import enum
import schrodinger
from schrodinger.application.msv.gui import gui_models
from schrodinger.application.msv.gui import popups
from schrodinger.application.msv.gui import stylesheets
from schrodinger.application.msv.gui.viewconstants import \
ALIGN_SELECTED_ONLY_CB_TT
from schrodinger.application.msv.gui.viewconstants import \
MULTI_ALIGN_DISABLED_TT
from schrodinger.application.msv.gui.viewconstants import \
PROF_ALIGN_DISABLED_TT
from schrodinger.application.msv.gui.viewconstants import AlignType
from schrodinger.application.msv.gui.viewconstants import MultAlnAlgorithm
from schrodinger.application.msv.gui.viewconstants import SeqAlnMode
from schrodinger.application.msv.gui.viewconstants import StructAlnMode
from schrodinger.application.msv.gui.viewconstants import StructAlnRefASLMode
from schrodinger.application.msv.gui.viewconstants import \
StructAlnSequenceRepresents
from schrodinger.application.msv.gui.viewconstants import StructAlnTransform
from schrodinger.models import mappers
from schrodinger.protein import annotation
from schrodinger.Qt import QtCore
from schrodinger.Qt import QtWidgets
from schrodinger.ui.qt import atomselector
from schrodinger.ui.qt import delegates
from schrodinger.ui.qt import mapperwidgets
from schrodinger.ui.qt import pop_up_widgets
from schrodinger.ui.qt import utils as qt_utils
from schrodinger.ui.qt import widgetmixins
from schrodinger.ui.qt.mapperwidgets import plptable
from . import alignment_pane_ui
from . import binding_site_aln_dialog_ui
from . import multiple_seq_aln_dialog_ui
from . import pairwise_seq_aln_dialog_ui
from . import protein_structure_aln_dialog_ui
maestro = schrodinger.get_maestro()
INFO_BTN_TOOLTIP = """This feature can only be used with the <i>Existing
entries</i> option, and only when the Reference sequence has structure.<br>The
Reference entry must have at least 2 chains that will be used in the
alignment. The entries to be aligned can have only 1 chain in the alignment.
"""
SELECTED_RES_TT = """
<p style='white-space:pre'>
This option pertains to sequence selection only.
Residue selection will automatically restrict the
sequence alignment to those residue blocks.
</p>"""
LOCK_GAPS_CB_TT = '''Preserve existing gaps in the Reference sequence (more gaps may still be
added). When multiple pairwise alignments are requested simultaneously,
gaps will be locked automatically after the first pair is aligned.'''
PAIRWISE_SUBST_MATRICES = [
"PAM250", "BLOSUM45", "BLOSUM62", "BLOSUM80", "GONNET", "Residue Identity"
]
SEQ_ANNO = annotation.ProteinSequenceAnnotations.ANNOTATION_TYPES
SEQ_MODE_TEXT = {
SeqAlnMode.Multiple: "Multiple sequence alignment",
SeqAlnMode.Pairwise: "Pairwise sequence alignment",
SeqAlnMode.Structure: "Current structure superposition",
SeqAlnMode.Residue: "Residue numbers",
SeqAlnMode.Profile: "Profile alignment",
SeqAlnMode.PairwiseSS: "Pairwise with secondary structure prediction",
} # yapf: disable
STRUCT_MODE_TEXT = [(StructAlnMode.Superimpose, "Current sequence alignment"),
(StructAlnMode.Structure, "Protein structure alignment"),
(StructAlnMode.BindingSite, "Binding site alignment")]
OPTIONS_PAGE = enum.IntEnum('OptionsPage', [
'multiple', 'pairwise', 'current_sequence', 'profile', 'prot_structure',
'binding_site', 'sel_binding_site', 'current_structure', 'residue_numbers',
'pairwise_ss'
],
start=0)
SETTINGS_PAGE = enum.IntEnum('SettingsPage', [
'multiple', 'no', 'pairwise', 'prot_structure', 'binding_site',
