def create_label_row(self):
"""
Row with two labels and a "Remove" button.
"""
# Create a first residue label that tells which residue has been selected.
self.res1_label = QtWidgets.QLabel(self.text1)
self.res1_label.setStyleSheet(small_font_style)
self.res1_label.setAlignment(QtCore.Qt.AlignCenter)
self.parent.loop_selector_frame_layout.addWidget(
self.res1_label, self.row, 0)
# Second residue label.
self.res2_label = QtWidgets.QLabel(self.text2)
self.res2_label.setStyleSheet(small_font_style)
self.res2_label.setAlignment(QtCore.Qt.AlignCenter)
self.parent.loop_selector_frame_layout.addWidget(
self.res2_label, self.row, 1)
# Adds the "Remove" button.
self.remove_loop_button = QtWidgets.QPushButton("Remove")
self.remove_loop_button.setStyleSheet(small_font_style)
self.remove_loop_button.clicked.connect(self.press_remove_button)
self.parent.loop_selector_frame_layout.addWidget(
self.remove_loop_button, self.row, 2)
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 __init__(
self,
label_text="New scalebar",
slider_value=1,
slider_from=1,
slider_to=10,
slider_resoution=1,
# slider_digits=3,
slider_tickinterval=1,
slider_use_float=False,
slider_use_float_val=100.0,
slider_binding=None,
slider_width=None):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Layout for the input widget and its label.
self.input = QtWidgets.QHBoxLayout()
# Adds a slider.
self.slider = QtWidgets.QSlider()
self.slider.setOrientation(QtCore.Qt.Horizontal)
self.slider.setTickPosition(QtWidgets.QSlider.TicksBelow)
self.slider_use_float = slider_use_float
self.slider_use_float_val = slider_use_float_val
self.slider.slider_resoution = slider_resoution
self.slider.setMinimum(self._get_slider_val(slider_from,
internal=True))
self.slider.setMaximum(self._get_slider_val(slider_to, internal=True))
self.slider.setValue(self._get_slider_val(slider_value, internal=True))
self.slider.setTickInterval(
self._get_slider_val(slider_tickinterval, internal=True))
self.slider.setSingleStep(
self._get_slider_val(slider_resoution, internal=True))
self.slider.setPageStep(
self._get_slider_val(slider_tickinterval, internal=True))
self.slider.valueChanged.connect(self._on_slider_change)
self.slider.sliderPressed.connect(self._on_slider_pressed)
self.slider.sliderReleased.connect(self._on_slider_release)
self.on_drag = False
self.input.addWidget(self.slider)
# Add a label on the right of the slider.
self.slider_label = QtWidgets.QLabel(str(slider_to))
self.input.addWidget(self.slider_label)
if slider_width:
self.slider.setFixedWidth(slider_width)
self.slider_label.setFixedWidth(
self.slider_label.sizeHint().width())
self.slider_label.setText(str(slider_value))
self.slider_binding = slider_binding
def build_modeling_protocol_main_page(self):
"""
Starts to insert content in the "Main" page.
"""
# Builds a frame for each modeling_cluster.
for (i, modeling_cluster) in enumerate(
self.protocol.modeling_clusters_list):
# Add a spacer to separate the sections for each modeling cluster.
if i != 0 and self.protocol.multiple_chain_mode:
spacer_frame = QtWidgets.QFrame()
spacer_frame.setFrameShape(QtWidgets.QFrame.HLine)
spacer_frame.setFrameShadow(QtWidgets.QFrame.Sunken)
self.main_page_interior_layout.addRow(spacer_frame)
show_symmetry_restraints_option = False
# Widgets necessary to choose the templates for a single target sequence.
modeling_option_label = QtWidgets.QLabel(
"Modeling options for target: %s" %
(modeling_cluster.target_name))
modeling_option_label.setStyleSheet(modeling_window_title_style)
self.main_page_interior_layout.addRow(modeling_option_label)
if self.protocol.multiple_chain_mode:
# Use symmetry restraints option.
if modeling_cluster.symmetry_restraints_id != None:
show_symmetry_restraints_option = True
symmetry_checkbox, symmetry_info = self.build_symmetry_restraints_option(
modeling_cluster)
if any((show_symmetry_restraints_option,
)): # This might include other flags in future releases.
