt5.QtWidgets import QLabel, QHBoxLayout, QVBoxLayout, QCheckBox, QStackedWidget
self.view = v = View(session.models.scene_root_model, window_size=(0, 0))
v.initialize_rendering(session.main_view.render.opengl_context)
# TODO: from chimerax.graphics.camera import OrthographicCamera
v.camera = OrthoCamera()
if self.display_name.startswith('Top'):
side = SideViewCanvas.TOP_SIDE
else:
side = SideViewCanvas.RIGHT_SIDE
self.opengl_canvas = SideViewCanvas(parent, v, session, self, side=side)
clip = QLabel(parent)
clip.setText("clip:")
self.clip_near = QCheckBox(parent)
self.clip_near.setText("near")
self.clip_near.down = False
# TODO: parent.Bind(wx.EVT_CHECKBOX, self.on_near, self.clip_near)
self.clip_near.clicked.connect(self.on_near)
self.clip_far = QCheckBox(parent)
self.clip_far.setText("far")
self.clip_far.down = False
# TODO: parent.Bind(wx.EVT_CHECKBOX, self.on_far, self.clip_far)
self.clip_far.clicked.connect(self.on_far)
button_layout = QHBoxLayout()
button_layout.addWidget(clip, alignment=Qt.AlignCenter)
button_layout.addWidget(self.clip_near)
button_layout.addWidget(self.clip_far)
button_layout.addStretch(1)
class graphics_area(QStackedWidget):
def sizeHint(self): # noqa
from PyQt5.QtCore import QSize
return QSize(200, 200)
layout = QVBoxLayout()
ga = graphics_area(parent)
ga.addWidget(self.opengl_canvas.widget)
layout.addWidget(ga, 1)
layout.addLayout(button_layout)
parent.setLayout(layout)
self.tool_window.manage(placement="side")
def take_snapshot(self, session, flags):
data = {
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
'models': self.models,
'attr_names': self.attr_names,
'scores_fetched': self.scores_fetched
}
return data
def take_snapshot(self, session, flags):
data = {
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
'alignment': self.alignment,
'region browser': self.region_browser.save_state(),
'seq canvas': self.seq_canvas.save_state()
}
return data
def __init__(self, session, title):
ToolInstance.__init__(self, session, title)
self.title = title
self._rows = None
self._columns = None
self._next_row_col = (1, 1)
self._fill_order = 'rows'
self._buttons = {} # Map (row,column) -> QPushButton
from chimerax.ui import MainToolWindow
tw = MainToolWindow(self)
self.tool_window = tw
from PyQt5.QtWidgets import QGridLayout
self._layout = layout = QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
tw.ui_area.setLayout(layout)
tw.manage(placement="side")
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
self.minimize_steps = 10
self.edge_thickness = 0.1 # Edge diameter as fraction of edge length.
self.display_name = 'Cage Builder'
from chimerax.ui import MainToolWindow
tw = MainToolWindow(self)
self.tool_window = tw
parent = tw.ui_area
from PyQt5.QtWidgets import QHBoxLayout, QLabel, QPushButton, QLineEdit
layout = QHBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
cp = QLabel('Create polygon')
layout.addWidget(cp)
b5 = QPushButton('5')
b5.clicked.connect(lambda e: self.attach_polygons(5))
layout.addWidget(b5)
b6 = QPushButton('6')
b6.clicked.connect(lambda e: self.attach_polygons(6))
layout.addWidget(b6)
mn = QPushButton('Minimize')
mn.clicked.connect(self.minimize_cb)
layout.addWidget(mn)
ell = QLabel(' Edge length')
layout.addWidget(ell)
self.edge_length = el = QLineEdit('50')
el.setMaximumWidth(30)
layout.addWidget(el)
dp = QPushButton('Delete')
dp.clicked.connect(self.delete_polygon_cb)
layout.addWidget(dp)
layout.addStretch(1) # Extra space at end of button row.
