def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _LinterSettings(self.session, name)
self._build_ui()
def __init__(self, session, name):
super().__init__(session, name)
self.settings = _InputGeneratorSettings(session,
"Build QM Input",
version="2")
self.tool_window = MainToolWindow(self)
self._build_ui()
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _VburSettings(self.session, name)
self.ligand_atoms = []
self._build_ui()
def __init__(self, session, name):
super().__init__(session, name)
self.settings = _EditStructureSettings(session, "Structure Modification")
self.tool_window = MainToolWindow(self)
self.close_previous_bool = self.settings.modify
self._build_ui()
def __init__(self, session, name):
super().__init__(session, name)
self.display_name = "SEQCROW Models"
self.tool_window = MainToolWindow(self)
self._build_ui()
self.fill_tree()
self._fr_change = self.session.filereader_manager.triggers.add_handler(FILEREADER_CHANGE,
lambda *args: self.fill_tree(*args))
self._add_models = self.session.triggers.add_handler(ADD_MODELS,
lambda *args: self.fill_tree(*args))
self._molid_change = self.session.triggers.add_handler(MODEL_ID_CHANGED,
lambda *args: self.fill_tree(*args))
self._molname_change = self.session.triggers.add_handler(MODEL_NAME_CHANGED,
lambda *args: self.fill_tree(*args))
def __init__(self, session, name):
super().__init__(session, name)
self.display_name = "Thermochemistry"
self.tool_window = MainToolWindow(self)
self.settings = _ComputeThermoSettings(self.session, name)
self.nrg_fr = {}
self.thermo_fr = {}
self.thermo_co = {}
self._build_ui()
self.set_sp()
self.set_thermo_mdl()
self.calc_relative_thermo()
def __init__(self, session, name):
super().__init__(session, name)
self.display_name = "Job Queue"
self.tool_window = MainToolWindow(self)
if not self.session.seqcrow_job_manager.initialized:
self.session.seqcrow_job_manager.init_queue()
self._build_ui()
self._job_queued = self.session.seqcrow_job_manager.triggers.add_handler(
JOB_QUEUED, lambda *args: self.fill_tree(*args))
self._job_started = self.session.seqcrow_job_manager.triggers.add_handler(
JOB_STARTED, lambda *args: self.fill_tree(*args))
self._job_finished = self.session.seqcrow_job_manager.triggers.add_handler(
JOB_FINISHED, lambda *args: self.fill_tree(*args))
self.fill_tree()
def __init__(self, session, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self.settings = _PrecisionRotateSettings(session, name)
self.bonds = {}
self.bond_centers = {}
self.groups = {}
self.perpendiculars = {}
self.perp_centers = {}
self.manual_center = {}
self._build_ui()
self._show_rot_vec = self.session.triggers.add_handler(
SELECTION_CHANGED, self.show_rot_vec)
global_triggers = get_triggers()
self._changes = global_triggers.add_handler("changes done",
self.show_rot_vec)
self.show_rot_vec()
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, name):
super().__init__(session, name)
self.tool_window = MainToolWindow(self)
self._build_ui()
def __init__(self, *args):
super().__init__(*args)
self.tool_window = MainToolWindow(self)
self._build_ui()