additional_options_label = QtWidgets.QLabel(
"Restraints options")
additional_options_label.setStyleSheet(
modeling_options_sections_style)
self.main_page_interior_layout.addRow(additional_options_label)
if show_symmetry_restraints_option:
self.main_page_interior_layout.addRow(
symmetry_checkbox, symmetry_info)
# Build a series of widgets for loop ranges selection.
modeling_option_label = QtWidgets.QLabel("Loop selection")
modeling_option_label.setStyleSheet(
modeling_options_sections_style)
self.main_page_interior_layout.addRow(modeling_option_label)
# Build a 'User_loop_selector_frame' object, which will contain information about
# user-defined loops for this target.
uls = User_loop_selector_frame_qt(
parent=None,
parent_window=self,
modeling_cluster=modeling_cluster)
modeling_cluster.user_loop_selector_frame = uls
self.main_page_interior_layout.addRow(uls)
def __init__(self, label_text="Input", value=""):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Second Entry.
self.right_label = QtWidgets.QLabel(value)
self.right_label.setWordWrap(True)
self.input = self.right_label
def initUI(self):
self.setWindowTitle(self.title)
vertical_layout = QtWidgets.QVBoxLayout()
self.thread_progressbar = QtWidgets.QProgressBar(self)
if self.progress:
self.thread_progressbar.setMinimum(0)
self.thread_progressbar.setMaximum(0)
progressbar_label = "Computing..." # "Wait for the protocol to complete."
self.thread_progressbar.setFormat(progressbar_label)
self.thread_progressbar.setValue(0)
vertical_layout.addWidget(self.thread_progressbar)
self.thread_progress_label = QtWidgets.QLabel(self.label_text, self)
self.thread_progress_label.setWordWrap(True)
vertical_layout.addWidget(self.thread_progress_label)
# Button for canceling the execution of the thread.
horizontal_layout = QtWidgets.QHBoxLayout()
self.cancel_button = QtWidgets.QPushButton('Cancel', self)
self.cancel_button.clicked.connect(self.on_cancel_button_click)
self.cancel_button.setEnabled(not self.lock)
horizontal_layout.addWidget(self.cancel_button)
vertical_layout.addLayout(horizontal_layout)
self.setLayout(vertical_layout)
def display_options(self, single_tool):
"""
Displays at list of option in the the target_frame contained in a target widget.
Used in the PyMod options window.
"""
# Check that at least one parameter
if not any([p.show_widget for p in single_tool.parameters]):
return None
self.tools_params_dict[single_tool.name] = {}
# Grids a label with the name of the tool.
tool_full_name_label = QtWidgets.QLabel(single_tool.full_name)
tool_full_name_label.setStyleSheet(options_title_style)
# print(dir(tool_full_name_label))
# print(tool_full_name_label.font().size())
self.middle_formlayout.addWidget(tool_full_name_label,
self.row_counter, 0)
self.row_counter += 1
# Actually grids the parmater widgets.
for parameter in single_tool.parameters:
if not parameter.show_widget:
continue
# If the display options return a widget, adds it ot the Tool list of parameter widgets.
w = self.display_paramenter_options(parameter)
self.row_counter += 1
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 __init__(self, label_text="Input", buttons=[]):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Buttons.
self.input = QtWidgets.QVBoxLayout()
if not buttons:
raise ValueError("Please provide a list of button names")
if len(buttons) != len(set(buttons)):
raise ValueError("Please provide a non redundant list of buttons")
self.button_group = QtWidgets.QButtonGroup()
self.buttons_names = []
self.buttons_dict = {}
for button_name in buttons:
button = QtWidgets.QPushButton(button_name)
button.setCheckable(True)
self.input.addWidget(button)
self.buttons_names.append(button_name)
self.buttons_dict[button_name] = button
self.button_group.addButton(button)
def __init__(self,
label_text="Input",
value="",
readonly=False,
style=None,
enter_command=None,
validate={}):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Entry.