parent.setLayout(layout)
tw.manage(placement="side")
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
from chimerax.ui import MainToolWindow
tw = MainToolWindow(self)
self.tool_window = tw
parent = tw.ui_area
from PyQt5.QtWidgets import QVBoxLayout, QLabel
layout = QVBoxLayout(parent)
layout.setContentsMargins(0,0,0,0)
layout.setSpacing(0)
parent.setLayout(layout)
# Heading
heading = QLabel('Placement of data array in x,y,z coordinate space:', parent)
layout.addWidget(heading)
# Make menus to choose molecule and map for fitting
mf = self._create_map_menu(parent)
layout.addWidget(mf)
# GUI for origin, step, angles, axis settings.
options = self._create_parameters_gui(parent)
layout.addWidget(options)
# Apply button
# bf = self._create_action_buttons(parent)
# layout.addWidget(bf)
# Status line
self._status_label = sl = QLabel(parent)
layout.addWidget(sl)
layout.addStretch(1) # Extra space at end
self._update_gui_values()
tw.manage(placement="side")
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
self.display_name = "Show Chain Sequence"
self.settings = SequencesSettings(session, "ChainSequences")
from chimerax.ui import MainToolWindow
self.tool_window = tw = MainToolWindow(self)
parent = tw.ui_area
from PyQt5.QtWidgets import QVBoxLayout, QCheckBox
layout = QVBoxLayout()
parent.setLayout(layout)
from chimerax.atomic.widgets import ChainListWidget
self.chain_list = ChainListWidget(session, group_identical=self.settings.grouping,
autoselect="first")
self.chain_list.value_changed.connect(self._update_show_button)
layout.addWidget(self.chain_list, stretch=1)
self.grouping_button = QCheckBox("Group identical sequences")
self.grouping_button.setChecked(self.settings.grouping)
self.grouping_button.stateChanged.connect(self._grouping_change)
layout.addWidget(self.grouping_button)
from PyQt5.QtWidgets import QDialogButtonBox as qbbox
bbox = qbbox()
self._show_button = bbox.addButton("Show", qbbox.AcceptRole)
bbox.addButton(qbbox.Cancel)
#bbox.addButton(qbbox.Help)
bbox.accepted.connect(self.show_seqs)
bbox.accepted.connect(self.delete) # slots executed in the order they are connected
bbox.rejected.connect(self.delete)
from chimerax.core.commands import run
bbox.helpRequested.connect(lambda run=run, ses=session: run(ses, "help " + self.help))
layout.addWidget(bbox)
self._update_show_button()
tw.manage(placement=None)
def __init__(self, session, tool_name):
# Standard template stuff
ToolInstance.__init__(self, session, tool_name)
self.display_name = "Toolshed"
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.tool_window.manage(placement=None)
parent = self.tool_window.ui_area
from PyQt5.QtWidgets import QGridLayout, QTabWidget
from chimerax.ui.widgets import HtmlView
layout = QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
self.tab_widget = QTabWidget()
self.html_view = HtmlView(size_hint=(1000, 600),
download=self._download)
self.tab_widget.addTab(self.html_view, "Toolshed")
layout.addWidget(self.tab_widget, 0, 0)
parent.setLayout(layout)
from PyQt5.QtCore import QUrl
self.html_view.setUrl(QUrl(self.url))
self._pending_downloads = []
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
from chimerax.ui import MainToolWindow
self.tool_window = tw = MainToolWindow(self)
parent = tw.ui_area
layout = QVBoxLayout()
