def run_expanded_command(session):
mall = session.models.list(type=model_class)
msel = [m for m in mall if m.selected]
mselvis = [m for m in msel if m.visible]
if len(mselvis) == 0:
# No selected visible models so run on all visible models.
mvis = [m for m in mall if m.visible]
if len(mvis) == len(mall):
target = 'all'
elif mvis:
# No selected models so target all visible models.
from chimerax.core.commands import concise_model_spec
target = concise_model_spec(session, mvis)
else:
# No visible models
target = None
elif len(msel) == len(mselvis):
# All selected models are visible.
target = 'sel'
else:
# Some but not all selected models are visible.
from chimerax.core.commands import concise_model_spec
target = 'sel & %s' % concise_model_spec(session, mselvis)
if target is None:
return # No visible models to run command on.
cmd = all_command if target == 'all' else command.replace(
' %s', ' ' + target)
run(session, cmd)
def _count_pbonds(self, query, finder, cat_name, column_name):
# Create hydrogen bonds between receptor(s) and ligands
from chimerax.core.commands import concise_model_spec, run
from chimerax.atomic import AtomicStructure
mine = concise_model_spec(self.session, self.structures)
all = self.session.models.list(type=AtomicStructure)
others = concise_model_spec(self.session,
set(all) - set(self.structures))
cmd = ("%s %s restrict %s "
"reveal true intersubmodel true" % (finder, mine, others))
run(self.session, cmd)
self._count_pb(cat_name, column_name)
def _show_hide(self, on, off):
if on or off:
from chimerax.core.commands import concise_model_spec, run
self._block_updates = True
cmd = []
if off:
models = concise_model_spec(self.session, off)
cmd.append("hide %s models" % models)
if on:
models = concise_model_spec(self.session, on)
cmd.append("show %s models" % models)
run(self.session, " ; ".join(cmd))
self._block_updates = False
self._update_display()
def fetch_additional_scores(self, refresh=False):
self.scores_fetched = True
from chimerax.core.commands import run, concise_model_spec
run(
self.session,
"modeller scores %s refresh %s" % (concise_model_spec(
self.session, self.models), str(refresh).lower()))
def close(models, session):
_mp.self_initiated = True
from chimerax.core.models import Model
# The 'close' command explicitly avoids closing grouping models where not
# all the child models are being closed so that "close ~#1.1" doesn't
# close the #1 grouping model. Therefore we need to change the '#!'s
# generated by concise_model_spec to just '#'s
run(session, "close %s" %
concise_model_spec(session, [m for m in models if isinstance(m, Model)]).replace('#!', '#'))
def shown_models_spec(session, model_class=None):
mlist = [m for m in session.models.list(type=model_class)]
mshown = [m for m in mlist if m.visible]
if len(mlist) == len(mshown):
spec = 'all' if mshown else ''
elif len(mshown) == 0:
spec = ''
else:
from chimerax.core.commands import concise_model_spec
spec = concise_model_spec(session, mshown)
return spec
def options_string(self):
models = self.structure_list.value
from chimerax.core.errors import UserError
if not models:
raise UserError("No models chosen for saving")
from chimerax.atomic import Structure
from chimerax.core.commands import concise_model_spec
spec = concise_model_spec(self.session, models, relevant_types=Structure)
if spec:
cmd = "models " + spec
else:
cmd = ""
if self.displayed_only.isChecked():
if cmd:
cmd += ' '
cmd += "displayedOnly true"
if self.selected_only.isChecked():
if cmd:
cmd += ' '
cmd += "selectedOnly true"
if self.rel_models.isChecked():
if cmd:
cmd += ' '
if self.simple_rel_models:
rel_model = models[0]
else:
rel_model = self.rel_model_menu.value
if rel_model is None:
raise UserError("No model chosen to save relative to")
cmd += "relModel #" + rel_model.id_string
large_handling = self.large_mb.text()
if large_handling == "Amber":
if cmd:
cmd += ' '
cmd += "serialNumbering amber"
return cmd
def view(objs, session):
from chimerax.core.models import Model
models = [o for o in objs if isinstance(o, Model)]
run(session, "view %s clip false" % concise_model_spec(session, models))
def show(models, session):
_mp.self_initiated = True
run(session, "show %s target m" % concise_model_spec(session, models))
def hide(models, session):
_mp.self_initiated = True
run(session, "hide %s target m" % concise_model_spec(session, models))
def get_command(self):
"""Used to generate the 'hbonds' command that can be run to produce the requested H-bonds.
Returns three strings:
1) The command name
2) The atom spec to provide just after the command name
3) The keyword/value pairs that follow that
The atom spec will be an empty string if no bond or model restriction was requested
(or those controls weren't shown).