self.entry = PyMod_entry_qt(value)
self.enter_command = enter_command
if self.enter_command is not None:
self.entry.returnPressed.connect(self.enter_command)
if readonly:
self.entry.setReadOnly(True)
if style is not None:
self.entry.setStyleSheet(style)
else:
self.entry.setStyleSheet(active_entry_style)
self.validate = validate
if self.validate:
self.entry.set_pmw_validator(self.validate)
self.input = self.entry
def show_advanced_button(self):
self.advance_options_button = QtWidgets.QPushButton(
"Show Advanced Options")
self.advance_options_button.clicked.connect(
self.toggle_advanced_options)
self._advanced_options_label = QtWidgets.QLabel("")
self.middle_formlayout.addRow(self.advance_options_button,
self._advanced_options_label)
def __init__(self, label_text="Input"):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Hbox.
self.hbox = QtWidgets.QHBoxLayout()
self.input = self.hbox
def _get_scene_image_label(self, scene_pix_map):
'''
Takes in the QPixmap from get_scene_png and uses it to create a label
displaying the thumbnail.
In the future, this function will generate its
own QPixmap object from the PNG buffer stored with the scene.
'''
scene_image_label = QtWidgets.QLabel(self)
scene_image_label.setPixmap(scene_pix_map)
return scene_image_label
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_alignment_mode_frame(self):
"""
Builds a frame with some options to choose the alignment mode.
"""
# Vbox which will store all the widgets for the alignment mode options.
self.alignment_mode_vbox = QtWidgets.QVBoxLayout()
self.alignment_mode_label = QtWidgets.QLabel("Alignment Mode")
self.alignment_mode_vbox.addWidget(self.alignment_mode_label)
self.alignment_mode_button_group = QtWidgets.QButtonGroup()
self.build_strategy_specific_modes_frames() # Defined in child classes.
self.middle_formlayout.addRow(self.alignment_mode_vbox)
def build_protocol_middle_frame(self):
# Add the buttons to choose the database in which to search for domain profiles.
if self.protocol.father_protocol.domain_search_mode == 'remote':
self.hmmer_database_rds = PyMod_radioselect_qt(
label_text="Database Selection", buttons=("PFAM", "Gene3D"))
for button in self.hmmer_database_rds.get_buttons():
button.clicked.connect(self.database_opt_cmd)
elif self.protocol.father_protocol.domain_search_mode == 'local':
# Build the list of database names.
self.protocol.hmmscan_db_dict = {
} # This dictionary associates a database code (displayed in the GUI) to its filename.
db_list = []
for db_filename in self.protocol.hmmscan_db_list:
db_name = "".join(db_filename.split(".")[0:-2])
db_list.append(db_name)
self.protocol.hmmscan_db_dict[db_name] = db_filename
# Packs the PHMMER database selection widget.
self.hmmer_database_rds = PyMod_radioselect_qt(
label_text="Database Selection", buttons=db_list)
self.middle_formlayout.add_widget_to_align(self.hmmer_database_rds)
# E-value selection.
self.e_value_threshold_enf = PyMod_entryfield_qt(
label_text="E-value Threshold",
value="1.0",
validate={
'validator': 'real',
'min': 0.0,
'max': 1000.0
})
self.middle_formlayout.add_widget_to_align(self.e_value_threshold_enf)
# Note about the Gene3D and Evalues.
if self.protocol.father_protocol.domain_search_mode == 'remote':
info_note = ('Note: The Gene3D online database will\n'
'ignore custom cut-off parameters since\n'
'they use a post processing step that\n'
'involves preset thresholds.')
self.notelabel = QtWidgets.QLabel(info_note)
self.middle_formlayout.addRow(self.notelabel)
self.middle_formlayout.set_input_widgets_width(140)
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 __init__(self, label_text="Input", items=[]):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Combobox.
self.combobox = QtWidgets.QComboBox()
if not items:
raise ValueError("Please provide a list of items for the combobox")
self.items = items
for item in self.items:
self.combobox.addItem(item)
self.combobox.setEditable(False)
self.input = self.combobox
def initUI(self):
self.setWindowTitle('Import PDB Options')
vertical_layout = QtWidgets.QVBoxLayout()
# Installation options label.
info_text = "Please select the 3D structure import mode:"
self.fetch_info_label = QtWidgets.QLabel(info_text, self)
# self.fetch_info_label.setStyleSheet(label_style_1)
vertical_layout.addWidget(self.fetch_info_label)
vertical_layout.addStretch(1)
# Import options radiobuttons.
horizontal_layout = QtWidgets.QHBoxLayout()
self.import_all_radiobutton = QtWidgets.QRadioButton(
"Import in PyMod the structure of every chain of the PDB files.")
