# -----------------------------------------------------------------------------
#
from chimera.extension import EMO, manager
# -----------------------------------------------------------------------------
#
class SAXS_EMO(EMO):
def name(self):
return 'Small-Angle X-Ray Profile'
def description(self):
return 'Compute small angle x-ray scattering profile'
def categories(self):
return ['Higher-Order Structure']
def icon(self):
return None
def activate(self):
self.module('gui').show_saxs_dialog()
return None
# -----------------------------------------------------------------------------
#
manager.registerExtension(SAXS_EMO(__file__))
from chimera.extension import EMO, manager
# -----------------------------------------------------------------------------
#
class ModelZ_Dialog_EMO(EMO):
def name(self):
return 'ecsudraft'
def description(self):
return "a draft for ecsu validation tool"
def categories(self):
return ['Utilities']
def icon(self):
return self.path('logo.jpg')
def activate(self):
# self.module('volumedialog').show_volume_dialog()
d = self.module('backbone').colorBB()
return None
# -----------------------------------------------------------------------------
# Register dialogs and menu entry.
#
manager.registerExtension(ModelZ_Dialog_EMO(__file__))
from chimera.extension import EMO, manager
# -----------------------------------------------------------------------------
#
class Hide_Dust_EMO(EMO):
def name(self):
return 'Hide Dust'
def description(self):
return 'Hide small surface pieces'
def categories(self):
return ['Volume Data']
def icon(self):
return None
def activate(self):
self.module('gui').show_dust_dialog()
return None
# -----------------------------------------------------------------------------
#
manager.registerExtension(Hide_Dust_EMO(__file__))
#
class BioMovie_EMO(EMO):
def name(self):
return 'BioMovie'
def description(self):
return self.categoryDescriptions()['Utilities']
def categories(self):
return self.categoryDescriptions().keys()
def categoryDescriptions(self):
# since we want to use specialized descriptions for certain categories...
return {
'Utilities': 'Run movie script',
}
def icon(self):
return None #self.path('volseg.png')
def activate(self):
# self.module('volumedialog').show_volume_dialog()
d = self.module('biomovie').show_dialog()
return None
# -----------------------------------------------------------------------------
# Register dialogs and menu entry.
#
manager.registerExtension(BioMovie_EMO(__file__))
from chimera.extension import EMO, manager
class XlinkAnalyzer_EMO(EMO):
def name(self):
return 'Xlink Analyzer'
def description(self):
return 'Xlink Analyzer modeling visualization'
def categories(self):
return ['Utilities']
def icon(self):
return None
def activate(self):
self.module('gui').show_dialog()
return None
manager.registerExtension(XlinkAnalyzer_EMO(__file__))
from chimera.extension import EMO, manager
# -----------------------------------------------------------------------------
#
class MapQ_Dialog_EMO ( EMO ):
def name(self):
return 'MapQ'
def description(self):
return self.categoryDescriptions()['Volume Data']
def categories(self):
return self.categoryDescriptions().keys()
def categoryDescriptions(self):
# since we want to use specialized descriptions for certain categories...
return {
'Volume Data': 'Evaluate map & model',
}
def icon(self):
return None #self.path('volseg.png')
def activate(self):
# self.module('volumedialog').show_volume_dialog()
d = self.module('mapq').show_dialog()
