class CastWindow(QWidget):
def __init__(self, parent, mode='normal'):
super().__init__()
self.parent = parent
self.mode = mode
if self.mode == 'wide':
self.MAX_CAST_NUM = 12
self.num_col = 6
self.num_row = 2
self.cast_num = 12
elif self.mode == 'long':
self.MAX_CAST_NUM = 12
self.cast_num = 12
else:
self.MAX_CAST_NUM = 10
self.cast_num = 10
self.cast_labels = [CastLabel(self) for i in range(self.MAX_CAST_NUM)]
print('init Cast Window.')
self.initUI()
def initUI(self):
if self.mode == 'wide':
self.layout = QGridLayout()
for i in range(self.num_col):
self.layout.setColumnStretch(i, 1)
for i in range(self.num_row):
self.layout.setRowStretch(i, 1)
positions = [(i, j) for i in range(self.num_row)
for j in range(self.num_col)]
for i in range(self.cast_num):
if i < self.MAX_CAST_NUM:
self.layout.addWidget(self.cast_labels[i], *positions[i])
else:
self.layout = QVBoxLayout()
for i in range(self.cast_num):
self.layout.addWidget(self.cast_labels[i])
self.setLayout(self.layout)
def update_cast(self, cast_list):
self.cast_num = len(cast_list)
for i in range(self.cast_num):
self.cast_labels[i].reset_pixmp(cast_list[i])
self.cast_labels[i].seltectable = True
for i in range(self.cast_num, self.MAX_CAST_NUM):
self.cast_labels[i].reset_pixmp()
self.cast_labels[i].seltectable = False
self.update()
def seletected_changed(self):
self.parent.cast_selected_changed()
def clean_seltected(self):
for i in range(self.cast_num):
self.cast_labels[i].isSelected = False
self.update()
def set_selected_idx(self, idx):
if idx < self.cast_num and idx >= 0:
self.cast_labels[idx].isSelected = True
else:
self.clean_seltected()
self.update()
def get_seletectd_idx(self):
sidx = -1
for i in range(self.cast_num):
if self.cast_labels[i].isSelected:
sidx = i
return sidx
def __init__(
self,
session,
name,
prox_word,
cmd_name,
color,
radius,
hbond_allowance,
overlap_cutoff,
has_apply_button,
*,
settings_name="",
# settings_name values:
# empty string: remembered across sessions and the same as for the main contacts/clashes
# GUI
# custom string (e.g. "rotamers"): remembered across sessions and specific to your
# interface, not shared with other contacts/clashes GUIs. The string "contacts GUI"
# or "clashes GUI" will be appended to the provided string to yield the final settings
# name.
# None: not remembered across sessions
#
# The settings will be saved when get_command() is called. The defaults for the
# settings will be the same as the values provided for the arguments below (i.e.
# can be overriden by providing explicit values when calling this function).
#
# Controls configured to not show in the interface will not have their corresponding
# keyword/value added to the command returned by get_command, nor will they have their
# settings value changed/saved. If needed, you will have to add the keyword/value to
# the command yourself.
#
# Your tool needs to call the GUI's destroy() method when it's deleted
attr_name=defaults["attr_name"],
bond_separation=defaults["bond_separation"],
continuous=False,
dashes=None,
distance_only=None,
inter_model=True,
inter_submodel=False,
intra_model=True,
intra_mol=defaults["intra_mol"],
intra_res=defaults["intra_res"],
log=defaults["action_log"],
make_pseudobonds=defaults["action_pseudobonds"],
res_separation=None,
restrict="any",
reveal=False,
save_file=None,
select=defaults["action_select"],
set_attrs=defaults["action_attr"],
show_dist=False,
summary=True,
test_atoms=None,
# what controls to show in the interface
#
# note that if 'test_atoms' is not None, then the selection-restriction control will be omitted
# regardless of the 'show_restrict' value
show_attr_name=True,
show_bond_separation=True,
show_checking_frequency=True,
show_color=True,
show_dashes=True,
show_distance_only=True,
show_hbond_allowance=True,
show_inter_model=True,
show_inter_submodel=False,
show_intra_model=True,
show_intra_mol=True,
show_intra_res=True,
show_log=True,
show_make_pseudobonds=True,
show_name=True,
show_overlap_cutoff=True,
show_radius=True,
show_res_separation=True,
show_restrict=True,
show_reveal=True,
show_save_file=True,
show_select=True,
show_set_attrs=True,
show_show_dist=True,
show_summary=False):
self.session = session
self.cmd_name = cmd_name
from inspect import getargvalues, currentframe
arg_names, var_args, var_kw, frame_dict = getargvalues(currentframe())
settings_defaults = {}
self.show_values = {}
for arg_name in arg_names:
if not arg_name.startswith(
'show_') or 'show_' + arg_name in arg_names:
settings_defaults[arg_name] = frame_dict[arg_name]
else:
self.show_values[arg_name[5:]] = frame_dict[arg_name]
if settings_name is None:
self.settings = settings = None
else:
self.settings = settings = _get_settings(session, settings_name,
settings_defaults,
cmd_name)
final_val = {}
for def_name in settings_defaults.keys():
final_val[def_name] = getattr(
settings, def_name) if settings else frame_dict[def_name]
super().__init__()
from PyQt5.QtWidgets import QVBoxLayout, QGridLayout, QGroupBox, QLabel, QPushButton, QButtonGroup
from PyQt5.QtWidgets import QRadioButton, QAbstractButton, QHBoxLayout, QDoubleSpinBox, QMenu
from PyQt5.QtWidgets import QSpinBox, QCheckBox
from PyQt5.QtCore import Qt
layout = QVBoxLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.setSpacing(0)
layout.setSizeConstraint(QVBoxLayout.SetFixedSize)
self.setLayout(layout)
from chimerax.core.commands import plural_of
self.prox_word = prox_word
self.prox_words = prox_words = plural_of(prox_word)
if test_atoms is not None:
show_restrict = False
show_bool_params = show_intra_model or show_intra_mol or show_intra_res or show_inter_model \
or show_inter_submodel
if show_overlap_cutoff or show_hbond_allowance or show_restrict or show_bond_separation \
or show_bool_params:
group = QGroupBox("Interaction parameters")
layout.addWidget(group)
group_layout = QVBoxLayout()
group_layout.setContentsMargins(0, 0, 0, 0)
group_layout.setSpacing(5)
group.setLayout(group_layout)
overlap_widgets = []
distance_only_widgets = []
