# -----------------------------------------------------------------------------
# Register GRASP surface file reader.
#
def open_cb(path):
import GraspSurface
m = GraspSurface.read_grasp_surface(path)
return [m]
import chimera
fi = chimera.fileInfo
fi.register('GRASP surface',
open_cb, ['.srf'], ['graspsurf'],
canDecompress=False,
category=fi.SURFACE)
# -----------------------------------------------------------------------------
# Register keyboard accelerator to write surfaces as a GRASP format file.
#
def write_grasp():
from GraspSurface.writegrasp import write_grasp_surface_file
write_grasp_surface_file()
from Accelerators import add_accelerator
add_accelerator('wg', 'Write GRASP surface file', write_grasp)
import chimera.extension
# -----------------------------------------------------------------------------
#
class Color_Zone_EMO(chimera.extension.EMO):
def name(self):
return 'Color Zone'
def description(self):
return 'Color piece of surface near selected atoms'
def categories(self):
return ['Volume Data', 'Depiction']
def icon(self):
return None
def activate(self):
self.module('gui').show_color_zone_dialog()
return None
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Color_Zone_EMO(__file__))
# ---------------------------------------------------------------------------
#
def split_map():
import ColorZone
ColorZone.split_volume_by_color_zone()
from Accelerators import add_accelerator
add_accelerator('sm', 'Split volume by color zones.', split_map)
# -----------------------------------------------------------------------------
# Register mask command.
#
def mask_cmd(cmdname, args):
from Mask.maskcommand import mask_command
mask_command(cmdname, args)
import Midas.midas_text
Midas.midas_text.addCommand('mask', mask_cmd, help=True)
# -----------------------------------------------------------------------------
# Register contour surface mask shortcut.
#
from Accelerators import add_accelerator
def mask_volume():
import Mask
Mask.mask_volume_using_selected_surfaces()
add_accelerator('vm', 'Mask volume using selected surfaces', mask_volume)
# -----------------------------------------------------------------------------
# Register shape command.
#
def shape_cmd(cmdname, args):
from Shape import shape_command
shape_command(cmdname, args)
from Midas.midas_text import addCommand
addCommand('shape', shape_cmd, help = True)
# -----------------------------------------------------------------------------
# Register surface resize mouse mode keyboard shortcut.
#
def resize_mouse_mode():
from Shape.resizemode import enable_resize_surface_mouse_mode as e
e(one_use = True)
from Accelerators import add_accelerator
add_accelerator('sz', 'Resize selected surfaces', resize_mouse_mode)
import chimera.extension
# -----------------------------------------------------------------------------
#
class Atom_Density_EMO(chimera.extension.EMO):
def name(self):
return 'Values at Atom Positions'
def description(self):
return 'Show volume data values at atom positions.'
def categories(self):
return ['Volume Data']
def icon(self):
return None
def activate(self):
self.module('gui').show_atom_density_dialog()
return None
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Atom_Density_EMO(__file__))
# -----------------------------------------------------------------------------
#
def oa():
import AtomDensity
AtomDensity.select_atoms_outside_map()
from Accelerators import add_accelerator
add_accelerator('oa', 'Reduce selected atoms to those outside map contour', oa)
def fillInUI(self, parent):
self.default_radius = 1
self.default_color = (1,0.6,0.8,.5) # Pink eraser
t = parent.winfo_toplevel()
self.toplevel_widget = t
t.withdraw()
parent.columnconfigure(0, weight = 1)
row = 0
import Tkinter
from CGLtk import Hybrid
sh = Hybrid.Checkbutton(parent, 'Show volume-erasing sphere ', True)
sh.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.show_sphere_var = sh.variable
sh.callback(self.show_sphere_cb)
crf = Tkinter.Frame(parent)
crf.grid(row = row, column = 0, sticky = 'ew')
crf.columnconfigure(2, weight = 1)
row = row + 1
cl = Tkinter.Label(crf, text = 'Color')
cl.grid(row = 0, column = 0, sticky = 'w')
from CGLtk.color import ColorWell
sc = ColorWell.ColorWell(crf, color = self.default_color,
callback = self.change_sphere_color_cb)
sc.grid(row = 0, column = 1, sticky = 'w')
self.sphere_color = sc
rs = Hybrid.Scale(crf, ' Radius ', 0, 30, .1, 2)
rs.frame.grid(row = 0, column = 2, sticky = 'ew')
row = row + 1
rs.callback(self.change_radius_cb)
rs.entry.bind('<KeyPress-Return>', self.change_radius_cb)
self.sphere_radius_scale = rs
mmf = Tkinter.Frame(parent)
mmf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
mb = Hybrid.Option_Menu(mmf, 'Use mouse ',
'button 1', 'button 2', 'button 3',
'ctrl button 1', 'ctrl button 2', 'ctrl button 3')
mb.variable.set('button 2')
mb.frame.grid(row = 0, column = 0, sticky = 'w')
mb.add_callback(self.bind_mouse_button_cb)
self.mouse_button = mb
mbl = Tkinter.Label(mmf, text = ' to move sphere')
mbl.grid(row = 0, column = 1, sticky = 'w')
ka = Tkinter.Label(parent, text = 'Erase using keyboard accelerator "es".')
