schrodinger.protein.helm.helm_renderer module¶

class schrodinger.protein.helm.helm_renderer.HexColor¶

Bases: Enum

Acidic = <PyQt6.QtGui.QColor object>¶

Basic = <PyQt6.QtGui.QColor object>¶

Aliphatic = <PyQt6.QtGui.QColor object>¶

Aromatic = <PyQt6.QtGui.QColor object>¶

Hydrophilic = <PyQt6.QtGui.QColor object>¶

Thiol = <PyQt6.QtGui.QColor object>¶

IminoAcid = <PyQt6.QtGui.QColor object>¶

VariablePolar = <PyQt6.QtGui.QColor object>¶

NABackBone = <PyQt6.QtGui.QColor object>¶

Adenine = <PyQt6.QtGui.QColor object>¶

Cytosine = <PyQt6.QtGui.QColor object>¶

Guanine = <PyQt6.QtGui.QColor object>¶

Thymine = <PyQt6.QtGui.QColor object>¶

Uracil = <PyQt6.QtGui.QColor object>¶

Other = <PyQt6.QtGui.QColor object>¶

Chem = <PyQt6.QtGui.QColor object>¶

Black = <PyQt6.QtGui.QColor object>¶

Gray3 = <PyQt6.QtGui.QColor object>¶

Gray4 = <PyQt6.QtGui.QColor object>¶

Gray6 = <PyQt6.QtGui.QColor object>¶

DarkRed = <PyQt6.QtGui.QColor object>¶

White = <PyQt6.QtGui.QColor object>¶

class schrodinger.protein.helm.helm_renderer.ZOrder¶

Bases: IntEnum

Enum describing which layer (Z value) each GraphicsItem is drawn on.

BehindMonomer = 1¶

DefaultMonomerItem = 2¶

InFrontMonomer = 3¶

schrodinger.protein.helm.helm_renderer.get_natural_analog(monomer: Atom) → str¶

schrodinger.protein.helm.helm_renderer.protect_painter(painter_method: Callable) → Callable¶

Decorator which can be applied to paint methods to ensure the state of the painter isn’t modified

Parameters:: painter_method – method to wrap. Should take a painter as its first argument
Returns:: wrapped function

class schrodinger.protein.helm.helm_renderer.HelmMonomer(*, res_name: str, polymer_type: schrodinger.protein.helm._helm_parser.PolymerType, is_branch: bool, is_smiles: bool, position: PyQt6.QtCore.QPointF, res_display_type=None)¶

Bases: object

__init__(*, res_name: str, polymer_type: PolymerType, is_branch: bool, is_smiles: bool, position: QPointF, res_display_type=None)¶

property is_standard: bool¶

property is_d_amino_acid: bool¶

property is_nucleotide_sugar: bool¶

property is_nucleotide_phosphate: bool¶

property is_nucleotide_backbone: bool¶

class schrodinger.protein.helm.helm_renderer.HelmMonomerTextLabel(text: str, size: int = 14, weight: Weight = Weight.Normal, color: HexColor = HexColor.Black, parent=None)¶

Bases: QGraphicsPathItem

GraphicsItem used for text labeling all monomers. Sets default font, etc., specific to the Helm rendering use case.

Text is rendered as a path for portability across platforms.

__init__(text: str, size: int = 14, weight: Weight = Weight.Normal, color: HexColor = HexColor.Black, parent=None)¶

class schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin(monomer: HelmMonomer)¶

Bases: object

Mixin which establishes the necessary methods to render the monomer item in the QGraphicsScene. Handles position offsets so that the center of the shape appears at the position set in the monomer object

Also defines default brush and pen settings

MAGNIFY_FACTOR = 1.0¶

DEFAULT_X_RADIUS = 12.5¶

DEFAULT_Y_RADIUS = 12.5¶

__init__(monomer: HelmMonomer)¶

getLabelText() → str¶

Get the text to be displayed in the monomer’s label.