"""
from chimerax.core.errors import UserError
settings = {}
command_values = {}
# never saved in settings
if self.__show_values['model_restrict']:
models = self.__model_restrict_option.value
if models is None:
atom_spec = ""
else:
if not models:
raise UserError("Model restriction enabled but no models chosen")
from chimerax.core.commands import concise_model_spec
atom_spec = concise_model_spec(self.session, models)
else:
atom_spec = ""
if self.__show_values['bond_restrict']:
bond_restrict = self.__bond_restrict_option.value
if bond_restrict is not None:
command_values['restrict'] = bond_restrict
if atom_spec:
atom_spec += " & sel"
else:
atom_spec = "sel"
if self.__show_values['save_file']:
if self.__save_file_option.value:
from PyQt5.QtWidgets import QFileDialog
fname = QFileDialog.getSaveFileName(self, "Save H-Bonds File")[0]
if fname:
command_values['save_file'] = fname
else:
from chimerax.core.errors import CancelOperation
raise CancelOperation("H-bonds save file cancelled")
else:
command_values['save_file'] = None
else:
command_values['save_file'] = None
# may be saved in settings
if self.__show_values['make_pseudobonds']:
settings['make_pseudobonds'] = self.__make_pb_group.isChecked()
if self.__show_values['color']:
settings['color'] = self.__color_option.value
if self.__show_values['radius']:
settings['radius'] = self.__radius_option.value
if self.__show_values['dashes']:
settings['dashes'] = self.__dashes_option.value
if self.__show_values['show_dist']:
settings['show_dist'] = self.__show_dist_option.value
else:
settings['color'] = None
settings['radius'] = None
settings['dashes'] = None
settings['show_dist'] = None
if self.__show_values['inter_model']:
settings['inter_model'] = self.__inter_model_option.value
else:
settings['inter_model'] = None
if self.__show_values['intra_model']:
settings['intra_model'] = self.__intra_model_option.value
else:
settings['intra_model'] = None
if self.__show_values['relax']:
settings['relax'] = self.__relax_group.isChecked()
if self.__show_values['slop']:
settings['dist_slop'] = self.__dist_slop_option.value
settings['angle_slop'] = self.__angle_slop_option.value
else:
settings['dist_slop'] = settings['angle_slop'] = None
if self.__show_values['slop_color']:
slop_color_value = self.__slop_color_option.value
if slop_color_value is None:
settings['two_colors'] = False
settings['slop_color'] = None
else:
settings['two_colors'] = True
settings['slop_color'] = slop_color_value
else:
settings['two_colors'] = settings['slop_color'] = None
else:
settings['relax'] = settings['dist_slop'] = settings['angle_slop'] = None
settings['two_colors'] = settings['slop_color'] = None
if self.__show_values['salt_only']:
settings['salt_only'] = self.__salt_only_option.value
else:
settings['salt_only'] = None
if self.__show_values['intra_mol']:
settings['intra_mol'] = self.__intra_mol_option.value
else:
settings['intra_mol'] = None
if self.__show_values['intra_res']:
settings['intra_res'] = self.__intra_res_option.value
else:
settings['intra_res'] = None
if self.__show_values['inter_submodel']:
settings['inter_submodel'] = self.__inter_submodel_option.value
else:
settings['inter_submodel'] = None
if self.__show_values['select']:
settings['select'] = self.__select_option.value
else:
settings['select'] = None
if self.__show_values['reveal']:
settings['reveal'] = self.__reveal_option.value
else:
settings['reveal'] = None
if self.__show_values['retain_current']:
settings['retain_current'] = self.__retain_current_option.value
else:
settings['retain_current'] = None
if self.__show_values['log']:
settings['log'] = self.__log_option.value
else:
settings['log'] = None
if self.__settings:
saveables = []
for attr_name, value in settings.items():
if value is not None:
setattr(self.__settings, attr_name, value)
saveables.append(attr_name)
if saveables:
self.__settings.save(settings=saveables)
def val_to_str(ses, val, kw):
from chimerax.core.commands import \
BoolArg, IntArg, FloatArg, ColorArg, StringArg, SaveFileNameArg
if type(val) == bool:
return BoolArg.unparse(val, ses)
if type(val) == int:
return IntArg.unparse(val, ses)
if type(val) == float:
return FloatArg.unparse(val, ses)
if kw.endswith('color'):
from chimerax.core.colors import Color
return ColorArg.unparse(Color(rgba=val), ses)
if kw == 'save_file':
return SaveFileNameArg.unparse(val, ses)
return StringArg.unparse(str(val), ses)
