HappyDoc Generated Documentation ./ModelClip/mclipcmd.py

. / ModelClip / mclipcmd.py 

Functions   
  parse_model_spec 
parse_model_spec ( mspec )
  mclip_command 
mclip_command ( cmdname,  args )

Per-model clipping Chimera command mclip.

mclip #1-3 # Model specifier can be "all". axis 0,0,1 # Can also be "x", "y", or "z". origin 3.2,1,5 # Can also be "center" (of bounding box). coords local # Can be "local" or "screen". offset 5.0 stagger 0.1 # Make non-coincident planes for multiple models. match #0 # Match clip plane of a specified model. # Can also be "focalplane", "near", or "nearfar". flip false # Flip plane 180 degrees. slab false thickness 10.0 # Slab thickness.

Only specified clipping parameters are changed, while unspecified ones remain at their current values. If a model has not been clipped before and the axis is not specified it defaults to "z", and if origin has not been specified it defaults to "center". The offset is not a remembered parameter -- it alters the origin which is remembed. The match option overrides other options except for offset, stagger and flip. Specifying no arguments turns on clipping for all models.

~mclip #2-4 # Turn off per-model clipping.

  unclip_models 
unclip_models ( models )
Exceptions   

MidasError, 'No models specified by "%s"' % str( models )

  match_settings 
match_settings (
        match,
        axis,
        origin,
        coord,
        slab,
        thickness,
        )
Exceptions   

MidasError, 'match value must be a model id or "near", "nearfar" or "focal", got "%s"' % str( match )

  center_of_models 
center_of_models ( models )

Screen coordinates. Transform each model box to coordinates of first box to compute center. Transforming boxes to screen coordinates is not as good as the result depends on the overall rotation.

  mclip 
mclip (
        models,
        axis=None,
        origin=None,
        coords=None,
        offset=None,
        stagger=None,
        match=None,
        flip=None,
        slab=None,
        thickness=None,
        )
Exceptions   

MidasError, 'No models specified by "%s"' % str( models )
MidasError, ('coords must be %s, got "%s"' %(' or '.join( csys ), str( coords ) ) )
MidasError, ('%s must be true/false, got "%s"' %(name, str( val ) ) )
MidasError, '%s must be number, got "%s"' %(name, str( val ) )

  clip_models 
clip_models (
        models,
        axis,
        origin,
        coord,
        offset,
        stagger,
        flip,
        slab,
        thickness,
        )
  clip_model 
clip_model (
        m,
        axis,
        origin,
        offset,
        slab,
        thickness,
        flip,
        )
  parse_floats 
parse_floats (
        value,
        name,
        count,
        default=None,
        )
Exceptions   

MidasError, ('%s value must be %d comma-separated numbers, got %s' %(name, count, str( value ) ) )

  apply_offset 
apply_offset (
        origin,
        axis,
        offset,
        )
  unclip_command 
unclip_command ( cmdname,  args )
Classes   

This document was automatically generated Wed Jul 9 15:49:02 2008 by HappyDoc version 3.1