If the assigned name is too long, truncate it and add an ellipsis.

setup()¶: Initialize the current monomer

getMonomerResizingProposal(text_x_radius: float, text_y_radius: float) → Tuple[float, float]¶: Method with class-specific logic to figure out how to resize the monomer given the final size of its text label. Args are the text label’s size; returns size of the smallest monomer that properly contains the text.

setupTextLabel()¶: Updates the geometry of the monomer and monomer label in order to prevent the label text from overflowing the monomer shape.

setShape() → None¶: Set the shape and/or bounding box of the monomer. Must be implemented by inheriting classes for them to be rendered in the scene

class schrodinger.protein.helm.helm_renderer.AminoAcidMonomerBase(monomer: HelmMonomer)¶

Bases: HelmMonomerItemMixin, QGraphicsRectItem

Item representing an amino acid’s position and graphical details in the scene

setShape()¶: Set the size of the monomer rectangle

paint(self, painter: Optional[QPainter], option: Optional[QStyleOptionGraphicsItem], widget: Optional[QWidget] = None)¶

class schrodinger.protein.helm.helm_renderer.StandardAminoAcidMonomerItem(monomer: HelmMonomer)¶: Bases: AminoAcidMonomerBase

class schrodinger.protein.helm.helm_renderer.DAminoAcidMonomerItem(monomer: HelmMonomer)¶

Bases: AminoAcidMonomerBase

DEFAULT_X_RADIUS = 16.0¶

class schrodinger.protein.helm.helm_renderer.OtherAminoAcidMonomerItem(monomer: HelmMonomer)¶: Bases: AminoAcidMonomerBase

class schrodinger.protein.helm.helm_renderer.BBPhosphateMonomerBase(monomer: HelmMonomer)¶

Bases: HelmMonomerItemMixin, QGraphicsEllipseItem

Item representing a nucleic acid backbone phosphate group’s position and graphical details in the scene

MAGNIFY_FACTOR = 1.05¶

getMonomerResizingProposal(text_x_radius: float, text_y_radius: float) → Tuple[float, float]¶: Compute the size of the smallest monomer GraphicsItem that can fit the text label, given that the monomer is ellipse-shaped.

setShape()¶: Set the size of the monomer ellipse

class schrodinger.protein.helm.helm_renderer.BBStandardPhosphateMonomerItem(monomer: HelmMonomer)¶: Bases: BBPhosphateMonomerBase

class schrodinger.protein.helm.helm_renderer.BBModifiedPhosphateMonomerItem(monomer: HelmMonomer)¶: Bases: BBPhosphateMonomerBase

class schrodinger.protein.helm.helm_renderer.BBSugarMonomerBase(monomer: HelmMonomer)¶

Bases: HelmMonomerItemMixin, QGraphicsRectItem

Item representing a nucleic acid backbone sugar group’s position and graphical details in the scene. Used for both ribose and deoxyribose.

setShape()¶: Set the size of the monomer rectangle

class schrodinger.protein.helm.helm_renderer.BBStandardSugarMonomerItem(monomer: HelmMonomer)¶: Bases: BBSugarMonomerBase

class schrodinger.protein.helm.helm_renderer.BBModifiedSugarMonomerItem(monomer: HelmMonomer)¶: Bases: BBSugarMonomerBase

class schrodinger.protein.helm.helm_renderer.NABaseMonomerBase(monomer: HelmMonomer)¶

Bases: HelmMonomerItemMixin, QGraphicsPolygonItem

Item representing a nucleobase’s position and graphical details in the scene

MAGNIFY_FACTOR = 1.15¶

getMonomerResizingProposal(text_x_radius: float, text_y_radius: float) → Tuple[float, float]¶: Compute the size of the smallest monomer GraphicsItem that can fit the text label, given that the monomer is diamond-shaped.

