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2016-4 Schrodinger Python API
Package schrodinger :: Package application :: Package bioluminate :: Module protein_structure_quality :: Class HomologyRama
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Class HomologyRama

ui.qt.rama.Rama --+
                  |
                 HomologyRama

A Ramachandran plot customized for the Protein Structure Quality Viewer

Nested Classes [hide private]

Inherited from ui.qt.rama.Rama: backbone_dihedral

Instance Methods [hide private]
 
__init__(self, *args, **kwargs)
Create a HomologyRama object.
 
change_current_pick(self, new_pick, multi=False)
React to picking a new point in the plot by changing the phi/psi counters if used and highlighting the selection in the workspace.
str
getCategory(self, xval, yval)
Get the favorable, allowed or disallowed status of a point
 
draw_regions(self)
Draw the various regions on the Ramachandran plot, and define the favorable, allowed and disallowed bins
 
recolorPlot(self, favorable, allowed, disallowed)
Change the color of the regions on the plot
tuple
makeBinPoint(self, xval, yval)
Return the bottom left corner of a 10x10 degree patch of the plot that contains xval, yval
 
defineBins(self, allowed, favorable)
Define the 10x10 degree bins for what is allowed and what is favorable
 
display_structure(self, ct, ca_list=None, chains='all')
Plot the dihedrals for a new structure
 
update_display(self)
Updates the plot to show the displayed structure.
 
find_closest_point(self, event)
Find the dihedral closes to the point (x, y).
bool
isInDisplayedChain(self, dihedral)
Returns True if the dihedral is from one of the displayed chains, False if not

Inherited from ui.qt.rama.Rama: adjust_phi, adjust_psi, adjust_symbol_size, apply_dihedral, clearGraph, clear_selection, display_residue, drag, find_connected_atom, get_connected_pair, get_picked, get_weight_symbol, minus, options_quit, pick_by_atom, pick_by_point, plus, revert_to_original, revert_to_saved, save, set_symbol_size, set_viewport, update_point_faces, update_point_xval, update_point_yval, write_file

Class Variables [hide private]

Inherited from ui.qt.rama.Rama: ALLOWED_COLOR, DEFAULT_CURSOR, DEFAULT_SYMBOL_SIZE, DEF_COLOR, ESC_KEY, FAVORABLE_COLOR, GLY_COLOR, PRO_COLOR, SYMBOL_SCALING_FACTOR, ZOOMSTEP

Method Details [hide private]

__init__(self, *args, **kwargs)
(Constructor)

 

Create a HomologyRama object.

See parent class for argument documentation

Parameters:
  • widget - the PyQt widget that 'owns' this plot
  • layout - the layout to place the plot into
  • size - size of square plot in pixels, (default=450).
  • dpi - dots per inch resolution of plot (default=100).
  • size - unused, kept for backward compatibility
  • show_status - If True, cursor location feedback is given in the matplotlib toolbar
  • show_counters - If True, show controls for changing the Phi and Psi values of the selected dihedral. Only one of multiselect and show_counters can be True.
  • zoom_on_pick - If True, zoom the Maestro workspace to the dihedral picked
  • multiselect - If True, the user can pick multiple points with shift/cntl-click. If False (default), only one point can be picked at a time. Only one of multiselect and show_counters can be True.
Overrides: ui.qt.rama.Rama.__init__

change_current_pick(self, new_pick, multi=False)

 

React to picking a new point in the plot by changing the phi/psi counters if used and highlighting the selection in the workspace.

Parameters:
  • new_pick (int) - the index of the picked point in self.dihedral_list
Overrides: ui.qt.rama.Rama.change_current_pick

getCategory(self, xval, yval)

 

Get the favorable, allowed or disallowed status of a point

Parameters:
  • xval (float) - the x value of the point
  • yval (float) - the y value of the point
Returns: str
one of HomologyRama.FAVORABLE, HomologyRama.ALLOWED, HomologyRama.DISALLOWED

draw_regions(self)

 

Draw the various regions on the Ramachandran plot, and define the favorable, allowed and disallowed bins

Overrides: ui.qt.rama.Rama.draw_regions

recolorPlot(self, favorable, allowed, disallowed)

 

Change the color of the regions on the plot

Parameters:
  • favorable (str) - matplotlib-recognized color string for the favorable regions
  • allowed (str) - matplotlib-recognized color string for the allowed regions
  • disallowed (str) - matplotlib-recognized color string for the disallowed regions

makeBinPoint(self, xval, yval)

 

Return the bottom left corner of a 10x10 degree patch of the plot that contains xval, yval

Parameters:
  • xval (float) - the x value of the point
  • yval (float) - the y value of the point
Returns: tuple
(X, Y) of the bottom left corner of the patch that contains (xval, yval). Will be integer multiples of 10.

defineBins(self, allowed, favorable)

 

Define the 10x10 degree bins for what is allowed and what is favorable

Parameters:
  • allowed (list) - matplotlib Polygon object defining an allowed region
  • favorable (list) - matplotlib Polygon object defining a favorable region

display_structure(self, ct, ca_list=None, chains='all')

 

Plot the dihedrals for a new structure

Parameters:
  • ct (schrodinger.structure.Structure) - structure with dihedrals to plot
  • ca_list (list) - list of Calpha carbons to plot (default is all)
  • chains ('all' or list of str) - What chains to display, default is 'all', otherwise should be a list of chain names
Overrides: ui.qt.rama.Rama.display_structure

update_display(self)

 

Updates the plot to show the displayed structure. Overrides the parent class method in order to only show dihedrals from the specified chains.

Overrides: ui.qt.rama.Rama.update_display

find_closest_point(self, event)

 

Find the dihedral closes to the point (x, y). Overrides the parent class method in order to only choose points from the displayed chain.

Parameters:
  • event (MouseEvent) - The matplotlib mouse event that generates this call
Overrides: ui.qt.rama.Rama.find_closest_point

isInDisplayedChain(self, dihedral)

 

Returns True if the dihedral is from one of the displayed chains, False if not

Parameters:
  • dihedral (rama.Rama.backbone_dihedral) - The object to test to see if it belongs to one of the displayed chains
Returns: bool
True if the dihedral is from one of the displayed chains, False if not

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2016-4 Schrodinger Python API
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