layout.setContentsMargins(0,0,0,0)
layout.setSpacing(3)
parent.setLayout(layout)
session.logger.status("Build Structure is a work in progress, more functions coming soon...",
color="blue")
self.category_button = QPushButton()
layout.addWidget(self.category_button, alignment=Qt.AlignCenter)
cat_menu = QMenu(parent)
self.category_button.setMenu(cat_menu)
cat_menu.triggered.connect(self._cat_menu_cb)
self.category_areas = QStackedWidget()
layout.addWidget(self.category_areas)
self.handlers = []
self.category_widgets = {}
for category in ["Start Structure", "Modify Structure"]:
self.category_widgets[category] = widget = QFrame()
widget.setLineWidth(2)
widget.setFrameStyle(QFrame.Panel | QFrame.Sunken)
getattr(self, "_layout_" + category.lower().replace(' ', '_'))(widget)
self.category_areas.addWidget(widget)
cat_menu.addAction(category)
initial_category = "Start Structure"
self.category_button.setText(initial_category)
self.category_areas.setCurrentWidget(self.category_widgets[initial_category])
tw.manage(placement="side")
def take_snapshot(self, session, flags):
import sys
data = {
'ToolInstance':
ToolInstance.take_snapshot(self, session, flags),
'mgr':
self.mgr,
'res_type':
self.res_type,
'lib_display_name':
session.rotamers.library(self.rot_lib).display_name,
'table info': (self.table.session_info(),
[(col_type, c.title, c.data_fetch, c.display_format)
for col_type, c in self.opt_columns.items()])
}
return data
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
self.display_name = "Models"
self.settings = ModelPanelSettings(session, "ModelPanel")
last = self.settings.last_use
from time import time
now = self.settings.last_use = time()
short_titles = last != None and now - last < 777700 # about 3 months
from chimerax.ui import MainToolWindow
self.tool_window = tw = MainToolWindow(self, close_destroys=False)
parent = tw.ui_area
from PyQt5.QtWidgets import QTreeWidget, QHBoxLayout, QVBoxLayout, QAbstractItemView, \
QFrame, QPushButton, QSizePolicy
class SizedTreeWidget(QTreeWidget):
def sizeHint(self):
from PyQt5.QtCore import QSize
# side buttons will keep the vertical size reasonable
if getattr(self, '_first_size_hint_call', True):
self._first_size_hint_call = False
width = 0
else:
width = self.header().length()
return QSize(width, 200)
self.tree = SizedTreeWidget()
self.tree.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.tree.keyPressEvent = session.ui.forward_keystroke
self.tree.expanded.connect(self._ensure_id_width)
layout = QHBoxLayout()
layout.setContentsMargins(0,0,0,0)
layout.setSpacing(0)
layout.addWidget(self.tree)
layout.setStretchFactor(self.tree, 1)
parent.setLayout(layout)
shown_title = "" if short_titles else "Shown"
sel_title = "" if short_titles else "Select"
self.tree.setHeaderLabels(["Name", "ID", " ", shown_title, sel_title])
from chimerax.ui.icons import get_qt_icon
self.tree.headerItem().setIcon(3, get_qt_icon("shown"))
self.tree.headerItem().setToolTip(3, "Shown")
self.tree.headerItem().setIcon(4, get_qt_icon("select"))
self.tree.headerItem().setToolTip(4, "Selected")
self.tree.setColumnWidth(self.NAME_COLUMN, 200)
self.tree.setSelectionBehavior(QAbstractItemView.SelectRows)
self.tree.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.tree.setAnimated(True)
self.tree.setUniformRowHeights(True)