# self.import_all_radiobutton.setChecked(True)
# self.import_all_radiobutton.setStyleSheet(label_font_1)
vertical_layout.addWidget(self.import_all_radiobutton)
self.import_fragment_radiobutton = QtWidgets.QRadioButton(
"Import in PyMod only the structure of the hit sequences fragments."
)
# label_font_1
self.import_fragment_radiobutton.setStyleSheet("margin-bottom: 10px")
vertical_layout.addWidget(self.import_fragment_radiobutton)
# Import fragments button.
self.import_button = QtWidgets.QPushButton("Import 3D Structures",
self)
# self.import_button.setStyleSheet(label_style_2)
self.import_button.clicked.connect(self.on_import_button_click)
horizontal_layout.addWidget(self.import_button)
horizontal_layout.addStretch(1)
# Cancel button.
self.cancel_button = QtWidgets.QPushButton('Cancel', self)
# self.cancel_button.setStyleSheet(label_style_2)
self.cancel_button.clicked.connect(self.on_cancel_button_click)
horizontal_layout.addWidget(self.cancel_button)
vertical_layout.addLayout(horizontal_layout)
self.setLayout(vertical_layout)
def __init__(self,
label_text="Input",
value=1,
spinbox_min=1,
spinbox_max=100):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Spinbox.
self.spinbox = QtWidgets.QSpinBox()
self.spinbox_min = spinbox_min
self.spinbox_max = spinbox_max
self.spinbox.setRange(self.spinbox_min, self.spinbox_max)
self.spinbox.setStyleSheet(active_entry_style)
self.input = self.spinbox
def __init__(self, label_text="Input", value="", style=None):
PyMod_form_item.__init__(self)
# Label.
self.label = QtWidgets.QLabel(label_text)
# Entry.
self.entry = QtWidgets.QPlainTextEdit(value)
if style is not None:
self.entry.setStyleSheet(style)
else:
self.entry.setStyleSheet(active_entry_style)
self.entry.setWordWrapMode(QtGui.QTextOption.WrapAnywhere)
expanding_size_policy = QtWidgets.QSizePolicy(
QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)
expanding_size_policy.setVerticalStretch(1)
self.entry.setSizePolicy(expanding_size_policy)
self.input = self.entry
def add_qt_menu_command(parent,
label,
command=None,
fg_color=None,
bg_color=None):
"""
Adds to a 'parent' QMenu widget a new menu item.
"""
# Color the label of the menu item.
if fg_color != None:
action = QtWidgets.QWidgetAction(parent)
label_widget = QtWidgets.QLabel(label)
s = """QLabel {
background-color: %s;
color: %s;
padding: 3px;
}
QLabel:hover {
background-color: #466e82;
color: %s;
}""" % (bg_color, fg_color, fg_color)
label_widget.setStyleSheet(s)
action.setDefaultWidget(label_widget)
# Don't color, use a regular 'QAction' object.
else:
action = QtWidgets.QAction(label, parent)
# Associates a command.
if command is not None:
action.triggered.connect(command)
parent.addAction(action)
return action
def load_aln_dialog(parent, filename, format):
_self = parent.cmd
import numpy
import difflib
import pymol.seqalign as seqalign
try:
# for fasta format, this only succeeds if all sequences have the
# same length, raises ValueError otherwise
alignment = seqalign.aln_magic_read(filename)
# a single sequence is not an aligment
if format == "fasta" and len(alignment) < 2:
raise ValueError
except ValueError:
# fasta files which don't contain alignments will be loaded as
# extended structures (fab command) instead
_self.load(filename)
return
# alignment record ids and PyMOL model names
ids = [rec.id for rec in alignment]
ids_remain = list(ids)
models = _self.get_object_list()
models_remain = list(models)
mapping = {}
N = len(ids)
M = len(models)
# ids -> models similarity matrix
similarity = numpy.zeros((N, M))
for i in range(N):
for j in range(M):
similarity[i, j] = difflib.SequenceMatcher(None, ids[i], models[j],
False).ratio()
# guess mapping
for _ in range(min(N, M)):
i, j = numpy.unravel_index(similarity.argmax(), similarity.shape)
mapping[ids_remain.pop(i)] = models_remain.pop(j)
similarity = numpy.delete(similarity, i, axis=0)
similarity = numpy.delete(similarity, j, axis=1)
form = parent.load_form('load_aln')
comboboxes = {}
# mapping GUI
for row, rec_id in enumerate(ids, 1):
label = QtWidgets.QLabel(rec_id, form._dialog)
combobox = QtWidgets.QComboBox(form._dialog)
combobox.addItem("")
combobox.addItems(models)
combobox.setCurrentText(mapping.get(rec_id, ""))
form.layout_mapping.addWidget(label, row, 0)
form.layout_mapping.addWidget(combobox, row, 1)
comboboxes[rec_id] = combobox
def run():
mapping = dict((rec_id, combobox.currentText())
for (rec_id, combobox) in comboboxes.items())
seqalign.load_aln_multi(filename, mapping=mapping, _self=_self)
form._dialog.close()
def cancel():
form._dialog.close()
if format == 'fasta' and QtWidgets.QMessageBox.question(
parent, "Load as structures?",
"Load sequences as extended structures instead?"
