def _log_place_marker(mset, center, color, radius):
c = '%.4g,%.4g,%.4g' % tuple(center)
from chimerax.core.colors import color_name
cmd = 'marker %s position %s color %s radius %.4g' % (
mset.atomspec, c, color_name(color), radius)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(mset.session, cmd)
def _log_marker_move(m):
mset = m.structure
pos = '%.4g,%.4g,%.4g' % tuple(m.scene_coord)
cmd = 'marker change %s:%d position %s' % (mset.atomspec, m.residue.number,
pos)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(mset.session, cmd)
def _log_link_delete(l):
mset = l.structure
m1, m2 = l.atoms
cmd = 'marker delete %s:%d,%d linksOnly true' % (
mset.atomspec, m1.residue.number, m2.residue.number)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(mset.session, cmd)
def _label_pick(self, pick, color = None, background = None,
size = None, height = None):
if pick is None:
from .label3d import label_delete
label_delete(self.session, object_type = 'residues')
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(self.session, 'label delete residues')
return
from chimerax import atomic
if isinstance(pick, atomic.PickedAtom):
atoms = pick.atom.residue.atoms
elif isinstance(pick, atomic.PickedResidue):
atoms = pick.residue.atoms
elif isinstance(pick, atomic.PickedBond):
atoms = atomic.Atoms(pick.bond.atoms) # Convert tuple to Atoms
elif isinstance(pick, atomic.PickedPseudobond):
atoms = atomic.Atoms(pick.pbond.atoms) # Convert tuple to Atoms
else:
return
from chimerax.core.objects import Objects
objects = Objects(atoms = atoms)
object_type = 'residues'
ses = self.session
from .label3d import label, label_delete
if label_delete(ses, objects, object_type) == 0:
label(ses, objects, object_type, color=color, bg_color=background,
size=size, height=height)
from chimerax.core.commands import log_equivalent_command, residues_specifier, options_text
rspec = residues_specifier(objects)
opts = options_text((('color',color), ('bg_color',background),
('size',size), ('height',height)))
log_equivalent_command(ses, 'label %s %s' % (rspec, opts))
def _log_link_resize(l):
mset = l.structure
m1, m2 = l.atoms
cmd = ('marker change %s:%d,%d radius %.4g markers false' %
(mset.atomspec, m1.residue.number, m2.residue.number, l.radius))
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(mset.session, cmd)
def _log_links_resize(session, links, radius):
if len(links) == 0:
return
from chimerax.core.commands import log_equivalent_command
for mspec in _link_specs(links):
cmd = 'marker change %s radius %.4g markers false' % (mspec, radius)
log_equivalent_command(session, cmd)
def log_volume_level_command(v):
if v.image_shown:
levels = ' '.join('level %.4g,%.4g' % sl for sl in v.image_levels)
elif v.surface_shown:
levels = ' '.join('level %.4g' % s.level for s in v.surfaces)
command = 'volume #%s %s' % (v.id_string, levels)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(v.session, command)
def _log_markers_resize(session, markers, radius):
if len(markers) == 0:
return
mspec = _markers_spec(markers)
lf = 'links false' if len(markers.intra_bonds) > 0 else ''
cmd = 'marker change %s radius %.4g %s' % (mspec, radius, lf)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(session, cmd)
def _log_link_command(marker1, marker2, rgba, radius):
mspec = '%s:%d,%d' % (marker1.structure.atomspec, marker1.residue.number,
marker2.residue.number)
from chimerax.core.colors import color_name
cmd = 'marker link %s color %s radius %.4g' % (mspec, color_name(rgba),
radius)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(marker1.structure.session, cmd)
def _log_markers_recolor(session, markers, color):
if len(markers) == 0:
return
mspec = _markers_spec(markers)
lf = 'links false' if len(markers.intra_bonds) > 0 else ''
from chimerax.core.colors import color_name
cmd = 'marker change %s color %s %s' % (mspec, color_name(color), lf)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(session, cmd)
def _log_links_recolor(session, links, color):
if len(links) == 0:
return
from chimerax.core.commands import log_equivalent_command
from chimerax.core.colors import color_name
cname = color_name(color)
for mspec in _link_specs(links):
cmd = 'marker change %s color %s markers false' % (mspec, cname)
log_equivalent_command(session, cmd)
def log_volume_command(self):
v = self._map
if v:
ro = v.rendering_options
options = (
