class ModellerLauncher(ToolInstance):
"""Generate the inputs needed by Modeller for comparative modeling"""
help = "help:user/tools/modeller.html"
SESSION_SAVE = False
def __init__(self, session, tool_name):
ToolInstance.__init__(self, session, tool_name)
from chimerax.ui import MainToolWindow
self.tool_window = MainToolWindow(self,
close_destroys=False,
statusbar=False)
parent = self.tool_window.ui_area
from PyQt5.QtWidgets import QListWidget, QFormLayout, QAbstractItemView, QGroupBox, QVBoxLayout
from PyQt5.QtWidgets import QDialogButtonBox as qbbox
interface_layout = QVBoxLayout()
interface_layout.setContentsMargins(0, 0, 0, 0)
interface_layout.setSpacing(0)
parent.setLayout(interface_layout)
alignments_area = QGroupBox("Sequence alignments")
interface_layout.addWidget(alignments_area)
interface_layout.setStretchFactor(alignments_area, 1)
alignments_layout = QVBoxLayout()
alignments_layout.setContentsMargins(0, 0, 0, 0)
alignments_area.setLayout(alignments_layout)
self.alignment_list = AlignmentListWidget(session)
self.alignment_list.setSelectionMode(
QAbstractItemView.ExtendedSelection)
self.alignment_list.keyPressEvent = session.ui.forward_keystroke
self.alignment_list.value_changed.connect(self._list_selection_cb)
self.alignment_list.alignments_changed.connect(
self._update_sequence_menus)
alignments_layout.addWidget(self.alignment_list)
alignments_layout.setStretchFactor(self.alignment_list, 1)
targets_area = QGroupBox("Target sequences")
self.targets_layout = QFormLayout()
targets_area.setLayout(self.targets_layout)
interface_layout.addWidget(targets_area)
self.seq_menu = {}
self._update_sequence_menus(session.alignments.alignments)
options_area = QGroupBox("Options")
options_layout = QVBoxLayout()
options_layout.setContentsMargins(0, 0, 0, 0)
options_area.setLayout(options_layout)
interface_layout.addWidget(options_area)
interface_layout.setStretchFactor(options_area, 2)
from chimerax.ui.options import CategorizedSettingsPanel, BooleanOption, IntOption, PasswordOption, \
OutputFolderOption
panel = CategorizedSettingsPanel(category_sorting=False, buttons=False)
options_layout.addWidget(panel)
from .settings import get_settings
settings = get_settings(session)
panel.add_option(
"Basic",
BooleanOption(
"Make multichain model from multichain template",
settings.multichain,
None,
balloon=
"If false, all chains (templates) associated with an alignment will be used in combination\n"
"to model the target sequence of that alignment, i.e. a monomer will be generated from the\n"
"alignment. If true, the target sequence will be modeled from each template, i.e. a multimer\n"
"will be generated from the alignment (assuming multiple chains are associated).",
attr_name="multichain",
settings=settings))
max_models = 1000
panel.add_option(
"Basic",
IntOption(
"Number of models",
settings.num_models,
None,
attr_name="num_models",
settings=settings,
min=1,
max=max_models,
balloon=
"Number of model structures to generate. Must be no more than %d.\n"
"Warning: please consider the calculation time" % max_models))
key = "" if settings.license_key is None else settings.license_key
panel.add_option(
"Basic",
PasswordOption(
"Modeller license key",
key,
None,
attr_name="license_key",
settings=settings,
balloon=
"Your Modeller license key. You can obtain a license key by registering at the Modeller web site"
))
panel.add_option(
"Advanced",
BooleanOption(
"Use fast/approximate mode (produces only one model)",
settings.fast,
None,
attr_name="fast",
settings=settings,
balloon=
"If enabled, use a fast approximate method to generate a single model.\n"
"Typically use to get a rough idea what the model will look like or\n"
"to check that the alignment is reasonable."))