if (show_overlap_cutoff
or show_hbond_allowance) and show_distance_only:
test_type_layout = QGridLayout()
test_type_layout.setContentsMargins(0, 0, 0, 0)
test_type_layout.setSpacing(0)
test_type_layout.setColumnStretch(1, 1)
group_layout.addLayout(test_type_layout)
overlap_rows = show_overlap_cutoff + show_hbond_allowance
self.overlap_radio = QRadioButton("")
test_type_layout.addWidget(self.overlap_radio, 0, 0,
overlap_rows, 1)
self.distance_radio = QRadioButton("")
test_type_layout.addWidget(self.distance_radio, overlap_rows,
0)
def enable_widgets(enabled, enabled_widgets, disabled_widgets):
for ew in enabled_widgets:
ew.setEnabled(enabled)
for dw in disabled_widgets:
dw.setEnabled(not enabled)
self.overlap_radio.toggled.connect(
lambda chk, *, ew=overlap_widgets, dw=
distance_only_widgets, f=enable_widgets: f(chk, ew, dw))
self.distance_radio.toggled.connect(
lambda chk, *, ew=distance_only_widgets, dw=
overlap_widgets, f=enable_widgets: f(chk, ew, dw))
row = 0
if show_overlap_cutoff:
cutoff_args = (row, 1)
row += 1
if show_hbond_allowance:
allowance_args = (row, 1)
row += 1
distance_args = (row, 1)
else:
test_type_layout = group_layout
cutoff_args = allowance_args = distance_args = ()
if show_overlap_cutoff:
overlap_layout = QHBoxLayout()
overlap_layout.setContentsMargins(0, 0, 0, 0)
overlap_layout.setSpacing(0)
test_type_layout.addLayout(overlap_layout, *cutoff_args)
lab = QLabel(
"Find pairs of atoms with VDW overlap \N{GREATER-THAN OR EQUAL TO}"
)
overlap_widgets.append(lab)
overlap_layout.addWidget(lab)
self.overlap_spinbox = QDoubleSpinBox()
self.overlap_spinbox.setDecimals(2)
self.overlap_spinbox.setSingleStep(0.1)
self.overlap_spinbox.setRange(-99, 99)
self.overlap_spinbox.setValue(final_val['overlap_cutoff'])
#self.overlap_spinbox.setSuffix('\N{ANGSTROM SIGN}')
overlap_widgets.append(self.overlap_spinbox)
overlap_layout.addWidget(self.overlap_spinbox)
lab2 = QLabel("\N{ANGSTROM SIGN}")
overlap_widgets.append(lab2)
overlap_layout.addWidget(lab2,
stretch=1,
alignment=Qt.AlignLeft)
if show_hbond_allowance:
hbond_layout = QHBoxLayout()
hbond_layout.setContentsMargins(0, 0, 0, 0)
hbond_layout.setSpacing(0)
test_type_layout.addLayout(hbond_layout, *allowance_args)
lab = QLabel("Subtract")
overlap_widgets.append(lab)
hbond_layout.addWidget(lab)
self.hbond_spinbox = QDoubleSpinBox()
self.hbond_spinbox.setDecimals(2)
self.hbond_spinbox.setSingleStep(0.1)
self.hbond_spinbox.setRange(-99, 99)
self.hbond_spinbox.setValue(final_val['hbond_allowance'])
#self.hbond_spinbox.setSuffix('\N{ANGSTROM SIGN}')
overlap_widgets.append(self.hbond_spinbox)
hbond_layout.addWidget(self.hbond_spinbox)
lab = QLabel("from overlap for potentially H-bonding pairs")
overlap_widgets.append(lab)
hbond_layout.addWidget(lab, stretch=1, alignment=Qt.AlignLeft)
if show_distance_only:
distance_layout = QHBoxLayout()
distance_layout.setContentsMargins(0, 0, 0, 0)
distance_layout.setSpacing(0)
test_type_layout.addLayout(distance_layout, *distance_args)
lab = QLabel(
"Find pairs of atoms with center-center distance \N{LESS-THAN OR EQUAL TO}"
)
distance_only_widgets.append(lab)
distance_layout.addWidget(lab)
self.dist_only_spinbox = QDoubleSpinBox()
self.dist_only_spinbox.setDecimals(2)
self.dist_only_spinbox.setSingleStep(0.1)
self.dist_only_spinbox.setRange(0, 1000000)
val = 4.0 if final_val['distance_only'] is None else final_val[
'distance_only']
self.dist_only_spinbox.setValue(val)
#self.dist_only_spinbox.setSuffix('\N{ANGSTROM SIGN}')
distance_only_widgets.append(self.dist_only_spinbox)
distance_layout.addWidget(self.dist_only_spinbox,
alignment=Qt.AlignLeft)
lab2 = QLabel("\N{ANGSTROM SIGN}")
distance_only_widgets.append(lab2)
distance_layout.addWidget(lab2,
stretch=1,
alignment=Qt.AlignLeft)
if overlap_widgets and distance_only_widgets:
if distance_only is None:
self.overlap_radio.setChecked(True)
enable_widgets(False, distance_only_widgets,
overlap_widgets)
else:
self.distance_radio.setChecked(True)
enable_widgets(True, distance_only_widgets,
overlap_widgets)
if show_restrict:
restrict_options = OptionsPanel(sorting=False,
scrolled=False,
contents_margins=(0, 0, 0, 0))
group_layout.addWidget(restrict_options,
alignment=Qt.AlignLeft)
if show_restrict:
self.sel_restrict_option = make_optional(