) == QtWidgets.QMessageBox.Yes:
_self.load(filename)
# hook up events
form.button_ok.clicked.connect(run)
form.button_cancel.clicked.connect(cancel)
form._dialog.setModal(True)
form._dialog.show()
def load_aln_dialog(parent, filename):
_self = parent.cmd
import numpy
import difflib
import pymol.seqalign as seqalign
try:
alignment = seqalign.aln_magic_read(filename)
except ValueError:
# fails for fasta files which don't contain alignments
_self.load(filename)
return
# alignment record ids and PyMOL model names
ids = [rec.id for rec in alignment]
ids_remain = list(ids)
models = _self.get_object_list()
models_remain = list(models)
mapping = {}
N = len(ids)
M = len(models)
# ids -> models similarity matrix
similarity = numpy.zeros((N, M))
for i in range(N):
for j in range(M):
similarity[i, j] = difflib.SequenceMatcher(None, ids[i], models[j],
False).ratio()
# guess mapping
for _ in range(min(N, M)):
i, j = numpy.unravel_index(similarity.argmax(), similarity.shape)
mapping[ids_remain.pop(i)] = models_remain.pop(j)
similarity = numpy.delete(similarity, i, axis=0)
similarity = numpy.delete(similarity, j, axis=1)
form = parent.load_form('load_aln')
comboboxes = {}
# mapping GUI
for row, rec_id in enumerate(ids, 1):
label = QtWidgets.QLabel(rec_id, form._dialog)
combobox = QtWidgets.QComboBox(form._dialog)
combobox.addItem("")
combobox.addItems(models)
combobox.setCurrentText(mapping.get(rec_id, ""))
form.layout_mapping.addWidget(label, row, 0)
form.layout_mapping.addWidget(combobox, row, 1)
comboboxes[rec_id] = combobox
def run():
mapping = dict((rec_id, combobox.currentText())
for (rec_id, combobox) in comboboxes.items())
seqalign.load_aln_multi(filename, mapping=mapping, _self=_self)
form._dialog.close()
# hook up events
form.button_ok.clicked.connect(run)
form.button_cancel.clicked.connect(form._dialog.close)
form._dialog.setModal(True)
form._dialog.show()
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 add_plot(self, x_data, y_data,
label=None,
additional_data=None):
"""
Adds a plot to the pyqtgraph PlotWidget.
"""
# Check and prepare the data.
if len(x_data) != len(y_data):
raise ValueError(("The x series and the y series do not have the same"
" number of elements (%s and %s respectively)" % (len(x_data), len(y_data))))
if additional_data:
if not len(x_data) == len(additional_data):
raise ValueError(("The 'additional_data' series does not have the"
" same number of elements of the data to plot"
" (%s and %s respectively)" % (len(x_data), len(additional_data))))
_x_data, _y_data = self.remove_none(x_data, y_data)
# Add the plot to the PlotWidget.
plot_color = self.plot_colors[self.plot_color_index]
self.change_plot_color_index()
curve_pen = pyqtgraph.mkPen(width=2, color=plot_color) # Color and width of the curve.
