Package schrodinger :: Package application :: Package phase :: Module phase_markers

[frames] | no frames]

Module phase_markers

Classes

[hide private]

WorkspaceSite
This is special class we use when adding sites manually in workspace.

PhaseFeatureMarker
Class defining a single Phase marker.

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

PhaseMarkers
Class for adding pharmacophore feature markers and controlling their visibility.

EditFeatureDialog
Class for Phase feature editor dialog.

ScreeningEditFeatureDialog
Advanced version of EditFeatureDialog that adds screening options for sites in Phase hypothesis.

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.

copy_site(from_site, to_site)
Copy data from one site to another.

list

copy_sites(sites)
Makes a copy of sites in a given list and returns it as new list.

int

get_fragment_for_sites(sites)
This function is called to create fragment structure for a given list of sites.

phase.PhpHypoAdaptor

set_hypo_ref_props(hypo, props_dict)
Sets the CT-level properties of the reference ligand of the hypothesis, and returns the new hypothesis.

PhaseMarkers

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

tuple

get_hypothesis_with_eid(entry_id)
Find Phase hypothesis with a given entry id in the Project Table

update_hypothesis(hypo, hypo_id)
This function is called to update hypothesis in the project table with a given hypo id after feature attributes have been modified.

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.

set_excluded_volume_visible(entry_id, visible)
Toggles hypothesis properties which can be shown in the workspace for hypothesis with a given entry id.

set_reference_ligand_visible(entry_id, visible)

show_phase_hover_markers(pick_id)
Show glow effect when mouse is hovered on a phase marker.

hide_phase_hover_markers(pick_id)
Remove glow effect when mouse is moved away from a phase marker.

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]

ENABLED_ROLE = 31

maestro = schrodinger.get_maestro()

markers = 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

copy_site(from_site, to_site)

Copy data from one site to another.

Parameters:

from_site (phase.PhpSite or WorkspaceSite) - site from which data will be copied.
to_site (phase.PhpSite or WorkspaceSite) - site to which data will be copied.

copy_sites(sites)

Makes a copy of sites in a given list and returns it as new list.

Parameters:

sites (list) - list of sites

Returns: list

copy of original list

get_fragment_for_sites(sites)

This function is called to create fragment structure for a given list of sites.

Parameters:

sites (list) - list of sites from which fragment will be created

Returns: int

fragment ct handle

set_hypo_ref_props(hypo, props_dict)

Sets the CT-level properties of the reference ligand of the hypothesis, and returns the new hypothesis.

Parameters:

hypo (phase.PhpHypoAdaptor) - Hypothesis to update
props_dict (dict) - Dictionary of CT-level properties.

Returns: phase.PhpHypoAdaptor

Updated hypothesis.

get_phase_markers()

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

Returns: PhaseMarkers: PhaseMarkers object

get_hypothesis_with_eid(entry_id)

Find Phase hypothesis with a given entry id in the Project Table

Parameters:

entry_id - Phase hypothesis entry id @type entry_id, int

Returns: tuple

tuple that contains Phase hypothesis and its id

update_hypothesis(hypo, hypo_id)

This function is called to update hypothesis in the project table with a given hypo id after feature attributes have been modified.

Parameters:

hypo (phase.PhpHypoAdaptor) - Phase hypothesis object
hypo_id (int) - hypothesis id

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

set_excluded_volume_visible(entry_id, visible)

Toggles hypothesis properties which can be shown in the workspace for hypothesis with a given entry id.

Parameters:

entry_id (int) - Phase hypothesis entry id
visible (bool) - whether to make visible in the workspace or not

show_phase_hover_markers(pick_id)

Show glow effect when mouse is hovered on a phase marker.

Parameters:

pick_id (int) - Phase marker pick id

hide_phase_hover_markers(pick_id)

Remove glow effect when mouse is moved away from a phase marker.

Parameters:

pick_id (int) - Phase marker pick 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