ka.grid(row = row, column = 0, sticky = 'w')
row = row + 1
from Accelerators import add_accelerator
add_accelerator('es', 'Erase volume data inside sphere', self.Erase)
add_accelerator('eo', 'Erase volume data outside sphere',
self.erase_outside_sphere)
#
class Unit_Cell_EMO(EMO):
def name(self):
return 'Unit Cell'
def description(self):
return 'Make molecule copies to for crystal unit cell'
def categories(self):
return ['Higher-Order Structure']
def icon(self):
return None
def activate(self):
self.module().show_unit_cell_dialog()
manager.registerExtension(Unit_Cell_EMO(__file__))
# -----------------------------------------------------------------------------
#
def show_unit_cell_dialog():
import UnitCell
UnitCell.show_unit_cell_dialog()
from Accelerators import add_accelerator
add_accelerator('uc', 'Show unit cell dialog', show_unit_cell_dialog)
from SpaceNavigator import sn
from Accelerators import add_accelerator
add_accelerator('nd', 'Space navigator only translate/rotate',
sn.toggle_dominant_mode)
add_accelerator('nz', 'Toggle space navigator zoom mode', sn.toggle_zoom_mode)
add_accelerator('na', 'Space navigator moves inactive models',
sn.toggle_all_models)
add_accelerator('nf', 'Toggle space navigator fly through mode',
sn.toggle_fly_mode)
return None
def activate(self):
self.module('gui').show_crystal_contacts_dialog()
return None
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Crystal_Contacts_EMO(__file__))
# -----------------------------------------------------------------------------
#
def show_contacts(distance = 1.0):
import chimera
for m in chimera.openModels.list(modelTypes = [chimera.Molecule]):
from CrystalContacts import show_crystal_contacts
show_crystal_contacts(m, distance)
from Accelerators import add_accelerator
add_accelerator('xx', 'Show crystal contacts', show_contacts)
# -----------------------------------------------------------------------------
#
def crystal_contacts_command(cmdname, args):
from CrystalContacts.command import crystal_contacts
crystal_contacts(cmdname, args)
# -----------------------------------------------------------------------------
#
from Midas.midas_text import addCommand
addCommand('crystalcontacts', crystal_contacts_command, help = True)
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Volume_Eraser_EMO(__file__))
# -----------------------------------------------------------------------------
#
def erase_box_cb():
import VolumeEraser
VolumeEraser.zero_volume_inside_selection_box()
def zero_boundary_cb(step=1):
import VolumeEraser
VolumeEraser.zero_volume_boundary(step)
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('eb', 'Erase volume data inside subregion selection box',
erase_box_cb)
add_accelerator('zb', 'Zero volume data boundary', zero_boundary_cb)
add_accelerator('zB2',
'Zero volume data boundary for step size 2',
lambda zb=zero_boundary_cb: zb(2))
add_accelerator('zB4',
'Zero volume data boundary for step size 4',
lambda zb=zero_boundary_cb: zb(4))
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Fit_Map_EMO(__file__))
# -----------------------------------------------------------------------------
#
def fit_map_cb():
import FitMap
FitMap.move_selected_atoms_to_maximum()
def fit_map_rotation_only_cb():
import FitMap
FitMap.move_selected_atoms_to_maximum(optimize_translation = False)
def fit_map_shift_only_cb():
import FitMap
FitMap.move_selected_atoms_to_maximum(optimize_rotation = False)
def move_atoms_to_maxima():
import FitMap
FitMap.move_atoms_to_maxima()
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('ft', 'Move model to maximize density at selected atoms',
fit_map_cb)
add_accelerator('fr', 'Rotate model to maximize density at selected atoms',
fit_map_rotation_only_cb)
add_accelerator('fs', 'Shift model to maximize density at selected atoms',
fit_map_shift_only_cb)
add_accelerator('mX', 'Move selected atoms to local maxima',
move_atoms_to_maxima)
# -----------------------------------------------------------------------------
#
def align_backbones():
'Superimpose molecules by pairing selected atoms from identical residues'
import MatchDomains
MatchDomains.align_backbones_using_selected_atoms()