plot_item = self.graphWidget.plot(_x_data, _y_data,
name=label,
connect="finite",
pen=curve_pen,
clickable=True)
plot_item._pymod_id = self.plot_count
plot_item.curve._pymod_id = self.plot_count
plot_item.curve.setClickable(True)
# plot_item.curve.sigClicked.connect(self.on_curve_click)
plot_item.sigClicked.connect(self.on_curve_click)
# Store information about the plot.
self.plot_items[self.plot_count] = {}
# The 'plot' key will store the pyqtgraph object for the plot.
self.plot_items[self.plot_count]["plot"] = plot_item
# The 'state' will be 1 if the plot is shown, and 0 it is hidden.
self.plot_items[self.plot_count]["state"] = 1
# Add a label.
if label is None:
label = "Plot %s" % self.plot_count
self.plot_items[self.plot_count]["label"] = label
# Data.
self.plot_items[self.plot_count]["x_data"] = x_data
self.plot_items[self.plot_count]["y_data"] = y_data
# Additional data.
self.plot_items[self.plot_count]["additional_data"] = additional_data
# Stores all the data in a single list.
for idx, (xi, yi) in enumerate(zip(x_data, y_data)):
if yi is not None:
self.all_points.append((xi, yi))
self.all_points_info.append((self.plot_count, idx))
# Add a checkbox in the controls frame. Used for showing/hiding the plot.
if self.use_controls:
plot_checkbox = QtWidgets.QCheckBox(label)
plot_checkbox.setStyleSheet(small_font_style)
plot_checkbox.setChecked(True)
plot_checkbox.clicked.connect(lambda a=None, i=self.plot_count: self.toggle_plot(i))
plot_color_label = QtWidgets.QLabel("---") # \u2796") # "\u25CF"
plot_color_label.setStyleSheet("color: %s; font-weight: bold" % plot_color)
self.controls_frame_layout.addWidget(plot_color_label, self.plot_count+1, 0, 1, 1)
self.controls_frame_layout.addWidget(plot_checkbox, self.plot_count+1, 1, 1, 1)
self.plot_items[self.plot_count]["checkbox"] = plot_checkbox
# Increase the plot counter.
self.plot_count += 1
def __init__(self): # noqa
QtWidgets.QMainWindow.__init__(self)
self.setDockOptions(QtWidgets.QMainWindow.AllowTabbedDocks
| QtWidgets.QMainWindow.AllowNestedDocks)
# resize Window before it is shown
options = pymol.invocation.options
self.resize(options.win_x + (220 if options.internal_gui else 0),
options.win_y + (246 if options.external_gui else 18))
# for thread-safe viewport command
self.viewportsignal.connect(self.pymolviewport)
# reusable dialogs
self.dialog_png = None
self.advanced_settings_dialog = None
self.props_dialog = None
self.builder = None
# setting index -> callable
self.setting_callbacks = defaultdict(list)
# "session_file" setting in window title
self.setting_callbacks[440].append(lambda v: self.setWindowTitle(
"PyMOL (" + os.path.basename(v) + ")"))
# "External" Command Line and Loggin Widget
self._setup_history()
self.lineedit = CommandLineEdit()
self.lineedit.setObjectName("command_line")
self.browser = QtWidgets.QPlainTextEdit()
self.browser.setObjectName("feedback_browser")
self.browser.setReadOnly(True)
# convenience: clicking into feedback browser gives focus to command
# line. Drawback: Copying with CTRL+C doesn't work in feedback
# browser -> clear focus proxy while text selected
self.browser.setFocusProxy(self.lineedit)
@self.browser.copyAvailable.connect
def _(yes):
self.browser.setFocusProxy(None if yes else self.lineedit)
self.browser.setFocus()
# Font
self.browser.setFont(getMonospaceFont())
connectFontContextMenu(self.browser)
lineeditlayout = QtWidgets.QHBoxLayout()
command_label = QtWidgets.QLabel("PyMOL>")
command_label.setObjectName("command_label")
lineeditlayout.addWidget(command_label)
lineeditlayout.addWidget(self.lineedit)
self.lineedit.setToolTip('''Command Input Area
Get the list of commands by hitting <TAB>
Get the list of arguments for one command with a question mark:
PyMOL> color ?
