Module phase_markers

Classes

[hide private]

PhaseFeatureMarker
Class defining a single Phase marker.

PhaseXvolMarkers
Class that defines group of spheres for the excluded volume.

PhaseFeatureMixin
A mixin for adding pharmacophore feature markers and controlling their visibility.

EditFeatureDialog
Class for Phase feature editor dialog.

Functions

[hide private]

tuple

get_site_coords(site)
This function returns site coordinates.

tuple

_calculate_arrow_tail(x, y, z, px, py, pz, rad, rcyl)
Calculate coordinates of the projected point arrow tail position.

PhaseFeatureMixin

get_phase_mixin()
This function returns global PhaseFeatureMixin object that should be used to generate Phase marker throughout Maestro session.

show_workspace_phase_markers(entry_ids)
Adds Phase pharmacophore site markers for given entries.

hide_workspace_phase_markers(entry_ids)
Removes Phase pharmacophore site markers for given entries.

project_close()
Delete all Phase feature markers.

setup_project_close()
Sets up function that should be called when project is closed.

toggle_excluded_volumes(entry_id)
Toggles excluded volumes on and off for hypothesis with a given entry id.

right_click_handler(pick_id, x, y)
Right click callback is called when user right clicks on a graphics object in the workspace at position (x,y) which has pick id as pick_id.

Variables

[hide private]

maestro = schrodinger.get_maestro()

marker_mixin = None
hash(x)

LABEL_FONT_NAME = maestro.get_font_names() [0]

__package__ = 'schrodinger.application.phase'

Function Details

[hide private]

get_site_coords(site)

This function returns site coordinates.

Returns: tuple: site xyz coordinates

_calculate_arrow_tail(x, y, z, px, py, pz, rad, rcyl)

Calculate coordinates of the projected point arrow tail position. Tail position is calculated in such a way that arrow cylinder 'grows' from the surface of the pharmacophore sphere.

Parameters:

x (float) - x-coordinate of the pharmacophore site
y (float) - y-coordinate of the pharmacophore site
z (float) - z-coordinate of the pharmacophore site
px (float) - x-coordinate of the projected point (arrow end point)
py (float) - y-coordinate of the projected point (arrow end point)
pz (float) - z-coordinate of the projected point (arrow end point)
rad (float) - pharmacophore feature sphere radius
rcyl (float) - radius of the arrow cylinder

Returns: tuple

tuple that contains xyz coordinates of the arrow tail point

get_phase_mixin()

This function returns global PhaseFeatureMixin object that should be used to generate Phase marker throughout Maestro session.

Returns: PhaseFeatureMixin: PhaseFeatureMixin object

show_workspace_phase_markers(entry_ids)

Adds Phase pharmacophore site markers for given entries. Phase hypothesis should be associated with entry in order for the sites to be added. If Phase markers already exist for a given entry id nothing needs to be done.

Parameters:

entry_ids (list) - list of Phase hypothesis entries

hide_workspace_phase_markers(entry_ids)

Removes Phase pharmacophore site markers for given entries.

Parameters:

entry_ids (list) - list of Phase hypothesis entries

toggle_excluded_volumes(entry_id)

Toggles excluded volumes on and off for hypothesis with a given entry id.

Parameters:

entry_ids (int) - Phase hypothesis entry id

right_click_handler(pick_id, x, y)

Right click callback is called when user right clicks on a graphics object in the workspace at position (x,y) which has pick id as pick_id.

Parameters:

pick_id (int) - Pick id
x (int) - X position in the workspace
y (int) - Y position in the workspace