# -----------------------------------------------------------------------------
#
def illustrate_alignment():
'Draw slabs to illustrate a the relative orientations of two domains'
import MatchDomains
MatchDomains.illustrate_backbone_alignment()
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('ab', 'Align backbones using selected atoms', align_backbones)
add_accelerator('ai', 'Illustrate backbone alignment based on selected atoms',
illustrate_alignment)
def icon(self):
return None
# return self.path('gumball.png')
def activate(self):
self.module('gui').show_surface_volume_dialog()
return None
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Surface_Volume_EMO(__file__))
# -----------------------------------------------------------------------------
#
def measure_area():
from MeasureVolume import report_selected_areas
report_selected_areas()
def measure_volume():
from MeasureVolume import report_selected_volumes
report_selected_volumes()
from Accelerators import add_accelerator
add_accelerator('ma', 'Measure area of selected surfaces', measure_area)
add_accelerator('mv', 'Measure volume of selected surfaces', measure_volume)
#
def mark_cofr():
from VolumePath import place_marker, show_volume_path_dialog
from chimera import openModels
place_marker(openModels.cofr.data())
show_volume_path_dialog()
# -----------------------------------------------------------------------------
#
def place_marker_at_mouse():
import VolumePath
VolumePath.place_marker_at_mouse()
# -----------------------------------------------------------------------------
#
def place_markers_on_atoms():
import VolumePath
VolumePath.place_markers_on_atoms()
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('mz', 'Place marker at position (0,0,0)', mark_zero)
add_accelerator('mc', 'Place marker at center of rotation', mark_cofr)
add_accelerator('mk', 'Place marker under mouse', place_marker_at_mouse)
add_accelerator('mS', 'Place markers on selected atoms',
place_markers_on_atoms)
def select_contacts_5():
select_contacts(5)
# -----------------------------------------------------------------------------
#
def select_sequence_copies():
from MultiScale import multiscale_model_dialog
d = multiscale_model_dialog()
if d:
d.select_sequence_copies()
# -----------------------------------------------------------------------------
#
def color_surfaces_to_match_atoms():
import MultiScale
MultiScale.color_surfaces_to_match_atoms()
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('bu', 'Show molecule biological unit using multiscale tool',
show_biounit)
add_accelerator('c3', 'Find 3A contacts between selected and unselected atoms',
select_contacts_3)
add_accelerator('c5', 'Find 5A contacts between selected and unselected atoms',
select_contacts_5)
add_accelerator('xc', 'Extend multiscale selection to sequence copies',
select_sequence_copies)
add_accelerator('c=', 'Color multiscale surfaces to match a chain atom',
color_surfaces_to_match_atoms)
return 'Values at Atom Positions'
def description(self):
return 'Show volume data values at atom positions.'
def categories(self):
return ['Volume Data']
def icon(self):
return None
def activate(self):
self.module('gui').show_atom_density_dialog()
return None
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Atom_Density_EMO(__file__))
# -----------------------------------------------------------------------------
#
def oa():
import AtomDensity
AtomDensity.select_atoms_outside_map()
from Accelerators import add_accelerator
add_accelerator('oa', 'Reduce selected atoms to those outside map contour', oa)
def symmetry_copies(cmdname, args):
import SymmetryCopies
SymmetryCopies.symmetry_copies_command(cmdname, args)
def undo_symmetry_copies(cmdname, args):
import SymmetryCopies
SymmetryCopies.undo_symmetry_copies_command(cmdname, args)
import Midas.midas_text
Midas.midas_text.addCommand('sym', symmetry_copies, undo_symmetry_copies,
help = True)
def icos_volume_sym():
import SymmetryCopies
SymmetryCopies.set_volume_icosahedral_symmetry()
from Accelerators import add_accelerator
add_accelerator('ic', 'Assigned icosahedral symmetry to active volume',
icos_volume_sym)
