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 fill_context_menu(self, menu, x, y):
from PyQt5.QtWidgets import QAction
file_menu = menu.addMenu("File")
save_as_menu = file_menu.addMenu("Save As")
from chimerax.core.commands import run, StringArg
fmts = [
fmt for fmt in self.session.save_command.save_data_formats
if fmt.category == "Sequence"
]
fmts.sort(key=lambda fmt: fmt.synopsis.casefold())
for fmt in fmts:
action = QAction(fmt.synopsis, save_as_menu)
action.triggered.connect(lambda arg, fmt=fmt: run(
self.session, "save browse format %s alignment %s" %
(fmt.nicknames[0], StringArg.unparse(self.alignment.ident))))
save_as_menu.addAction(action)
scf_action = QAction("Load Sequence Coloring File...", file_menu)
scf_action.triggered.connect(lambda arg: self.load_scf_file(None))
file_menu.addAction(scf_action)
structure_menu = menu.addMenu("Structure")
assoc_action = QAction("Associations...", structure_menu)
assoc_action.triggered.connect(lambda arg: self.show_associations())
from chimerax.atomic import AtomicStructure
for m in self.session.models:
if isinstance(m, AtomicStructure):
break
else:
assoc_action.setEnabled(False)
structure_menu.addAction(assoc_action)
headers_menu = menu.addMenu("Headers")
headers = self.alignment.headers
headers.sort(key=lambda hdr: hdr.ident.casefold())
from chimerax.core.commands import run
for hdr in headers:
action = QAction(hdr.name, headers_menu)
action.setCheckable(True)
action.setChecked(hdr.shown)
if not hdr.relevant:
action.setEnabled(False)
align_arg = "%s " % self.alignment if len(
self.session.alignments.alignments) > 1 else ""
action.triggered.connect(
lambda checked, hdr=hdr, align_arg=align_arg, self=self: run(
self.session, "seq header %s%s %s" %
(align_arg, hdr.ident, "show" if checked else "hide")))
headers_menu.addAction(action)
headers_menu.addSeparator()
hdr_save_menu = headers_menu.addMenu("Save")
for hdr in headers:
if not hdr.relevant:
continue
action = QAction(hdr.name, hdr_save_menu)
align_arg = "%s " % self.alignment if len(
self.session.alignments.alignments) > 1 else ""
action.triggered.connect(
lambda checked, hdr=hdr, align_arg=align_arg, self=self: run(
self.session, "seq header %s%s save browse" %
(align_arg, hdr.ident)))
hdr_save_menu.addAction(action)
# Whenever Region Browser and UniProt Annotations happen, the thought is to
# put them in an "Annotations" menu (rather than "Info")
tools_menu = menu.addMenu("Tools")
comp_model_action = QAction("Modeller Comparative Modeling...",
tools_menu)
comp_model_action.triggered.connect(lambda arg: run(
self.session, "ui tool show 'Modeller Comparative'"))
if not self.alignment.associations:
comp_model_action.setEnabled(False)
tools_menu.addAction(comp_model_action)
if len(self.alignment.seqs) == 1:
blast_action = QAction("Blast Protein...", tools_menu)
blast_action.triggered.connect(lambda arg: run(
self.session, "blastprotein %s" %
(StringArg.unparse("%s:1" % self.alignment.ident))))
tools_menu.addAction(blast_action)
else:
blast_menu = tools_menu.addMenu("Blast Protein")
for i, seq in enumerate(self.alignment.seqs):
blast_action = QAction(seq.name, blast_menu)
blast_action.triggered.connect(lambda arg: run(
self.session, "blastprotein %s" % (StringArg.unparse(
"%s:%d" % (self.alignment.ident, i + 1)))))
blast_menu.addAction(blast_action)
settings_action = QAction("Settings...", menu)
settings_action.triggered.connect(lambda arg: self.show_settings())
menu.addAction(settings_action)
def callback(ses = self.session, tool_name=tool.name, vmenu = self):
from chimerax.core.commands import run, StringArg
run(ses, "ui tool show %s" % StringArg.unparse(tool_name))