self.tree.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.tree.itemChanged.connect(self._tree_change_cb)
buttons_layout = QVBoxLayout()
layout.addLayout(buttons_layout)
self._items = []
for model_func in [close, hide, show, view]:
button = QPushButton(model_func.__name__.capitalize())
buttons_layout.addWidget(button)
button.clicked.connect(lambda chk, self=self, mf=model_func, ses=session:
mf([self.models[row] for row in [self._items.index(i)
for i in self.tree.selectedItems()]] or self.models, ses))
self.simply_changed_models = set()
self.check_model_list = True
self.countdown = 1
self.self_initiated = False
from chimerax.core.models import ADD_MODELS, REMOVE_MODELS, \
MODEL_DISPLAY_CHANGED, MODEL_ID_CHANGED, MODEL_NAME_CHANGED
from chimerax.core.selection import SELECTION_CHANGED
session.triggers.add_handler(SELECTION_CHANGED,
lambda *args: self._initiate_fill_tree(*args, countdown=3))
session.triggers.add_handler(MODEL_DISPLAY_CHANGED,
lambda *args: self._initiate_fill_tree(*args, simple_change=True, countdown=(0,3)))
session.triggers.add_handler(ADD_MODELS,
lambda *args: self._initiate_fill_tree(*args, always_rebuild=True, countdown=(3,10)))
session.triggers.add_handler(REMOVE_MODELS,
lambda *args: self._initiate_fill_tree(*args, always_rebuild=True))
session.triggers.add_handler(MODEL_ID_CHANGED,
lambda *args: self._initiate_fill_tree(*args, always_rebuild=True, countdown=3))
session.triggers.add_handler(MODEL_NAME_CHANGED,
lambda *args: self._initiate_fill_tree(*args, simple_change=True, countdown=3))
from chimerax import atomic
atomic.get_triggers().add_handler("changes", self._changes_cb)
self._frame_drawn_handler = None
tw.manage(placement="side")
tw.shown_changed = self._shown_changed
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
self.display_name = "ISOLDE"
from chimerax.ui.gui import MainToolWindow
self.tool_window = MainToolWindow(self)
self.tool_window.manage(placement=None)
parent = self.tool_window.ui_area
pp = parent.parent().parent()
pp.resize(540, 850)
import os
basedir = os.path.dirname(os.path.abspath(__file__))
from PyQt5 import uic
uifile = os.path.join(basedir, 'ui', 'IsoldeFrame.ui')
from Qt import QtWidgets, QtGui
#from . import isoldewidget
from .resources import resources_rc
mw = self.mainwin = QtWidgets.QFrame(parent=parent)
iw = self.iw = uic.loadUi(uifile, mw)
# iw = self.iw = isoldewidget.Ui_isolde_widget()
#iw = w.Ui_isolde_widget()
# iw.setupUi(self.mainwin)
import os
icon_file = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'resources/logo_small.png')
isolde_icon = QtGui.QPixmap(icon_file)
iw._isolde_icon.setPixmap(isolde_icon)
layout = QtWidgets.QHBoxLayout()
layout.addWidget(self.mainwin)
layout.setStretchFactor(self.mainwin, 1)
layout.setContentsMargins(1, 1, 1, 3)
parent.setLayout(layout)
self.tool_window.manage(placement=None)
# Should load saved state here
combo_boxes = (
iw._tutorials_combo_box,
iw._master_model_combo_box,
iw._real_space_map_volume_combo_box,
iw._sim_basic_xtal_settings_map_combo_box,
iw._sim_force_field_combo_box,
iw._sim_platform_combo_box,
iw._experience_level_combo_box,
iw._rebuild_sel_res_rot_backrub_map_combo_box,
iw._validate_rama_case_combo_box,
iw._validate_rama_sel_combo_box,
)
from .ui.util import win_auto_resize_combo_box_hack