AtomPairRestrictOption)("Limit by selection",
None,
None,
atom_word="end")
restrict_options.add_option(self.sel_restrict_option)
if show_bond_separation:
bond_sep_layout = QHBoxLayout()
bond_sep_layout.setContentsMargins(0, 0, 0, 0)
bond_sep_layout.setSpacing(0)
group_layout.addLayout(bond_sep_layout)
bond_sep_layout.addWidget(
QLabel("Ignore interactions between atoms"))
self.bond_sep_button = QPushButton()
bond_sep_layout.addWidget(self.bond_sep_button)
bond_sep_menu = QMenu(self)
for bond_sep in range(2, 6):
bond_sep_menu.addAction(str(bond_sep))
bond_sep_menu.triggered.connect(
lambda action, but=self.bond_sep_button: but.setText(
action.text()))
self.bond_sep_button.setMenu(bond_sep_menu)
self.bond_sep_button.setText(str(bond_separation))
bond_sep_layout.addWidget(QLabel("or fewer bonds apart"),
stretch=1,
alignment=Qt.AlignLeft)
if show_res_separation:
res_sep_layout = QHBoxLayout()
res_sep_layout.setContentsMargins(0, 0, 0, 0)
#res_sep_layout.setSpacing(0)
group_layout.addLayout(res_sep_layout)
self.res_sep_checkbox = QCheckBox(
"Ignore interactions between residues <")
final_rs_val = final_val['res_separation']
self.res_sep_checkbox.setChecked(final_rs_val is not None)
res_sep_layout.addWidget(self.res_sep_checkbox)
val = 5 if final_rs_val is None else final_rs_val
self.res_sep_spinbox = rs_box = QSpinBox()
rs_box.setMinimum(1)
rs_box.setValue(val)
res_sep_layout.addWidget(rs_box)
res_sep_layout.addWidget(QLabel("apart in sequence"),
stretch=1,
alignment=Qt.AlignLeft)
if show_bool_params:
bool_param_options = OptionsPanel(sorting=False,
scrolled=False,
contents_margins=(10, 0, 10,
0))
group_layout.addWidget(bool_param_options,
alignment=Qt.AlignCenter)
if show_inter_model:
self.inter_model_option = BooleanOption(
"Include intermodel",
None if settings else inter_model,
None,
attr_name="inter_model",
settings=settings)
bool_param_options.add_option(self.inter_model_option)
if show_inter_submodel:
self.inter_submodel_option = BooleanOption(
"Include intersubmodel",
None if settings else inter_submodel,
None,
attr_name="inter_submodel",
settings=settings)
bool_param_options.add_option(self.inter_submodel_option)
if show_intra_model:
self.intra_model_option = BooleanOption(
"Include intramodel",
None if settings else intra_model,
None,
attr_name="intra_model",
settings=settings)
bool_param_options.add_option(self.intra_model_option)
if show_intra_mol:
self.intra_mol_option = BooleanOption(
"Include intramolecule",
None if settings else intra_mol,
None,
attr_name="intra_mol",
settings=settings)
bool_param_options.add_option(self.intra_mol_option)
if show_intra_res:
self.intra_res_option = BooleanOption(
"Include intraresidue",
None if settings else intra_res,
None,
attr_name="intra_res",
settings=settings)
bool_param_options.add_option(self.intra_res_option)
if show_select or show_make_pseudobonds or show_color or show_dashes or show_radius \
or show_show_dist or show_name or show_reveal or show_attr_name or show_set_attrs or show_log \
or show_save_file:
group = QGroupBox("Treatment of results")
layout.addWidget(group)
group_layout = QVBoxLayout()
group_layout.setContentsMargins(0, 0, 0, 0)
group_layout.setSpacing(5)
group.setLayout(group_layout)
treatment_options = OptionsPanel(sorting=False,
scrolled=False,
contents_margins=(10, 0, 10, 0))
group_layout.addWidget(treatment_options)
if show_select:
self.select_option = BooleanOption(
"Select atoms",
None if settings else select,
None,
attr_name="select",
settings=settings)
treatment_options.add_option(self.select_option)
if show_make_pseudobonds:
if show_color or show_dashes or show_radius or show_show_dist or show_name:
# checkable group
self.make_pseudobonds_widget, sub_options = treatment_options.add_option_group(
group_label="Display as pseudobonds",
checked=final_val['make_pseudobonds'],
contents_margins=(10, 0, 10, 0),
sorting=False)
subgroup_layout = QVBoxLayout()
subgroup_layout.setContentsMargins(0, 0, 0, 0)
subgroup_layout.setSpacing(5)
self.make_pseudobonds_widget.setLayout(subgroup_layout)
subgroup_layout.addWidget(sub_options)
if show_color:
self.color_option = ColorOption(
"Color",
None if settings else color,
None,
attr_name="color",
settings=settings)
sub_options.add_option(self.color_option)