panel.add_option(
"Advanced",
BooleanOption(
"Include non-water HETATM residues from template",
settings.het_preserve,
None,
attr_name="het_preserve",
settings=settings,
balloon=
"If enabled, all non-water HETATM residues in the template\n"
"structure(s) will be transferred into the generated models."))
panel.add_option(
"Advanced",
BooleanOption(
"Build models with hydrogens",
settings.hydrogens,
None,
attr_name="hydrogens",
settings=settings,
balloon=
"If enabled, the generated models will include hydrogen atoms.\n"
"Otherwise, only heavy atom coordinates will be built.\n"
"Increases computation time by approximately a factor of 4."))
panel.add_option(
"Advanced",
OutputFolderOption(
"Temporary folder location (optional)",
settings.temp_path,
None,
attr_name="temp_path",
settings=settings,
balloon=
"Specify a folder for temporary files. If not specified,\n"
"a location will be generated automatically."))
panel.add_option(
"Advanced",
BooleanOption(
"Include water molecules from template",
settings.water_preserve,
None,
attr_name="water_preserve",
settings=settings,
balloon="If enabled, all water molecules in the template\n"
"structure(s) will be included in the generated models."))
from PyQt5.QtCore import Qt
from chimerax.ui.widgets import Citation
interface_layout.addWidget(Citation(
session, "A. Sali and T.L. Blundell.\n"
"Comparative protein modelling by satisfaction of spatial restraints.\n"
"J. Mol. Biol. 234, 779-815, 1993.",
prefix="Publications using Modeller results should cite:",
pubmed_id=18428767),
alignment=Qt.AlignCenter)
bbox = qbbox(qbbox.Ok | qbbox.Cancel | qbbox.Help)
bbox.accepted.connect(self.launch_modeller)
bbox.rejected.connect(self.delete)
from chimerax.core.commands import run
bbox.helpRequested.connect(
lambda run=run, ses=session: run(ses, "help " + self.help))
interface_layout.addWidget(bbox)
self.tool_window.manage(None)
def delete(self):
ToolInstance.delete(self)
def launch_modeller(self):
from chimerax.core.commands import run, FileNameArg, StringArg
from chimerax.core.errors import UserError
alignments = self.alignment_list.value
if not alignments:
raise UserError("No alignments chosen for modeling")
aln_seq_args = []
for aln in alignments:
seq_menu = self.seq_menu[aln]
seq = seq_menu.value
if not seq:
raise UserError("No target sequence chosen for alignment %s" %
aln.ident)
aln_seq_args.append(
StringArg.unparse("%s:%d" %
(aln.ident, aln.seqs.index(seq) + 1)))
from .settings import get_settings
settings = get_settings(self.session)
run(
self.session,
"modeller comparative %s multichain %s numModels %d fast %s hetPreserve %s"
" hydrogens %s%s waterPreserve %s" %
(" ".join(aln_seq_args), repr(
settings.multichain).lower(), settings.num_models,
repr(settings.fast).lower(), repr(settings.het_preserve).lower(),
repr(settings.hydrogens).lower(), " tempPath %s" %
FileNameArg.unparse(settings.temp_path) if settings.temp_path else
"", repr(settings.water_preserve).lower()))
self.delete()
def _list_selection_cb(self):
layout = self.targets_layout
while layout.count() > 0:
item = layout.takeAt(0)
if not item:
break
widget = item.widget()
if isinstance(widget, AlignSeqMenuButton):
widget.setHidden(True)
else:
widget.deleteLater()
for sel_aln in self.alignment_list.value:
mb = self.seq_menu[sel_aln]
mb.setHidden(False)
layout.addRow(sel_aln.ident, mb)
def _update_sequence_menus(self, alignments):
alignment_set = set(alignments)
for aln, mb in list(self.seq_menu.items()):
if aln not in alignment_set:
row, role = self.targets_layout.getWidgetPosition(mb)
if row >= 0:
self.targets_layout.removeRow(row)
del self.seq_menu[aln]
for aln in alignments:
if aln not in self.seq_menu:
self.seq_menu[aln] = AlignSeqMenuButton(
aln, no_value_button_text="No target chosen")