Read the online help for a command with "help":
PyMOL> help color
Get autocompletion for many arguments by hitting <TAB>
PyMOL> color ye<TAB> (will autocomplete "yellow")
''')
layout = QtWidgets.QVBoxLayout()
layout.addWidget(self.browser)
layout.addLayout(lineeditlayout)
quickbuttonslayout = QtWidgets.QVBoxLayout()
quickbuttonslayout.setSpacing(2)
extguilayout = QtWidgets.QBoxLayout(QtWidgets.QBoxLayout.LeftToRight)
extguilayout.setContentsMargins(2, 2, 2, 2)
extguilayout.addLayout(layout)
extguilayout.addLayout(quickbuttonslayout)
class ExtGuiFrame(QtWidgets.QFrame):
def mouseDoubleClickEvent(_, event):
self.toggle_ext_window_dockable(True)
_size_hint = QtCore.QSize(options.win_x, options.ext_y)
def sizeHint(self):
return self._size_hint
dockWidgetContents = ExtGuiFrame(self)
dockWidgetContents.setLayout(extguilayout)
dockWidgetContents.setObjectName("extgui")
self.ext_window = \
dockWidget = QtWidgets.QDockWidget(self)
dockWidget.setWindowTitle("External GUI")
dockWidget.setWidget(dockWidgetContents)
if options.external_gui:
dockWidget.setTitleBarWidget(QtWidgets.QWidget())
else:
dockWidget.hide()
self.addDockWidget(Qt.TopDockWidgetArea, dockWidget)
# rearrange vertically if docking left or right
@dockWidget.dockLocationChanged.connect
def _(area):
if area == Qt.LeftDockWidgetArea or area == Qt.RightDockWidgetArea:
extguilayout.setDirection(QtWidgets.QBoxLayout.BottomToTop)
quickbuttonslayout.takeAt(quickbuttons_stretch_index)
else:
extguilayout.setDirection(QtWidgets.QBoxLayout.LeftToRight)
if quickbuttons_stretch_index >= quickbuttonslayout.count():
quickbuttonslayout.addStretch()
# OpenGL Widget
self.pymolwidget = PyMOLGLWidget(self)
self.setCentralWidget(self.pymolwidget)
cmd = self.cmd = self.pymolwidget.cmd
'''
# command completion
completer = QtWidgets.QCompleter(cmd.kwhash.keywords, self)
self.lineedit.setCompleter(completer)
'''
# overload <Tab> action
self.lineedit.installEventFilter(self)
self.pymolwidget.installEventFilter(self)
# Quick Buttons
for row in [
[
('Reset', cmd.reset),
('Zoom', lambda: cmd.zoom(animate=1.0)),
('Orient', lambda: cmd.orient(animate=1.0)),
# render dialog will be constructed when the menu is shown
# for the first time. This way it's populated with the current
# viewport and settings. Also defers parsing of the ui file.
('Draw/Ray', WidgetMenu(self).setSetupUi(self.render_dialog)),
],
[
('Unpick', cmd.unpick),
('Deselect', cmd.deselect),
('Rock', cmd.rock),
('Get View', self.get_view),
],
[
('|<', cmd.rewind),
('<', cmd.backward),
('Stop', cmd.mstop),
('Play', cmd.mplay),
('>', cmd.forward),
('>|', cmd.ending),
('MClear', cmd.mclear),
],
[
('Builder', self.open_builder_panel),
('Properties', self.open_props_dialog),
('Rebuild', cmd.rebuild),
],
]:
hbox = QtWidgets.QHBoxLayout()
hbox.setSpacing(2)
for name, callback in row:
btn = QtWidgets.QPushButton(name)
btn.setProperty("quickbutton", True)
btn.setAttribute(Qt.WA_LayoutUsesWidgetRect) # OS X workaround
hbox.addWidget(btn)
if callback is None:
btn.setEnabled(False)
elif isinstance(callback, QtWidgets.QMenu):
btn.setMenu(callback)
else:
btn.released.connect(callback)
quickbuttonslayout.addLayout(hbox)
# progress bar
hbox = QtWidgets.QHBoxLayout()
self.progressbar = QtWidgets.QProgressBar()
self.progressbar.setSizePolicy(QtWidgets.QSizePolicy.Minimum,
QtWidgets.QSizePolicy.Minimum)
hbox.addWidget(self.progressbar)
self.abortbutton = QtWidgets.QPushButton('Abort')
self.abortbutton.setStyleSheet("background: #FF0000; color: #FFFFFF")
self.abortbutton.released.connect(cmd.interrupt)
hbox.addWidget(self.abortbutton)
quickbuttonslayout.addLayout(hbox)
quickbuttonslayout.addStretch()
quickbuttons_stretch_index = quickbuttonslayout.count() - 1