'tiltedSlabAxis %.4g,%.4g,%.4g' % tuple(ro.tilted_slab_axis) +
' tiltedSlabOffset %.4g' % ro.tilted_slab_offset)
command = 'volume #%s %s' % (v.id_string, options)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(v.session, command)
def _unlabel(self, log_command = True):
res = self._labeled_residues
if res is None:
return False
from chimerax.label.label3d import label_delete
label_delete(self.session, res, 'residues')
self._labeled_residues = None
if log_command:
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(self.session, 'zone label False')
return True
def _log_tape_command(self):
m1, m2 = self._markers
label, h = self._label_text_and_height()
mset = m1.structure
p1 = '%.4g,%.4g,%.4g' % tuple(m1.scene_coord)
p2 = '%.4g,%.4g,%.4g' % tuple(m2.scene_coord)
from chimerax.core.colors import color_name
cname = color_name(self._color)
cmd = (
'marker segment %s position %s toPosition %s color %s radius %.4g label %s labelHeight %.4g labelColor %s'
% (mset.atomspec, p1, p2, cname, self._radius, label, h, cname))
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(mset.session, cmd)
def _unzone(self, log_command = True):
r = self._zone_center_residue
if r is None:
return
self._restore_original_display()
self._unlabel(log_command = False)
from chimerax.map_filter.vopcommand import volume_unzone
volume_unzone(self.session, self._shown_volumes())
if log_command:
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(self.session, 'zone clear')
self._zone_center_residue = None
def _log_label_move_command(self):
lbl = self._label
from .label2d import Label
from .arrows import Arrow
if isinstance(lbl, Label):
command = '2dlabel #%s xpos %.3f ypos %.3f' % (
lbl.drawing.id_string, lbl.xpos, lbl.ypos)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(self.session, command)
elif isinstance(lbl, Arrow):
x, y = self._get_arr_xy()
command = '2dlabel arrow #%s %s %.3f,%.3f' % (
lbl.drawing.id_string, self._arr_part, x, y)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(self.session, command)
def log_volume_region_command(v):
ro = v.rendering_options
if v.showing_image('orthoplanes'):
planes = ''.join(
[n for n, s in zip(('x', 'y', 'z'), ro.orthoplanes_shown) if s])
region = ('orthoplanes %s' % planes +
' positionPlanes %d,%d,%d' % ro.orthoplane_positions)
elif v.showing_image('tilted slab'):
region = ('tiltedSlabOffset %.4g' % ro.tilted_slab_offset +
' tiltedSlabPlaneCount %d' % ro.tilted_slab_plane_count)
else:
ijk_min, ijk_max = v.region[:2]
region = 'region %d,%d,%d,%d,%d,%d' % (tuple(ijk_min) + tuple(ijk_max))
command = 'volume #%s %s' % (v.id_string, region)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(v.session, command)
def _show_zone(self, residue, label=True, ribbon=True, log_command = True):
'''Show nearby residues, labels, and surfaces.'''
if self._zone_center_residue is None:
# Remember original display state.
s = residue.structure
self._original_atom_display = s.atoms.displays
self._original_residue_display = s.residues.ribbon_displays
self._zone_center_residue = residue
ratoms = residue.atoms
nres = self._show_near_residues(residue, show_ligands=ribbon)
if label:
self._show_labels()
if ribbon:
self._show_ribbons(nres)
self._show_volume_zone(ratoms)
# Set center of rotation
v = self.session.main_view
c = residue.structure.scene_position * residue.center
v.center_of_rotation = c
if log_command:
rspec = residue.string(style='command line')
options = ' '.join(('' if ribbon else 'ribbon False',
'' if label else 'label False'))
if log_command == 'include distances':
options = ' '.join((options,
'residueDistance %.3g' % self._residue_distance,
'labelDistance %.3g' % self._label_distance,
'surfaceDistance %.3g' % self._surface_distance))
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(self.session, 'zone %s %s' % (rspec, options))
def _log_marker_resize(m):
mset = m.structure
cmd = 'marker change %s:%d radius %.4g' % (mset.atomspec, m.residue.number,
m.radius)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(mset.session, cmd)
def _log_clear_command(self):
mset = self._marker_set
cmd = 'marker delete %s' % mset.atomspec
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(mset.session, cmd)
def _log_marker_delete(m):
mset = m.structure
cmd = 'marker delete %s:%d' % (mset.atomspec, m.residue.number)
from chimerax.core.commands import log_equivalent_command
log_equivalent_command(mset.session, cmd)