for cb in combo_boxes:
win_auto_resize_combo_box_hack(cb)
###
# Selection manipulation buttons
###
# Grow selection at N-terminus
self._sel_grow_n_terminal_buttons = (iw._sel_extend_N_button, )
# Shrink selection at N-terminus
self._sel_shrink_n_terminal_buttons = (iw._sel_shrink_N_button, )
# Shrink selection at C-terminus
self._sel_shrink_c_terminal_buttons = (iw._sel_shrink_C_button, )
# Grow selection at C-terminus
self._sel_grow_c_terminal_buttons = (iw._sel_extend_C_button, )
# Define intermediate and expert frames
self._intermediate_frames = [
iw._sim_platform_frame,
iw._sim_basic_load_cif_templates_button,
]
self._expert_frames = [
iw._force_field_selection_frame,
]
# Any other frames/widgets that should be hidden at the start
self._hidden_at_start = [
iw._validate_rama_main_frame,
iw._validate_pep_main_frame,
iw._validate_rota_main_frame,
iw._validate_unparameterised_residues_main_frame,
iw._sim_basic_xtal_init_open_button,
iw._sim_basic_xtal_init_main_frame,
iw._sim_basic_xtal_settings_live_recalc_checkbox,
iw._sim_basic_xtal_map_settings_frame,
iw._real_space_map_from_volume_frame,
iw._live_map_control_frame,
iw._sim_status_indicator,
]
for f in self._hidden_at_start:
f.hide()
# Any frames/widgets that should be disabled at the start
self._disabled_at_start = [
#iw._sim_basic_xtal_map_settings_frame,
iw._map_masking_frame,
iw._rebuild_sel_res_pep_flip_button,
iw._rebuild_sel_res_cis_trans_flip_button,
iw._rebuild_cycle_rotamer_frame,
#iw._rebuild_sel_res_last_rotamer_button,
#iw._rebuild_sel_res_next_rotamer_button,
iw._rebuild_sel_res_rot_commit_button,
iw._rebuild_sel_res_rot_target_button,
iw._rebuild_sel_res_rot_discard_button,
iw._rebuild_sel_res_rot_release_button,
#~ iw._rebuild_pos_restraint_one_atom_frame,
#iw._rebuild_pin_atom_container,
iw._rebuild_pin_atom_to_current_pos_button,
iw._rebuild_pin_atom_to_pivot_button,
iw._rebuild_pos_restraint_clear_button,
iw._rebuild_2ry_struct_restr_container,
iw._rebuild_2ry_struct_restr_clear_button,
iw._rebuild_register_shift_container,
iw._rebuild_dist_restraint_container,
iw._rebuild_dist_restraint_apply_button,
iw._rebuild_grow_shrink_sel_frame,
iw._right_mouse_modes_frame,
iw._live_map_recalc_button,
iw._live_map_update_sim_button,
]
for f in self._disabled_at_start:
f.setEnabled(False)
# Apply custom palettes to intermediate and expert frames
from . import palettes
self._pi = palettes.IntermediatePalette()
self._pe = palettes.ExpertPalette()
for f in self._intermediate_frames:
f.setPalette(self._pi.palette)
f.setAutoFillBackground(True)
for f in self._expert_frames:
f.setPalette(self._pe.palette)
f.setAutoFillBackground(True)
from . import isolde
self.isolde = isolde.Isolde(self)
def __init__(self, session):
tool_name = "Help Viewer"
ToolInstance.__init__(self, session, tool_name)
self._pending_downloads = []
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self)
parent = self.tool_window.ui_area
# UI content code
from PyQt5.QtWidgets import QToolBar, QVBoxLayout, QAction, QLineEdit, QTabWidget, QShortcut, QStatusBar
from PyQt5.QtGui import QIcon
from PyQt5.QtCore import Qt
shortcuts = (
(Qt.CTRL + Qt.Key_0, self.page_reset_zoom),
(Qt.CTRL + Qt.Key_T, lambda: self.create_tab(empty=True)),
(Qt.CTRL + Qt.Key_W, self.close_current_tab),