return None
# -----------------------------------------------------------------------------
# Register dialogs and menu entry.
#
manager.registerExtension ( MapQ_Dialog_EMO ( __file__ ) )
return 'Electrostatic Surface Coloring'
def description(self):
return 'Color surface using an electrostatic potential data file'
def categories(self):
return ['Surface/Binding Analysis']
def icon(self):
return self.path('gumball.png')
def activate(self):
m = self.module('gui')
d = m.show_surface_color_dialog()
d.use_electrostatics_colormap()
return None
# -----------------------------------------------------------------------------
#
manager.registerExtension(Surface_Color_EMO(__file__))
manager.registerExtension(Electrostatic_Surface_Color_EMO(__file__))
# -----------------------------------------------------------------------------
#
def register_file_types():
from VolumeData import file_types, electrostatics_types
ftypes = filter(lambda ft: ft[1] in electrostatics_types, file_types)
for descrip, name, prefix_list, suffix_list, batch in ftypes:
def open_cb(path, ftype=name):
from VolumeViewer import open_volume_file
vlist = open_volume_file(path, ftype, open_models = False,
show_data = False, show_dialog = False)
import chimera
if len(vlist) > 0 and not chimera.nogui:
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)
# -----------------------------------------------------------------------------
#
from chimera.extension import EMO, manager
# -----------------------------------------------------------------------------
#
class SAXS_EMO(EMO):
def name(self):
return 'Small-Angle X-Ray Profile'
def description(self):
return 'Compute small angle x-ray scattering profile'
def categories(self):
return ['Higher-Order Structure']
def icon(self):
return None
def activate(self):
self.module('gui').show_saxs_dialog()
return None
# -----------------------------------------------------------------------------
#
manager.registerExtension(SAXS_EMO(__file__))
from chimera.extension import EMO, manager
class CHEWD_EMO(EMO):
def name(self):
return 'CHEWD'
def description(self):
return 'Molecular Surface Viewer for the residues wise energies'
def categories(self):
return ['Utilities']
def icon(self):
return None
def activate(self):
from chimera.dialogs import display
display(self.module('gui').CHEWDDialog.name)
return None
manager.registerExtension(CHEWD_EMO(__file__))
#
from chimera.extension import EMO, manager
class Volume_Filter_EMO(EMO):
def name(self):
return 'Volume Filter'
def description(self):
return 'Filter volume data'
def categories(self):
return ['Volume Data']
def icon(self):
return None
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
from chimera.extension import EMO, manager
# -----------------------------------------------------------------------------
#
class Hide_Dust_EMO(EMO):
def name(self):
return 'Hide Dust'
def description(self):
return 'Hide small surface pieces'
def categories(self):
return ['Volume Data']
def icon(self):
return None
def activate(self):
self.module('gui').show_dust_dialog()
return None
# -----------------------------------------------------------------------------
#
manager.registerExtension(Hide_Dust_EMO(__file__))
'Volume Data': 'Fit structures into segmented regions',
}
def icon(self):
return self.path('fitseg.png')
def activate(self):
# self.module('volumedialog').show_volume_dialog()
d = self.module('fit_dialog').show_fit_segments_dialog()
return None
# -----------------------------------------------------------------------------
# Register dialogs and menu entry.
#
manager.registerExtension(Fit_Segments_EMO(__file__))
manager.registerExtension(Segment_Map_EMO(__file__))
# -----------------------------------------------------------------------------
# Register segmentation file reader.
#
def open_seg(path):
from Segger import segment_dialog as sd
d = sd.show_volume_segmentation_dialog()
d.OpenSegFiles([(path, 'Segmentation')])
return []
import chimera
fi = chimera.fileInfo
# -----------------------------------------------------------------------------
#
from chimera.extension import EMO, manager
# -----------------------------------------------------------------------------
#
class NMWiz_EMO(EMO):
def name(self):
return 'Normal Mode Wizard'
def description(self):
return 'Visualization of Normal Mode'
def categories(self):
return ['Structure Analysis']
def icon(self):
return None
def activate(self):
self.module('gui').show_nmwiz_dialog()
return None
# -----------------------------------------------------------------------------
#
manager.registerExtension(NMWiz_EMO(__file__))
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)
from chimera.extension import EMO, manager
class XlinkAnalyzer_EMO(EMO):
def name(self):
return 'Xlink Analyzer'
def description(self):
return 'Xlink Analyzer modeling visualization'
def categories(self):
return ['Utilities']
def icon(self):
return None
def activate(self):
self.module('gui').show_dialog()
return None
manager.registerExtension(XlinkAnalyzer_EMO(__file__))
#
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)