# -----------------------------------------------------------------------------
# Register shape command.
#
def shape_cmd(cmdname, args):
from Shape import shape_command
shape_command(cmdname, args)
from Midas.midas_text import addCommand
addCommand('shape', shape_cmd, help=True)
# -----------------------------------------------------------------------------
# Register surface resize mouse mode keyboard shortcut.
#
def resize_mouse_mode():
from Shape.resizemode import enable_resize_surface_mouse_mode as e
e(one_use=True)
from Accelerators import add_accelerator
add_accelerator('sz', 'Resize selected surfaces', resize_mouse_mode)
def surfdist():
import SurfaceDistance
SurfaceDistance.selection_surface_distance()
from Accelerators import add_accelerator
add_accelerator('sd', 'Report distance between selected atoms and displayed surfaces', surfdist)
def activate(self):
self.module('gui').show_volume_filter_dialog()
return None
manager.registerExtension(Volume_Filter_EMO(__file__))
# -----------------------------------------------------------------------------
# Register vop command.
#
def vop_cmd(cmdname, args):
from VolumeFilter.vopcommand import vop_command
vop_command(cmdname, args)
from Midas.midas_text import addCommand
addCommand('vop', vop_cmd, help = True)
# ---------------------------------------------------------------------------
# Register keyboard shortcuts for filtering.
#
def fourier():
from VolumeFilter import fourier_transform
fourier_transform()
def laplace():
from VolumeFilter import laplacian
laplacian()
from Accelerators import add_accelerator
add_accelerator('FT', 'Fourier transform active volume', fourier)
add_accelerator('LT', 'Calculate Laplacian active volume', laplace)
from median import make_test_volume
add_accelerator('tv', 'Make test volume', make_test_volume)
def description(self):
return 'Calculates mean, standard deviation, and root mean square for volume data'
def categories(self):
return ['Volume Data']
def icon(self):
return None
def activate(self):
self.module().show_volume_statistics()
return None
# -----------------------------------------------------------------------------
#
manager.registerExtension(Volume_Statistics_EMO(__file__))
# -----------------------------------------------------------------------------
#
def show_stats():
from VolumeStatistics import show_volume_statistics
show_volume_statistics(show_reply_log=False)
from Accelerators import add_accelerator
add_accelerator('md', 'Print mean and standard deviation of volume data',
show_stats)
# -----------------------------------------------------------------------------
# Register GRASP surface file reader.
#
def open_cb(path):
import GraspSurface
m = GraspSurface.read_grasp_surface(path)
return [m]
import chimera
fi = chimera.fileInfo
fi.register('GRASP surface', open_cb, ['.srf'], ['graspsurf'],
canDecompress = False, category = fi.SURFACE)
# -----------------------------------------------------------------------------
# Register keyboard accelerator to write surfaces as a GRASP format file.
#
def write_grasp():
from GraspSurface.writegrasp import write_grasp_surface_file
write_grasp_surface_file()
from Accelerators import add_accelerator
add_accelerator('wg', 'Write GRASP surface file', write_grasp)
def name(self):
return 'Measure Volume and Area'
def description(self):
return 'Compute volume enclosed by a surface and surface area.'
def categories(self):
return ['Volume Data', 'Surface/Binding Analysis']
def icon(self):
return None
# return self.path('gumball.png')
def activate(self):
self.module('gui').show_surface_volume_dialog()
return None
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Surface_Volume_EMO(__file__))
# -----------------------------------------------------------------------------
#
def measure_area():
from MeasureVolume import report_selected_areas
report_selected_areas()
def measure_volume():
from MeasureVolume import report_selected_volumes
report_selected_volumes()
from Accelerators import add_accelerator
add_accelerator('ma', 'Measure area of selected surfaces', measure_area)
add_accelerator('mv', 'Measure volume of selected surfaces', measure_volume)
def surfdist():
import SurfaceDistance
SurfaceDistance.selection_surface_distance()
from Accelerators import add_accelerator
add_accelerator(
'sd', 'Report distance between selected atoms and displayed surfaces',
surfdist)