getPolygonVertices() → List[QPointF]¶

Get the polygon vertices to create the required diamond shape

Returns:: A list of vertices in clockwise order

setShape()¶: Set the size and vertices of the monomer item diamond

class schrodinger.protein.helm.helm_renderer.NAStandardBaseMonomerItem(monomer: HelmMonomer)¶: Bases: NABaseMonomerBase

class schrodinger.protein.helm.helm_renderer.NAUnnaturalBaseMonomerItem(monomer: HelmMonomer)¶: Bases: NABaseMonomerBase

class schrodinger.protein.helm.helm_renderer.ChemMonomerItem(monomer: HelmMonomer)¶

Bases: HelmMonomerItemMixin, QGraphicsRectItem

Catchall class for non-peptide, non-nucleotide elements.

setShape()¶: Set the size of the monomer rectangle

schrodinger.protein.helm.helm_renderer.monomer_item_factory(monomer: HelmMonomer) → HelmMonomerItemMixin¶

Implement logic specifying different graphical styles (implemented by each child class) for a monomer.

Parameters:: monomer – Monomer properties, determined by HelmScene.getMonomerData.
Returns:: Graphics item to be added to the current QtWidgets.QGraphicsScene.

class schrodinger.protein.helm.helm_renderer.HelmConnector(start: HelmMonomerItemMixin, end: HelmMonomerItemMixin, is_cyclic: bool = True)¶

Bases: object

start: HelmMonomerItemMixin¶

end: HelmMonomerItemMixin¶

is_cyclic: bool = True¶

getMonomers() → Tuple[HelmMonomer, HelmMonomer]¶: Convenience function returning a 2-tuple of the (start, end) monomer definitions.

getMonomerTypes() → Tuple[PolymerType, PolymerType]¶: Convenience function returning a 2-tuple of the PolymerType of the start and end monomers.

property has_branch: bool¶

property is_disulfide_bridge: bool¶

property polymer_type: PolymerType¶: Determine the PolymerType of the connector, based on the PolymerType of the two monomers it connects.

__init__(start: HelmMonomerItemMixin, end: HelmMonomerItemMixin, is_cyclic: bool = True) → None¶

class schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin(connector: HelmConnector, parent=None)¶

Bases: object

Base class for all connectors.

__init__(connector: HelmConnector, parent=None)¶

getStartPos() → QPointF¶

getEndPos() → QPointF¶

setup() → None¶

class schrodinger.protein.helm.helm_renderer.LineHelmConnectorItem(connector: HelmConnector, parent=None)¶

Bases: HelmConnectorItemMixin, QGraphicsLineItem

Base class for all connectors rendered as a straight line.

setup() → None¶

class schrodinger.protein.helm.helm_renderer.PolylineHelmConnectorItem(connector: HelmConnector, parent=None)¶

Bases: HelmConnectorItemMixin, QGraphicsPathItem

Base class for all connectors rendered as a polyline (”／‾＼”).

setup() → None¶

class schrodinger.protein.helm.helm_renderer.ArrowheadConnectorMixin¶

Bases: object

Mixin for adding arrowheads to the start or end of a HelmConnectorItemMixin graphics item.

add_arrowhead(pos: QPointF) → QAbstractGraphicsShapeItem¶

getArrowheadPos(monomer: HelmMonomerItemMixin, other_monomer: HelmMonomerItemMixin) → QPointF¶: Logic for determining where the arrowhead should be attached to monomer, given that the other end of the connector is attached to other_monomer. Returns a position in the global QGraphicsScene coordinate system.

class schrodinger.protein.helm.helm_renderer.AALinearConnectorItem(connector: HelmConnector, parent=None)¶

Bases: LineHelmConnectorItem

Graphics Item representing a non-branching connector between two amino acids.

class schrodinger.protein.helm.helm_renderer.AABranchingConnectorItem(connector: HelmConnector, parent=None)¶

Bases: ArrowheadConnectorMixin, LineHelmConnectorItem

Graphics Item representing a branching connector between two amino acids.

__init__(connector: HelmConnector, parent=None)¶

getStartPos() → QPointF¶

getEndPos() → QPointF¶

class schrodinger.protein.helm.helm_renderer.DisulfideConnectorMixin(connector: HelmConnector, parent=None)¶

Bases: ArrowheadConnectorMixin

Mixin for representing disulfide bridges.