(Qt.CTRL + Qt.Key_Tab, lambda: self.cycle_tab(1)),
(Qt.CTRL + Qt.SHIFT + Qt.Key_Tab, lambda: self.cycle_tab(-1)),
(Qt.CTRL + Qt.Key_1, lambda: self.tab_n(0)),
(Qt.CTRL + Qt.Key_2, lambda: self.tab_n(1)),
(Qt.CTRL + Qt.Key_3, lambda: self.tab_n(2)),
(Qt.CTRL + Qt.Key_4, lambda: self.tab_n(3)),
(Qt.CTRL + Qt.Key_5, lambda: self.tab_n(4)),
(Qt.CTRL + Qt.Key_6, lambda: self.tab_n(5)),
(Qt.CTRL + Qt.Key_7, lambda: self.tab_n(6)),
(Qt.CTRL + Qt.Key_8, lambda: self.tab_n(7)),
(Qt.CTRL + Qt.Key_9, lambda: self.tab_n(-1)),
)
for shortcut, callback in shortcuts:
sc = QShortcut(shortcut, parent)
sc.activated.connect(callback)
self.toolbar = tb = QToolBar()
# tb.setToolButtonStyle(Qt.ToolButtonTextUnderIcon)
layout = QVBoxLayout()
layout.setContentsMargins(0, 1, 0, 0)
layout.addWidget(tb)
parent.setLayout(layout)
import os.path
icon_dir = os.path.dirname(__file__)
# attribute, text, tool tip, callback, shortcut(s), enabled
buttons = (
("back", "Back", "Back to previous page", self.page_back,
Qt.Key_Back, False),
("forward", "Forward", "Next page", self.page_forward,
Qt.Key_Forward, False),
("reload", "Reload", "Reload page", self.page_reload,
Qt.Key_Reload, True),
("new_tab", "New Tab", "New Tab",
lambda: self.create_tab(empty=True), Qt.Key_Reload, True),
("zoom_in", "Zoom in", "Zoom in", self.page_zoom_in,
[Qt.CTRL + Qt.Key_Plus, Qt.Key_ZoomIn,
Qt.CTRL + Qt.Key_Equal], True),
("zoom_out", "Zoom out", "Zoom out", self.page_zoom_out,
[Qt.CTRL + Qt.Key_Minus, Qt.Key_ZoomOut], True),
("home", "Home", "Home page", self.page_home, Qt.Key_HomePage,
True),
(None, None, None, None, None, None),
("search", "Search", "Search in page", self.page_search,
Qt.Key_Search, True),
)
for attribute, text, tooltip, callback, shortcut, enabled in buttons:
if attribute is None:
tb.addSeparator()
continue
icon_path = os.path.join(icon_dir, "%s.svg" % attribute)
setattr(self, attribute, QAction(QIcon(icon_path), text, tb))
a = getattr(self, attribute)
a.setToolTip(tooltip)
a.triggered.connect(callback)
if shortcut:
if isinstance(shortcut, list):
a.setShortcuts(shortcut)
else:
a.setShortcut(shortcut)
a.setEnabled(enabled)
tb.addAction(a)
self.url = QLineEdit()
self.url.setPlaceholderText("url")
self.url.setClearButtonEnabled(True)
self.url.returnPressed.connect(self.go_to)
tb.insertWidget(self.reload, self.url)
self.search_terms = QLineEdit()
self.search_terms.setClearButtonEnabled(True)
self.search_terms.setPlaceholderText("search in page")
self.search_terms.setMaximumWidth(200)
self.search_terms.returnPressed.connect(self.page_search)
tb.addWidget(self.search_terms)
self.tabs = QTabWidget(parent)
self.tabs.setTabsClosable(True)
self.tabs.setUsesScrollButtons(True)
self.tabs.setTabBarAutoHide(True)
self.tabs.setDocumentMode(False)
self.tabs.currentChanged.connect(self.tab_changed)
self.tabs.tabCloseRequested.connect(self.close_tab)
layout.addWidget(self.tabs)
self.status_bar = QStatusBar()
layout.addWidget(self.status_bar)
self.tool_window.manage(placement=None)
self.profile = create_chimerax_profile(
self.tabs,
interceptor=self.intercept,
download=self.download_requested)
def delete(self):
global _singleton
_singleton = None
ToolInstance.delete(self)
def delete(self):
self.opengl_canvas.close()
self.view.delete()
self.view = None
ToolInstance.delete(self)