# Delay importing module until function is actually called.
#
def function(name):
def f(*args, **kw):
from VolumeViewer import shortcuts
getattr(shortcuts, name)(*args, **kw)
return f
# -----------------------------------------------------------------------------
# Register keyboard shortcuts.
#
ks = (('bv', 'Make volume bounding selected atoms from periodic volume',
'bounding_map'),
('cv', 'Clip volume', 'clip_volume'),
('ez', 'Copy map with erased zone', 'erase_zone'),
('fv', 'Change volume subregion to full data', 'full_volume'),
('Im', 'Invert map shown in volume viewer', 'invert_map'),
('ob', 'Toggle volume outline box', 'outline_box'),
('u8', 'Make MRC signed 8-bit volume unsigned',
'mrc_signed8_to_unsigned8'),
('vh', 'Hide volume', 'hide_volume'),
('vR', 'Remove volume', 'remove_volume'),
('vs', 'Show volume', 'show_volume'),
('vv', 'Show volume viewer dialog', 'show_volume_dialog'),
('wv', 'Make writable copy of volume data', 'writable_volume'),
('zv', 'Copy map including only zone', 'zone_volume'),
)
from Accelerators import add_accelerator
for keys, descrip, fname in ks:
add_accelerator(keys, descrip, function(fname))
# -----------------------------------------------------------------------------
# Register mask command.
#
def mask_cmd(cmdname, args):
from Mask.maskcommand import mask_command
mask_command(cmdname, args)
import Midas.midas_text
Midas.midas_text.addCommand('mask', mask_cmd, help = True)
# -----------------------------------------------------------------------------
# Register contour surface mask shortcut.
#
from Accelerators import add_accelerator
def mask_volume():
import Mask
Mask.mask_volume_using_selected_surfaces()
add_accelerator('vm', 'Mask volume using selected surfaces', mask_volume)
def register_accelerators():
accelerators = [
('a0', 'Activate model 0 (toggle)', activate_model_0),
('a1', 'Activate model 1 (toggle)', activate_model_1),
('a2', 'Activate model 2 (toggle)', activate_model_2),
('a3', 'Activate model 3 (toggle)', activate_model_3),
('aa', 'Activate all models', activate_all),
('ad', 'Accelerator dialog', show_accelerator_dialog),
('af', 'Accelerators off', turn_off_accelerators),
('ao', 'Activate only selected models', activate_only),
('ar', 'Activate reverse', activate_reverse),
('at', 'Activate toggle', activate_toggle_and_remember),
('bb', 'Backbone only', backbone_only),
('bk', 'Set background to black', set_black_background),
('bs', 'Ball & stick representation', ball_and_stick_representation),
('c2', 'Color secondary structure', color_secondary_structure),
('Ca', 'Close all models', close_all_models),
('ca', 'Adjust clip planes with mouse', clip_adjust),
('cc', 'Clip selected models', clip_selected_models),
('ce', 'Color by element', color_by_element),
('cl', 'Show command line', show_command_line),
('cm', 'Show surface color dialog', show_surface_color_dialog),
('cp', 'Show surface capper dialog', show_surface_capper_dialog),
('cr', 'Set center of rotation', set_center_of_rotation),
('cs', 'Clear selection', clear_selection),
('Cs', 'Close session', close_session),
('ct', 'Show chain trace only', show_chain_trace_only),
('da', 'Display atoms', display_atoms),
('Da', 'Delete atoms and bonds', delete_atoms),
('dc', 'Toggle depth cueing', toggle_depth_cueing),
('dp', 'Display path tracer markers', show_all_markers),
('ds', 'Display surface', show_surface),
('ff', 'Fetch file from web', fetch_file),
('fo', 'Focus', focus),
('gb', 'Set gray background', set_gray_background),
('gl', 'Toggle glossy lighting', glossy_lighting),
('ha', 'Hide atoms', hide_atoms),
('hc', 'Hide command line', hide_command_line),
('hp', 'Hide path tracer markers', hide_all_markers),
('hr', 'Hide ribbon', hide_ribbon),
('hs', 'Hide surface', hide_surface),
('ir', 'Independent center of rotation', independent_cofr),
('is', 'Invert selection (selected models)', invert_selection),
('iS', 'Invert selection (all models)', invert_selection_all_models),
('kl', 'Show per-model clipping dialog',
show_per_model_clipping_dialog),
('lo', 'Show names of last opened files', names_of_last_opened),
('ls', 'Open last session file', open_last_session),