'pairwise_ss'
],
start=0)
COMBO_PAGE_MAPPING = {
SeqAlnMode.Multiple: (OPTIONS_PAGE.multiple, SETTINGS_PAGE.multiple),
SeqAlnMode.Pairwise: (OPTIONS_PAGE.pairwise, SETTINGS_PAGE.pairwise),
SeqAlnMode.Structure: (OPTIONS_PAGE.current_structure, SETTINGS_PAGE.no),
SeqAlnMode.Residue: (OPTIONS_PAGE.residue_numbers, SETTINGS_PAGE.no),
SeqAlnMode.Profile: (OPTIONS_PAGE.profile, SETTINGS_PAGE.no),
SeqAlnMode.PairwiseSS: (OPTIONS_PAGE.pairwise_ss, SETTINGS_PAGE.pairwise_ss),
StructAlnMode.Superimpose: (OPTIONS_PAGE.current_sequence, SETTINGS_PAGE.no),
StructAlnMode.Structure: (OPTIONS_PAGE.prot_structure, SETTINGS_PAGE.prot_structure),
StructAlnMode.BindingSite: (OPTIONS_PAGE.binding_site, SETTINGS_PAGE.binding_site)
} # yapf: disable
def _set_not_implemented(widget):
"""
Mark a widget as not implemented
"""
widget.setEnabled(False)
font = widget.font()
font.setStrikeOut(True)
widget.setFont(font)
widget.setToolTip("Not implemented")
[docs]class MsvComboBoxMixin:
[docs] def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.setStyleSheet(stylesheets.LIGHT_COMBOBOX)
# MSV-1962: Workaround for a bug where the combobox background color
# was being applied to the selected item background on Linux
self.setItemDelegate(QtWidgets.QStyledItemDelegate(self))
def _getWidth(self):
"""
Return the correct width for the text.
This method is needed to prevent Macs from truncating text that is too
long
"""
text_items = (self.itemText(i) for i in range(self.count()))
font_metrics = self.fontMetrics()
text_width = max((font_metrics.width(item) for item in text_items),
default=0)
padding = 20
return text_width + padding
[docs]class MsvMappableComboBox(MsvComboBoxMixin, mapperwidgets.MappableComboBox):
pass
[docs]class MsvEnumComboBox(MsvComboBoxMixin, mapperwidgets.EnumComboBox):
pass
[docs]class AlignmentPane(mappers.MapperMixin, widgetmixins.InitMixin, BasePopUp):
"""
Alignment pane for align options
:ivar alignmentRequested: Signal emitted when "Align" is clicked.
:vartype sequenceAlignmentRequested: QtCore.pyqtSignal
"""
model_class = gui_models.PageModel
ui_module = alignment_pane_ui
alignmentRequested = QtCore.pyqtSignal()
[docs] def initSetUp(self):
super().initSetUp()
self._previous_align_selected = True
self.setObjectName('alignment_pane')
self.setStyleSheet(stylesheets.ALIGNMENT_PANE)
self._setUpComboBoxes()
self._setUpProteinStructureAlnDialog()
self._setUpBindingSiteAlnDialog()
self._setUpMultipleSeqAlnDialog()
self._setUpPairwiseSeqAlnDialog()
ui = self.ui
ui.dropdown_options_stacked_widget.setEnum(AlignType)
self._mode_btn_grp = mapperwidgets.MappableButtonGroup({
ui.sequences_rb: AlignType.Sequence,
ui.structures_rb: AlignType.Structure,
})
ui.selected_res_info_btn.setToolTip(SELECTED_RES_TT)
ui.clear_constraints_btn.pressed.connect(
self._onClearConstraintsClicked)
ui.ss_clear_constraints_btn.pressed.connect(
self._onClearConstraintsClicked)
ui.align_btn.clicked.connect(self._onAlignClicked)
self.structure_dialog.alignBtnUpdateRequested.connect(
self.updateAlignBtnVisibility)
self.ui.lock_gaps_cb.setToolTip(LOCK_GAPS_CB_TT)
self.ui.selected_only_cb.setToolTip(ALIGN_SELECTED_ONLY_CB_TT)
self.ui.help_btn.clicked.connect(self._showHelp)
def _showHelp(self):
qt_utils.help_dialog('MSV_ALIGN_PANE', parent=self)
[docs] def updateAlignBtnVisibility(self, valid):
"""
Enable/disable the Align button. Also, set the tooltip when disabled.
:param valid: Whether to enable or disable the Align button.
