def view_model(self,
tool='chimera',
savefig=None,
cmd=None,
center_of_mass=False,
gyradius=False,
color='index',
**kwargs):
"""
Visualize a selected model in the three dimensions. (either with Chimera
or through matplotlib).
:param model_num: model to visualize
:param 'chimera' tool: path to the external tool used to visualize the
model. Can also be 'plot', to use matplotlib.
:param None savefig: path to a file where to save the image OR movie
generated (depending on the extension; accepted formats are png, mov
and webm). if set to None, the image or movie will be shown using
the default GUI.
:param 'index' color: can be:
* a string as:
* '**index**' to color particles according to their position in the
model (:func:`pytadbit.utils.extraviews.color_residues`)
* '**tad**' to color particles according to the TAD they belong to
(:func:`pytadbit.utils.extraviews.tad_coloring`)
* '**border**' to color particles marking borders. Color according to
their score (:func:`pytadbit.utils.extraviews.tad_border_coloring`)
coloring function like.
* a function, that takes as argument a model and any other parameter
passed through the kwargs.
* a list of (r, g, b) tuples (as long as the number of particles).
Each r, g, b between 0 and 1.
:param False center_of_mass: draws a dot representing the center of
mass of the model
:param False gyradius: draws the center of mass of the model as a sphere
with radius equal to the radius of gyration of the model
:param None cmd: list of commands to be passed to the viewer.
The chimera list is:
::
focus
set bg_color white
windowsize 800 600
bonddisplay never #0
represent wire
shape tube #0 radius 5 bandLength 100 segmentSubdivisions 1 followBonds on
clip yon -500
~label
set subdivision 1
set depth_cue
set dc_color black
set dc_start 0.5
set dc_end 1
scale 0.8
Followed by the movie command to record movies:
::
movie record supersample 1
turn y 3 120
wait 120
movie stop
movie encode output SAVEFIG
Or the copy command for images:
::
copy file SAVEFIG png
Passing as the following list as 'cmd' parameter:
::
cmd = ['focus', 'set bg_color white', 'windowsize 800 600',
'bonddisplay never #0',
'shape tube #0 radius 10 bandLength 200 segmentSubdivisions 100 followBonds on',
'clip yon -500', '~label', 'set subdivision 1',
'set depth_cue', 'set dc_color black', 'set dc_start 0.5',
'set dc_end 1', 'scale 0.8']
will return the default image (other commands can be passed to
modified the final image/movie).
:param kwargs: see :func:`pytadbit.utils.extraviews.plot_3d_model` or
:func:`pytadbit.utils.extraviews.chimera_view` for other arguments
to pass to this function
"""
if gyradius:
gyradius = self.radius_of_gyration()
center_of_mass = True
if tool == 'plot':
x, y, z = self['x'], self['y'], self['z']
plot_3d_model(x, y, z, color=color, **kwargs)
return
self.write_cmm('/tmp/', color=color, **kwargs)
chimera_view(['/tmp/model.%s.cmm' % (self['rand_init'])],
savefig=savefig,
chimera_bin=tool,
chimera_cmd=cmd,
center_of_mass=center_of_mass,
gyradius=gyradius)
def view_model(self, tool='chimera', savefig=None, cmd=None,
center_of_mass=False, gyradius=False, color='index',
**kwargs):
"""
Visualize a selected model in the three dimensions. (either with Chimera
or through matplotlib).
:param model_num: model to visualize
:param 'chimera' tool: path to the external tool used to visualize the
model. Can also be 'plot', to use matplotlib.
:param None savefig: path to a file where to save the image OR movie
generated (depending on the extension; accepted formats are png, mov
and webm). if set to None, the image or movie will be shown using
the default GUI.
:param 'index' color: can be:
* a string as:
* '**index**' to color particles according to their position in the
model (:func:`pytadbit.utils.extraviews.color_residues`)
* '**tad**' to color particles according to the TAD they belong to
(:func:`pytadbit.utils.extraviews.tad_coloring`)
* '**border**' to color particles marking borders. Color according to
their score (:func:`pytadbit.utils.extraviews.tad_border_coloring`)
coloring function like.
* a function, that takes as argument a model and any other parameter
passed through the kwargs.
* a list of (r, g, b) tuples (as long as the number of particles).
Each r, g, b between 0 and 1.
:param False center_of_mass: draws a dot representing the center of
mass of the model
:param False gyradius: draws the center of mass of the model as a sphere
with radius equal to the radius of gyration of the model
:param None cmd: list of commands to be passed to the viewer.
The chimera list is:
::
focus
set bg_color white
windowsize 800 600
bonddisplay never #0
represent wire
shape tube #0 radius 5 bandLength 100 segmentSubdivisions 1 followBonds on
clip yon -500
~label
set subdivision 1
set depth_cue
set dc_color black
set dc_start 0.5
set dc_end 1
scale 0.8
Followed by the movie command to record movies:
::
movie record supersample 1
turn y 3 120
wait 120
movie stop
movie encode output SAVEFIG
Or the copy command for images:
::
copy file SAVEFIG png
Passing as the following list as 'cmd' parameter:
::
cmd = ['focus', 'set bg_color white', 'windowsize 800 600',
'bonddisplay never #0',
'shape tube #0 radius 10 bandLength 200 segmentSubdivisions 100 followBonds on',
'clip yon -500', '~label', 'set subdivision 1',
'set depth_cue', 'set dc_color black', 'set dc_start 0.5',
'set dc_end 1', 'scale 0.8']
will return the default image (other commands can be passed to
modified the final image/movie).
:param kwargs: see :func:`pytadbit.utils.extraviews.plot_3d_model` or
:func:`pytadbit.utils.extraviews.chimera_view` for other arguments
to pass to this function
"""
if gyradius:
gyradius = self.radius_of_gyration()
center_of_mass = True
if tool == 'plot':
x, y, z = self['x'], self['y'], self['z']
plot_3d_model(x, y, z, color=color, **kwargs)
return
self.write_cmm('/tmp/', color=color, **kwargs)
chimera_view(['/tmp/model.%s.cmm' % (self['rand_init'])],
savefig=savefig, chimera_bin=tool, chimera_cmd=cmd,
center_of_mass=center_of_mass, gyradius=gyradius)