command_values.update(settings)
from .cmd import cmd_hbonds
kw_values = ""
for kw, val in command_values.items():
if val is None:
continue
if is_default(cmd_hbonds, kw, val):
continue
# 'dashes' default checking requires special handling
if kw == 'dashes' and val == AtomicStructure.default_hbond_dashes \
and not command_values['retain_current']:
continue
camel = ""
next_upper = False
for c in kw:
if c == '_':
next_upper = True
else:
if next_upper:
camel += c.upper()
else:
camel += c
next_upper = False
kw_values += (" " if kw_values else "") + camel + " " + val_to_str(self.session, val, kw)
return "hbonds", atom_spec, kw_values
def run_matchmaker(self):
from chimerax.core.commands import StringArg, BoolArg, FloatArg, DynamicEnum, NoneArg
from .settings import defaults, get_settings
settings = get_settings(self.session)
chain_pairing = self.chain_pairing_option.value
ref_widget, match_widget = self.matching_widgets[chain_pairing]
ref_value = ref_widget.value
match_value = match_widget.value
if chain_pairing == CP_SPECIFIC_SPECIFIC:
ref_spec = "".join([rchain.atomspec for rchain, mchain in match_value])
else:
ref_spec = ref_value.atomspec
if not ref_spec:
raise UserError("No reference and/or match structure/chain chosen")
if self.ref_sel_restrict.isChecked():
ref_spec = ref_spec + " & sel"
if chain_pairing == CP_SPECIFIC_SPECIFIC:
match_spec = "".join([mchain.atomspec for rchain, mchain in match_value])
else:
from chimerax.core.commands import concise_model_spec
match_spec = concise_model_spec(self.session, match_value)
if not match_spec:
raise UserError("No match structure/chain(s) chosen")
if self.match_sel_restrict.isChecked():
match_spec = match_spec + " & sel"
cmd = "matchmaker " + match_spec + " to " + ref_spec
if chain_pairing != defaults['chain_pairing']:
cmd += ' pairing ' + chain_pairing
alg = settings.alignment_algorithm
if alg != defaults['alignment_algorithm']:
cmd += ' alg ' + StringArg.unparse(alg)
verbose = settings.verbose_logging
if verbose != defaults['verbose_logging']:
cmd += ' verbose ' + BoolArg.unparse(verbose)
use_ss = settings.use_ss
if use_ss:
ss_fraction = settings.ss_mixture
if ss_fraction != defaults['ss_mixture']:
cmd += ' ssFraction ' + FloatArg.unparse(ss_fraction)
else:
cmd += ' ssFraction ' + BoolArg.unparse(use_ss)
matrix = settings.matrix
if matrix != defaults['matrix']:
from chimerax import sim_matrices
cmd += ' matrix ' + DynamicEnum(
lambda ses=self.session: sim_matrices.matrices(ses.logger).keys()).unparse(matrix)
gap_open = settings.gap_open
if not use_ss and gap_open != defaults['gap_open']:
cmd += ' gapOpen ' + FloatArg.unparse(gap_open)
helix_open = settings.helix_open
from chimerax.core.commands import run
if helix_open != defaults['helix_open']:
cmd += ' hgap ' + FloatArg.unparse(helix_open)
strand_open = settings.strand_open
from chimerax.core.commands import run
if strand_open != defaults['strand_open']:
cmd += ' sgap ' + FloatArg.unparse(strand_open)
other_open = settings.other_open
from chimerax.core.commands import run
if other_open != defaults['other_open']:
cmd += ' ogap ' + FloatArg.unparse(other_open)
iterate = settings.iterate
if iterate:
iter_cutoff = settings.iter_cutoff
if iter_cutoff != defaults['iter_cutoff']:
cmd += ' cutoffDistance ' + FloatArg.unparse(iter_cutoff)
else:
cmd += ' cutoffDistance ' + NoneArg.unparse(None)
gap_extend = settings.gap_extend
if gap_extend != defaults['gap_extend']:
cmd += ' gapExtend ' + FloatArg.unparse(gap_extend)
if self.bring_model_list.isEnabled():
models = self.bring_model_list.value
if models:
cmd += ' bring ' + concise_model_spec(self.session, models)
show_alignment = settings.show_alignment
if show_alignment != defaults['show_alignment']:
cmd += ' showAlignment ' + BoolArg.unparse(show_alignment)
compute_ss = settings.compute_ss
if compute_ss != defaults['compute_ss']:
cmd += ' computeSs ' + BoolArg.unparse(compute_ss)
overwrite_ss = settings.overwrite_ss
if compute_ss and overwrite_ss != defaults['overwrite_ss']:
cmd += ' keepComputedSs ' + BoolArg.unparse(overwrite_ss)
ss_matrix = settings.ss_scores
if ss_matrix != defaults['ss_scores']:
for key, val in ss_matrix.items():
order = ['H', 'S', 'O']
if val != defaults['ss_scores'][key]:
let1, let2 = key
if order.index(let1) > order.index(let2):
continue
cmd += ' mat' + let1 + let2.lower() + ' ' + FloatArg.unparse(val)
run(self.session, cmd)