# menu top level
self.menubar = menubar = self.menuBar()
# action groups
actiongroups = {}
def _addmenu(data, menu):
'''Fill a menu from "data"'''
menu.setTearOffEnabled(True)
menu.setWindowTitle(menu.title()) # needed for Windows
for item in data:
if item[0] == 'separator':
menu.addSeparator()
elif item[0] == 'menu':
_addmenu(item[2], menu.addMenu(item[1].replace('&', '&&')))
elif item[0] == 'command':
command = item[2]
if command is None:
print('warning: skipping', item)
else:
if isinstance(command, str):
command = lambda c=command: cmd.do(c)
menu.addAction(item[1], command)
elif item[0] == 'check':
if len(item) > 4:
menu.addAction(
SettingAction(self, cmd, item[2], item[1], item[3],
item[4]))
else:
menu.addAction(
SettingAction(self, cmd, item[2], item[1]))
elif item[0] == 'radio':
label, name, value = item[1:4]
try:
group, type_, values = actiongroups[item[2]]
except KeyError:
group = QtWidgets.QActionGroup(self)
type_, values = cmd.get_setting_tuple(name)
actiongroups[item[2]] = group, type_, values
action = QtWidgets.QAction(label, self)
action.triggered.connect(lambda _=0, args=(name, value):
cmd.set(*args, log=1, quiet=0))
self.setting_callbacks[cmd.setting._get_index(
name)].append(
lambda v, V=value, a=action: a.setChecked(v == V))
group.addAction(action)
menu.addAction(action)
action.setCheckable(True)
if values[0] == value:
action.setChecked(True)
elif item[0] == 'open_recent_menu':
self.open_recent_menu = menu.addMenu('Open Recent...')
else:
print('error:', item)
# recent files menu
self.open_recent_menu = None
# for plugins
self.menudict = {'': menubar}
# menu
for _, label, data in self.get_menudata(cmd):
assert _ == 'menu'
menu = menubar.addMenu(label)
self.menudict[label] = menu
_addmenu(data, menu)
# hack for macOS to hide "Edit > Start Dictation"
# https://bugreports.qt.io/browse/QTBUG-43217
if pymol.IS_MACOS:
self.menudict['Edit'].setTitle('Edit_')
QtCore.QTimer.singleShot(
10, lambda: self.menudict['Edit'].setTitle('Edit'))
# recent files menu
if self.open_recent_menu:
@self.open_recent_menu.aboutToShow.connect
def _():
self.open_recent_menu.clear()
for fname in self.recent_filenames:
self.open_recent_menu.addAction(
fname if len(fname) < 128 else '...' + fname[-120:],
lambda fname=fname: self.load_dialog(fname))
# some experimental window control
menu = self.menudict['Display'].addSeparator()
menu = self.menudict['Display'].addMenu('External GUI')
menu.addAction('Toggle floating', self.toggle_ext_window_dockable,
QtGui.QKeySequence('Ctrl+E'))
ext_vis_action = self.ext_window.toggleViewAction()
ext_vis_action.setText('Visible')
menu.addAction(ext_vis_action)
# extra key mappings (MacPyMOL compatible)
QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+O'),
self).activated.connect(self.file_open)
QtWidgets.QShortcut(QtGui.QKeySequence('Ctrl+S'),
self).activated.connect(self.session_save)
# feedback
self.feedback_timer = QtCore.QTimer()
self.feedback_timer.setSingleShot(True)
self.feedback_timer.timeout.connect(self.update_feedback)
self.feedback_timer.start(100)
# legacy plugin system
self.menudict['Plugin'].addAction('Initialize Plugin System',
self.initializePlugins)
# focus in command line
if options.external_gui:
self.lineedit.setFocus()
else:
self.pymolwidget.setFocus()
# Apply PyMOL stylesheet
try:
with open(
cmd.exp_path('$PYMOL_DATA/pmg_qt/styles/pymol.sty')) as f:
style = f.read()
except IOError:
print('Could not read PyMOL stylesheet.')
print('DEBUG: PYMOL_DATA=' + repr(os.getenv('PYMOL_DATA')))
style = ""
if style:
self.setStyleSheet(style)
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 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
}