if show_radius:
self.radius_option = FloatOption(
"Radius",
None if settings else radius,
None,
attr_name="radius",
settings=settings)
sub_options.add_option(self.radius_option)
if show_dashes:
self.dashes_option = IntOption(
"Dashes",
None if settings else dashes,
None,
attr_name="dashes",
min=0,
settings=settings)
sub_options.add_option(self.dashes_option)
if show_show_dist:
self.show_dist_option = BooleanOption(
"Distance label",
None if settings else show_dist,
None,
attr_name="show_dist",
settings=settings)
sub_options.add_option(self.show_dist_option)
if show_name:
self.name_option = StringOption(
"Group name", name, None)
sub_options.add_option(self.name_option)
else:
# boolean
self.make_pseudobonds_widget = BooleanOption(
"Draw pseudobonds",
None if settings else make_pseudobonds,
None,
attr_name="make_pseudobonds",
settings=settings)
treatment_options.add_option(self.make_pseudobonds_widget)
else:
if show_color:
self.color_option = ColorOption(
"Pseudobond color",
None if settings else color,
None,
attr_name="color",
settings=settings)
treatment_options.add_option(self.color_option)
if show_radius:
self.radius_option = FloatOption(
"Pseudobond radius",
None if settings else radius,
None,
attr_name="radius",
settings=settings)
treatment_options.add_option(self.radius_option)
if show_dashes:
self.dashes_option = IntOption(
"Pseudobond dashes",
None if settings else dashes,
None,
attr_name="dashes",
min=0,
settings=settings)
sub_options.add_option(self.dashes_option)
if show_show_dist:
self.show_dist_option = BooleanOption(
"Pseudobond distance label",
None if settings else show_dist,
None,
attr_name="show_dist",
settings=settings)
sub_options.add_option(self.show_dist_option)
if show_name:
self.name_option = StringOption("Pseudobond group name",
name, None)
sub_options.add_option(self.name_option)
if show_reveal:
self.reveal_option = BooleanOption(
"Reveal atoms of interacting residues",
None if settings else reveal,
None,
attr_name="reveal",
settings=settings)
treatment_options.add_option(self.reveal_option)
if show_set_attrs:
if show_attr_name:
combo_option = make_optional(StringOption)
option = self.attr_name_option = combo_option(
"Assign atomic attribute named",
final_val['attr_name'], None)
if not final_val['set_attrs']:
# done this way so that attr name is not blank
option.value = None
else:
option = self.set_attrs_option = BooleanOption(
"Assign attribute", final_val['set_attrs'], None)
treatment_options.add_option(option)
elif show_attr_name:
self.attr_name_option = StringOption("Attribute name",
final_val['attr_name'],
None)
treatment_options.add_option(self.attr_name_option)
if show_log or show_save_file:
group = QGroupBox("Write information to:")
layout.addWidget(group)
info_layout = QVBoxLayout()
info_layout.setContentsMargins(0, 0, 0, 0)
info_layout.setSpacing(0)
group.setLayout(info_layout)
info_options = OptionsPanel(sorting=False,
scrolled=False,
contents_margins=(0, 0, 0, 0))
info_layout.addWidget(info_options)
if show_log:
self.log_option = BooleanOption("Log",
None if settings else log,
None,
attr_name="log",
settings=settings)
info_options.add_option(self.log_option)
if show_save_file:
self.save_file_option = BooleanOption("File", False, None)
info_options.add_option(self.save_file_option)
if show_summary:
self.summary_option = BooleanOption(
"Log total number of %s" % prox_words,
None if settings else summary,
None,
attr_name="summary",
settings=settings)
treatment_options.add_option(self.summary_option)
if show_checking_frequency:
group = QGroupBox("Frequency of checking")
layout.addWidget(group)
group_layout = QGridLayout()
group_layout.setContentsMargins(0, 0, 0, 0)
group_layout.setSpacing(5)
group_layout.setColumnStretch(0, 1)
group_layout.setColumnStretch(3, 1)
group.setLayout(group_layout)
group_layout.addWidget(QLabel("Check..."),
0,
1,
2,
1,
alignment=Qt.AlignRight | Qt.AlignVCenter)
self.ok_radio = QRadioButton(
"when OK%s clicked" % ("/Apply" if has_apply_button else ""))
self.ok_radio.setChecked(True)
group_layout.addWidget(self.ok_radio, 0, 2, alignment=Qt.AlignLeft)
self.ok_radio.toggled.connect(self._checking_change)
group_layout.addWidget(
QRadioButton("continuously (until dialog closed)"),
1,
2,
alignment=Qt.AlignLeft)