:type valid: bool
"""
self.ui.align_btn.setEnabled(valid)
tooltip = "" if valid else (
"Chain mapping is invalid - correct values or toggle off option")
self.ui.align_btn.setToolTip(tooltip)
[docs] def initLayOut(self):
super().initLayOut()
g = self.geometry()
g.setWidth(0) # Force the pane to resize to the minimum width
self.setGeometry(g)
[docs] def defineMappings(self):
M = self.model_class
settings = M.options.align_settings
page_target = mappers.TargetSpec(slot=self._updatePanelState)
align_type_lhs = (self._mode_btn_grp,
self.ui.dropdown_options_stacked_widget, page_target)
can_aln_tgt = mappers.TargetSpec(slot=self._updateCanAlign)
can_aln_params = (M.menu_statuses.can_only_multiple_align,
M.menu_statuses.can_only_profile_align,
M.menu_statuses.can_aln_set_align)
can_clear_constraints_tgt = mappers.TargetSpec(
setter=self._updateClearConstraintsBtn)
can_set_constraints_tgt = mappers.TargetSpec(
setter=self._updateSetConstraintsBtn)
return [
(align_type_lhs, settings.align_type),
((self.sequence_combo, page_target), settings.seq_align_mode),
((self.structure_combo, page_target), settings.struct_align_mode),
(self.ui.selected_only_cb, settings.align_only_selected_seqs),
(self.pairwise_dialog, settings.pairwise),
(self.multiple_dialog, settings.multiple),
(self.structure_dialog, settings.protein_structure),
(self.binding_site_aln_dialog, settings.binding_site),
(self.ui.globally_conserved_residues_cb, settings.multiple.find_globally_conserved),
(self.ui.multiple_superimpose_structures_cb, settings.multiple.superimpose_after),
(self.ui.set_constraints_cb, settings.pairwise.set_constraints),
(self.ui.ss_set_constraints_cb, settings.pairwise_ss.set_constraints),
(self.ui.gpcr_cb,settings.pairwise_ss.use_gpcr_aln),
(can_set_constraints_tgt, M.menu_statuses.can_set_constraints),
(can_clear_constraints_tgt, M.menu_statuses.can_clear_constraints),
(self.ui.lock_gaps_cb, settings.pairwise.lock_gaps),
(self.ui.pairwise_superimpose_structures_cb, settings.pairwise.superimpose_after),
(self.ui.resnum_superimpose_structures_cb, settings.residue_number.superimpose_after),
(self.ui.align_sequences_cb, settings.protein_structure.align_seqs),
(self.ui.force_alignment_cb, settings.protein_structure.force),
(self.ui.superimpose_selected_cb, settings.superimpose.align_sel_res_only),
(self.ui.align_following_superposition_cb, settings.binding_site.align_seqs),
(self.ui.align_sel_res_sequences_cb, settings.binding_site.align_seqs),
((self.binding_site_cutoff_combo, page_target), settings.binding_site.binding_site_cutoff),
(can_aln_tgt, can_aln_params),
] # yapf: disable
[docs] def getSignalsAndSlots(self, model):
# MSV-2583: Figure out why `res_selection_model` is getting
# garbage collected
self._res_sel_model_reference = model.aln.res_selection_model
resSelectionChanged = model.aln.res_selection_model.selectionChanged
ss = [
(resSelectionChanged, self._updateSelectedResInfoIconVisibility),
(model.menu_statuses.can_align_binding_siteChanged, self._updateCanAlign),
(model.menu_statuses.can_align_selected_seqsChanged, self._updateSelectedSeqCb),
(model.menu_statuses.can_only_multiple_alignChanged, self._updateSelectedSeqCb),
(model.menu_statuses.can_only_profile_alignChanged, self._updateSelectedSeqCb),
(model.options.align_settings.binding_site.align_sel_res_onlyChanged, self._updatePanelState),
] # yapf: disable
return ss
[docs] def setModel(self, model):
super().setModel(model)
if model is None:
return
self._updateSelectedResInfoIconVisibility()
def _setUpComboBoxes(self):
self.sequence_combo = MsvMappableComboBox()
for enum_member in SeqAlnMode:
text = SEQ_MODE_TEXT[enum_member]
self.sequence_combo.addItem(text, enum_member)
self.ui.sequence_combo_layout.addWidget(self.sequence_combo)
self.structure_combo = MsvEnumComboBox(enum=StructAlnMode)
self.structure_combo.updateItemTexts(STRUCT_MODE_TEXT)
self.ui.structure_combo_layout.addWidget(self.structure_combo)
self.binding_site_cutoff_combo = popups.BindingSiteDistanceComboBox(
parent=self)
self.ui.binding_site_cutoff_layout.addWidget(
self.binding_site_cutoff_combo)
post_lbl = QtWidgets.QLabel(' of ligand')
self.ui.binding_site_cutoff_layout.addWidget(post_lbl)
def _setUpProteinStructureAlnDialog(self):
"""
Add settings button to create protein structure aln dialog
"""
protein_structure_aln_btn = popups.make_pop_up_tool_button(
parent=self,
pop_up_class=ProteinStructureAlnPopUp,
obj_name='protein_structure_aln_btn',
)
protein_structure_aln_btn.setPopupValign(
protein_structure_aln_btn.ALIGN_BOTTOM)
self.ui.protein_structure_alignment_settings_widget.layout().addWidget(
protein_structure_aln_btn)
self.structure_dialog = protein_structure_aln_btn.popup_dialog
def _setUpBindingSiteAlnDialog(self):
"""
Add settings button that opens the binding site aln dialog
"""
binding_site_aln_btn = popups.make_pop_up_tool_button(
parent=self,
pop_up_class=BindingSiteAlnPopup,
obj_name='binding_site_aln_btn',
)
binding_site_aln_btn.setPopupValign(binding_site_aln_btn.ALIGN_BOTTOM)
self.ui.binding_site_alignment_settings_widget.layout().addWidget(
binding_site_aln_btn)
self.binding_site_aln_dialog = binding_site_aln_btn.popup_dialog
def _setUpMultipleSeqAlnDialog(self):
"""
Add settings button to create multiple seq aln dialog
"""
multiple_seq_aln_btn = popups.make_pop_up_tool_button(
parent=self,
pop_up_class=MultipleAlignSettingsPopUp,
obj_name='multiple_seq_aln_btn')
multiple_seq_aln_btn.setPopupValign(multiple_seq_aln_btn.ALIGN_BOTTOM)
self.ui.Multiple_sequence_alignment_settings_widget.layout().addWidget(
multiple_seq_aln_btn)
self.multiple_dialog = multiple_seq_aln_btn.popup_dialog
def _setUpPairwiseSeqAlnDialog(self):
"""
Add settings button to create pairwise seq aln dialog
"""
pairwise_seq_aln_btn = popups.make_pop_up_tool_button(
parent=self,
pop_up_class=PairwiseAlignSettingsPopUp,
obj_name='pairwise_seq_aln_btn')
pairwise_seq_aln_btn.setPopupValign(pairwise_seq_aln_btn.ALIGN_BOTTOM)
self.ui.pairwise_sequence_alignment_settings_widget.layout().addWidget(
pairwise_seq_aln_btn)
self.pairwise_dialog = pairwise_seq_aln_btn.popup_dialog
##############################################
# Mapper callbacks
##############################################
@QtCore.pyqtSlot()
def _updateSelectedSeqCb(self):
"""
Manage state of "Selected seqs" checkbox
"""
menu_statuses = self.model.menu_statuses
align_restricted = (menu_statuses.can_only_multiple_align or
menu_statuses.can_only_profile_align)
enable = menu_statuses.can_align_selected_seqs and not align_restricted
self.ui.selected_only_cb.setEnabled(enable)
settings = self.model.options.align_settings
if enable:
# If we're enabling the checkbox, restore the value to what it was
# when we disabled it.
settings.align_only_selected_seqs = self._previous_align_selected
else:
# If we're disabling the checkbox, save the state first so
# we can restore it later.
self._previous_align_selected = settings.align_only_selected_seqs
settings.align_only_selected_seqs = align_restricted
@QtCore.pyqtSlot()
def _updateSelectedResInfoIconVisibility(self):
"""
Manage the visibility of the info icon next to the "Selected Only"
checkbox.
The info icon will be shown for sequence alignment modes if any
residues are selected.