('mm', 'Mouse modes', show_mouse_modes),
('mp', 'Show model panel dialog', show_model_panel),
('mw', 'Molecular weight', molecular_weight),
('o2', 'Open last 2 files', open_last_2_files),
('o3', 'Open last 3 files', open_last_3_files),
('oc', 'Type one command', one_command),
('oj', 'Open 3nd to last file', open_3rd_to_last_file),
('ok', 'Open 2nd to last file', open_2nd_to_last_file),
('ol', 'Open last file', open_last_file),
('Op', 'Original model positions', original_positions),
('op', 'Open file', open_file),
('or', 'Orthographic projection', toggle_ortho_projection),
('os', 'Open session', open_session),
('ov', 'Open volume', open_file),
('Qt', 'Quit Chimera', quit),
('pf', 'Preferences dialog', show_preferences_dialog),
('ps', 'Python shell', show_python_shell),
('ra', 'Render by attribute', show_render_by_attribute_dialog),
('rc', 'Rainbow chain', rainbow_chain),
('re', 'Edged ribbon', edged_ribbon),
('rf', 'Flat ribbon', flat_ribbon),
('rh', 'Hide ribbon', hide_ribbon),
('rl', 'Reply log', show_reply_log),
('rr', 'Round ribbon', round_ribbon),
('sa', 'Select all', select_all),
('sc', 'Select connected atoms/bonds', select_connected),
('se', 'Toggle silhouette edges', toggle_silhouette_edges),
('sf', 'Show surface', show_surface),
('sF', 'Surface selected atoms', surface_selected_atoms),
('si', 'Save image...', save_image),
('sl', 'Show/Hide status line', toggle_status_line),
('so', 'Standard orientation', standard_orientation),
('sp', 'Sphere representation', sphere_representation),
('ss', 'Save session as...', save_session_as),
('Ss', 'Save session', save_session),
('st', 'Stick representation', stick_representation),
('sv', 'Show side view dialog', show_side_view),
('sx', 'Show side chains only', show_side_chains_only),
('t0', 'Transparent surface 0%', transparent_surface_0),
('t5', 'Transparent surface 50%', transparent_surface_50),
('ug', "User's guide", show_users_guide),
('va', 'View all models', view_all),
('vp', 'Show volume path tracer dialog',
show_volume_path_tracer_dialog),
('wb', 'Set background to white', set_white_background),
('wr', 'Wire representation', wire_representation),
('xs', 'Export scene', export_scene),
('x9', 'Turn 90 degrees about x axis', turn_x_90),
('y9', 'Turn 90 degrees about y axis', turn_y_90),
('z9', 'Turn 90 degrees about z axis', turn_z_90),
('zn', 'Select zone using zone dialog settings', select_zone),
('zd', 'Show zone dialog', show_zone_dialog),
]
from Accelerators import add_accelerator
for (keys, descrip, func) in accelerators:
add_accelerator(keys, descrip, func)
from chimera.extension import EMO, manager
# -----------------------------------------------------------------------------
#
class Unit_Cell_EMO(EMO):
def name(self):
return 'Unit Cell'
def description(self):
return 'Make molecule copies to for crystal unit cell'
def categories(self):
return ['Higher-Order Structure']
def icon(self):
return None
def activate(self):
self.module().show_unit_cell_dialog()
manager.registerExtension(Unit_Cell_EMO(__file__))
# -----------------------------------------------------------------------------
#
def show_unit_cell_dialog():
import UnitCell
UnitCell.show_unit_cell_dialog()
from Accelerators import add_accelerator
add_accelerator('uc', 'Show unit cell dialog', show_unit_cell_dialog)
# -----------------------------------------------------------------------------
#
def print_path_length():
import PathLength
PathLength.print_path_length()
def print_model_path_lengths():
import PathLength
PathLength.print_model_path_lengths()
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('pl', 'Show total length of selected bonds', print_path_length)
add_accelerator('pL', 'Show total length of selected bonds for each model',
print_model_path_lengths)
#
chimera.extension.manager.registerExtension(Crystal_Contacts_EMO(__file__))
# -----------------------------------------------------------------------------
#
def show_contacts(distance=1.0):
import chimera
for m in chimera.openModels.list(modelTypes=[chimera.Molecule]):
from CrystalContacts import show_crystal_contacts