__init__(connector: HelmConnector, parent=None)¶

getStartPos() → QPointF¶

getEndPos() → QPointF¶

class schrodinger.protein.helm.helm_renderer.DisulfideLinearConnectorItem(connector: HelmConnector, parent=None)¶

Bases: DisulfideConnectorMixin, PolylineHelmConnectorItem

Graphics Item representing disulfide bridges between two amino acids that have been laid out in a linear arrangement.

class schrodinger.protein.helm.helm_renderer.DisulfideCyclicConnectorItem(connector: HelmConnector, parent=None)¶

Bases: DisulfideConnectorMixin, LineHelmConnectorItem

Graphics Item representing disulfide bridges between two amino acids that have been laid out in a cyclic arrangement, in which the bridge closes the cycle.

class schrodinger.protein.helm.helm_renderer.NABackboneConnectorItem(connector: HelmConnector, parent=None)¶

Bases: LineHelmConnectorItem

Graphics Item representing backbone connections between nucleotides.

class schrodinger.protein.helm.helm_renderer.NABackboneBaseConnectorItem(connector: HelmConnector, parent=None)¶

Bases: LineHelmConnectorItem

Graphics Item representing a connection between a nucleotide backbone and base.

class schrodinger.protein.helm.helm_renderer.NABaseConnectorItem(connector: HelmConnector, parent=None)¶

Bases: LineHelmConnectorItem

Graphics Item representing a connection between two base pairs.

class schrodinger.protein.helm.helm_renderer.ChemConnectorItem(connector: HelmConnector, parent=None)¶

Bases: LineHelmConnectorItem

Catchall class for all connectors where one or both endpoints is a Chem (non-peptide, non-nucleotide) element.

schrodinger.protein.helm.helm_renderer.connector_item_factory(connector: HelmConnector) → QAbstractGraphicsShapeItem¶

Implement logic specifying different graphical styles (implemented by each child class) for a connector.

Parameters:: connector – Connector properties, determined by HelmScene.getConnectorData.
Returns:: Graphics item to be added to the current QtWidgets.QGraphicsScene.

class schrodinger.protein.helm.helm_renderer.HelmScene¶

Bases: QGraphicsScene

Scene object for rendering a helm molecule

__init__()¶

setHelmMolecule(helm_mol: Mol)¶

Set the helm molecule to render and add bond and monomer representations to the scene.

Parameters:

helm_mol – Helm data represented by a 2D coarse-grained molecule.
fallback_entity – entity class to use for a fallback image

getMonomerData(monomer: Atom) → Tuple[int, HelmMonomer]¶

Compute the properties of monomer needed for the logic that determines its graphical representation: the HelmMonomerItemMixin child class that monomer_item_factory should dispatch to.

Parameters:: monomer – Representation of the monomer in the input rdkit molecule.
Returns:: 2-tuple of the index of the monomer in the conformer object and a HelmMonomer object with the needed properties.

getConnectorData(bond: Bond, monomer_lookup: dict) → HelmConnector¶

Compute the properties of bond needed for the logic that determines its graphical representation: the HelmConnectorItemMixin child class that connector_item_factory should dispatch to.

Parameters:

bond – Representation of the connector in the input rdkit molecule.
monomer_lookup – A dict mapping the monomer’s index in the conformer to its HelmMonomer representation.

Returns:

A HelmConnector object with the needed properties.

class schrodinger.protein.helm.helm_renderer.HelmWidget(helm_mol: Optional[Mol] = None, *args, **kwargs)¶

Bases: QWidget

A widget which creates a visual representation of a coarse-grained 2D helm molecule

__init__(helm_mol: Optional[Mol] = None, *args, **kwargs)¶

setViewSize(size)¶: Set view size to requested width and height and rescale to show the entire scene :param size: the requested size in pixels

getScaleFactor(size: QSizeF) → float¶

Get the scaling factor to make a view of the requested width and height: fit the scene

Parameters:: size – width and height of the view
Returns:: Factor by which to rescale the view