"""
should_show = (
self.model.aln.res_selection_model.hasSelection() and
self.model.options.align_settings.align_type is AlignType.Sequence)
self.ui.selected_res_info_btn.setVisible(should_show)
@QtCore.pyqtSlot()
def _updatePanelState(self):
"""
Change options and settings pages based on current mode
"""
ui = self.ui
settings = self.model.options.align_settings
align_mode = settings.getAlignMode()
options_page, settings_page = COMBO_PAGE_MAPPING[align_mode]
if options_page == OPTIONS_PAGE.binding_site \
and settings.binding_site.align_sel_res_only:
options_page = OPTIONS_PAGE.sel_binding_site
ui.checkable_options_stacked_widget.setCurrentIndex(options_page)
ui.settings_stacked_widget.setCurrentIndex(settings_page)
self._updateCanAlign()
self._updateSelectedResInfoIconVisibility()
@QtCore.pyqtSlot()
def _updateCanAlign(self):
"""
Update whether aligning is allowed
"""
enable_align = True
settings = self.model.options.align_settings
statuses = self.model.menu_statuses
align_type = settings.align_type
align_mode = settings.getAlignMode()
align_btn_tooltip = ''
if not statuses.can_aln_set_align:
enable_align = False
align_btn_tooltip = PROF_ALIGN_DISABLED_TT
elif align_type is AlignType.Sequence:
is_profile = align_mode is SeqAlnMode.Profile
must_profile = statuses.can_only_profile_align
if is_profile or must_profile:
enable_align = is_profile and must_profile
if not enable_align:
align_btn_tooltip = (PROF_ALIGN_DISABLED_TT if is_profile
else MULTI_ALIGN_DISABLED_TT)
elif not self.model.split_chain_view:
enable_align = False
align_btn_tooltip = "Profile alignment not enabled in combined chain mode"
elif statuses.can_only_multiple_align:
enable_align = align_mode is SeqAlnMode.Multiple
elif align_type is AlignType.Structure:
if (statuses.can_only_multiple_align or
statuses.can_only_profile_align):
enable_align = False
elif align_mode == StructAlnMode.Superimpose:
enable_align = bool(maestro)
elif align_mode == StructAlnMode.BindingSite and settings.binding_site.align_sel_res_only:
enable_align = statuses.can_align_binding_site
self.ui.align_btn.setEnabled(enable_align)
self.ui.align_btn.setToolTip(align_btn_tooltip)
@QtCore.pyqtSlot(bool)
def _updateClearConstraintsBtn(self, can_clear_constraints):
"""
Update the enabled state of the clear constraints btn
"""
self.ui.clear_constraints_btn.setEnabled(can_clear_constraints)
self.ui.ss_clear_constraints_btn.setEnabled(can_clear_constraints)
@QtCore.pyqtSlot(bool)
def _updateSetConstraintsBtn(self, can_set_constraints):
"""
Update the enabled state of the set constraints btn
"""
self.ui.set_constraints_cb.setEnabled(can_set_constraints)
self.ui.ss_set_constraints_cb.setEnabled(can_set_constraints)
##############################################
# Widget slots
##############################################
def _onClearConstraintsClicked(self):
self.model.aln.resetPairwiseConstraints()
def _onAlignClicked(self):
self.close()
self.alignmentRequested.emit()
[docs]class MappableAtomSelector(mappers.TargetMixin, atomselector.AtomSelector):
[docs] def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.aslTextModified.connect(self.targetValueChanged)
[docs] def targetGetValue(self):
return self.getAsl()
[docs] def targetSetValue(self, value):
self.setAsl(value)
[docs]class ChainMapTableSpec(plptable.TableSpec):
@plptable.FieldColumn(gui_models.ChainName.seq_chain,
title="Sequence (1 per entry)")
def sequence_chain(self, field):
return f"{field[0]}_{field[1]}"
reference = plptable.FieldColumn(gui_models.ChainName.reference,
title="Reference Chain",
editable=True)
[docs] @reference.data_method(role=delegates.ComboBoxDelegate.COMBOBOX_ROLE)
def populateComboBox(self, field):
return self._reference_chains
[docs] def setReferenceChains(self, ref_chains):
"""
Set all the available chains from the reference structure ready to
be added to the combobox delegate.
:param ref_chains: list of chains.
:type ref_chains: list(str)
"""
self._reference_chains = ref_chains