show_crystal_contacts(m, distance)
from Accelerators import add_accelerator
add_accelerator('xx', 'Show crystal contacts', show_contacts)
# -----------------------------------------------------------------------------
#
def crystal_contacts_command(cmdname, args):
from CrystalContacts.command import crystal_contacts
crystal_contacts(cmdname, args)
# -----------------------------------------------------------------------------
#
from Midas.midas_text import addCommand
addCommand('crystalcontacts', crystal_contacts_command, help=True)
import FitMap
FitMap.move_selected_atoms_to_maximum()
def fit_map_rotation_only_cb():
import FitMap
FitMap.move_selected_atoms_to_maximum(optimize_translation=False)
def fit_map_shift_only_cb():
import FitMap
FitMap.move_selected_atoms_to_maximum(optimize_rotation=False)
def move_atoms_to_maxima():
import FitMap
FitMap.move_atoms_to_maxima()
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('ft', 'Move model to maximize density at selected atoms',
fit_map_cb)
add_accelerator('fr', 'Rotate model to maximize density at selected atoms',
fit_map_rotation_only_cb)
add_accelerator('fs', 'Shift model to maximize density at selected atoms',
fit_map_shift_only_cb)
add_accelerator('mX', 'Move selected atoms to local maxima',
move_atoms_to_maxima)
from SpaceNavigator import sn
from Accelerators import add_accelerator
add_accelerator('nd', 'Space navigator only translate/rotate',
sn.toggle_dominant_mode)
add_accelerator('nz', 'Toggle space navigator zoom mode',
sn.toggle_zoom_mode)
add_accelerator('na', 'Space navigator moves inactive models',
sn.toggle_all_models)
add_accelerator('nf', 'Toggle space navigator fly through mode',
sn.toggle_fly_mode)
place_marker(m0)
show_volume_path_dialog()
# -----------------------------------------------------------------------------
#
def mark_cofr():
from VolumePath import place_marker, show_volume_path_dialog
from chimera import openModels
place_marker(openModels.cofr.data())
show_volume_path_dialog()
# -----------------------------------------------------------------------------
#
def place_marker_at_mouse():
import VolumePath
VolumePath.place_marker_at_mouse()
# -----------------------------------------------------------------------------
#
def place_markers_on_atoms():
import VolumePath
VolumePath.place_markers_on_atoms()
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('mz', 'Place marker at position (0,0,0)', mark_zero)
add_accelerator('mc', 'Place marker at center of rotation', mark_cofr)
add_accelerator('mk', 'Place marker under mouse', place_marker_at_mouse)
add_accelerator('mS', 'Place markers on selected atoms', place_markers_on_atoms)
return 'Color Zone'
def description(self):
return 'Color piece of surface near selected atoms'
def categories(self):
return ['Volume Data', 'Depiction']
def icon(self):
return None
def activate(self):
self.module('gui').show_color_zone_dialog()
return None
# -----------------------------------------------------------------------------
#
chimera.extension.manager.registerExtension(Color_Zone_EMO(__file__))
# ---------------------------------------------------------------------------
#
def split_map():
import ColorZone
ColorZone.split_volume_by_color_zone()
from Accelerators import add_accelerator
add_accelerator('sm', 'Split volume by color zones.', split_map)
# -----------------------------------------------------------------------------
#
def align_backbones():
'Superimpose molecules by pairing selected atoms from identical residues'
import MatchDomains
MatchDomains.align_backbones_using_selected_atoms()
# -----------------------------------------------------------------------------
#
def illustrate_alignment():
'Draw slabs to illustrate a the relative orientations of two domains'
import MatchDomains
MatchDomains.illustrate_backbone_alignment()
# -----------------------------------------------------------------------------
#
from Accelerators import add_accelerator
add_accelerator('ab', 'Align backbones using selected atoms', align_backbones)
add_accelerator('ai', 'Illustrate backbone alignment based on selected atoms',
illustrate_alignment)