schrodinger.application.glide.gui module¶

Classes and functions that are shared between the Glide GridGen and Docking panels.

schrodinger.application.glide.gui.find_equivalent_atoms(st, anum)¶: Given a structure atom, return a list of atoms that are identical to it. If no identical atoms are found, and empty list is returned.

class schrodinger.application.glide.gui.GlideWorkspaceMarkers¶

Bases: MarkerMixin

Class for marking constraints and excluded volumes in the Workspace. Along with the marker, optional labels are also drawn.

__init__()¶

clear()¶: Remove all added labels.

add(center: Optional[Union[GridCenter, List[float]]] = None, radius=None, atom=None, color=None, name=None, opacity=0.8)¶

Add another marker to draw.

Either center and radius need to be specified (to draw a sphere) or an atom object (to draw atom markers).

show()¶: Show the markers in the Workspace.

hide()¶: Hide the markers from the Workspace.

setVisible(visible)¶: Show the markers if “visible” is True, hide otherwise.

showLabels()¶: Enable labels.

hideLabels()¶: Disable labels.

setLabelsVisible(visible)¶: Show the labels if “visible” is True, hide otherwise.

class schrodinger.application.glide.gui.GridCenter(*args, _param_type=<object object>, **kwargs)¶

Bases: CompoundParam

x: float¶: A parameter of the class.

y: float¶: A parameter of the class.

z: float¶: A parameter of the class.

is_center_set: bool¶: A parameter of the class.

setXYZ(x: float, y: float, z: float)¶

Set the x, y, and z coordinates of the grid center.

Parameters:

x – X coordinate.
y – Y coordinate.
z – Z coordinate.

is_center_setChanged¶: A pyqtSignal emitted by instances of the class.

is_center_setReplaced¶: A pyqtSignal emitted by instances of the class.

xChanged¶: A pyqtSignal emitted by instances of the class.

xReplaced¶: A pyqtSignal emitted by instances of the class.

yChanged¶: A pyqtSignal emitted by instances of the class.

yReplaced¶: A pyqtSignal emitted by instances of the class.

zChanged¶: A pyqtSignal emitted by instances of the class.

zReplaced¶: A pyqtSignal emitted by instances of the class.

class schrodinger.application.glide.gui.GridSite(*args, _param_type=<object object>, **kwargs)¶

Bases: CompoundParam

Class representing a grid box. The values get set either when picking a new ligand in the Receptor tab, or by making changes in the Site tab. When a new ligand is picked, ligand_picked signal is emitted. When the user makes changes in the Site tab, the site_changed signal is emitted.

center: GridCenter¶: A parameter of the class.

entry_id: int¶: A parameter of the class.

asl: str¶: A parameter of the class.

inner_box: tuple¶: A parameter of the class.

size: float¶: A parameter of the class.

site_changed¶: A pyqtSignal emitted by instances of the class.

ligand_picked¶: A pyqtSignal emitted by instances of the class.

initializeValue()¶: Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

initConcrete()¶: Override to customize initialization of concrete params.

reset()¶: Reset the Gridsite instance to its initial state.

setCustomCenter(center: tuple[float] | None)¶

Set the center of the grid box to the specified values or (0,0,0) if None.

Parameters:: center – Optional tuple of three floats.

getBoxSizes() → tuple[tuple, tuple]¶

Get the sizes of the inner and outer boxes.

Returns:: A tuple containing the xyz sizes of the inner box and outer box.

ligandPicked(ligmol: _Molecule = None, entry: ProjectRow = None)¶

Called by the receptor tab when a new ligand is picked. Either ligmol or entry (but not both) must be specified.

Parameters:

ligmol – Optional; A _Molecule instance for the picked ligand molecule.
entry – Optional; An instance of ProjectRow class.

Raises:

ValueError – If neither ligmol nor entry is specified.

setCenterToLigand()¶: Set the center of the grid box to the center of the picked ligand (if a ligand was picked). Used by the SiteTab.

setSizeToLigand()¶: Set the size of the grid box to the size of the picked ligand (if a ligand was picked). Used by the SiteTab.

findLigandAtoms(st: Structure) → List[int]¶

Given a Structure, return a list of the ligand atoms in it.

Parameters:: st – A Structure containing atoms containing ligand atoms.
Returns:: A list of ligand atoms in the structure.

isDefined() → bool¶

Check if the active site is defined.

Returns:: True if the active site is defined; False otherwise.

isSphereInBox(xyz: tuple[float] | schrodinger.application.glide.gui.GridCenter, radius: float) → bool¶

Determine if a sphere is fully within the grid box.

Parameters:

xyz – XYZ coordinates representing the center of the sphere.
radius – Radius of the sphere.

Returns:

True if the sphere is inside the grid box; False otherwise.

isPointInBox(xyz: tuple[float] | schrodinger.application.glide.gui.GridCenter) → bool¶

Check if a coordinate is within the grid box.

Parameters:: xyz – A list or class representing XYZ coordinates.
Returns:: True if the coordinates are inside the grid box; False otherwise.

hasLigandsInBox(st: Structure) → bool¶

Determine whether there are unidentified ligands in the workspace. Used to warn the user before starting a job.

Parameters:: st – A Structure containing atoms containing ligand atoms.
Returns:: True if there are ligands in the box; False otherwise.

aslChanged¶: A pyqtSignal emitted by instances of the class.

aslReplaced¶: A pyqtSignal emitted by instances of the class.

centerChanged¶: A pyqtSignal emitted by instances of the class.

centerReplaced¶: A pyqtSignal emitted by instances of the class.

entry_idChanged¶: A pyqtSignal emitted by instances of the class.

entry_idReplaced¶: A pyqtSignal emitted by instances of the class.

inner_boxChanged¶: A pyqtSignal emitted by instances of the class.

inner_boxReplaced¶: A pyqtSignal emitted by instances of the class.

sizeChanged¶: A pyqtSignal emitted by instances of the class.

sizeReplaced¶: A pyqtSignal emitted by instances of the class.