schrodinger.protein.helm.helm_renderer module¶
- class schrodinger.protein.helm.helm_renderer.HexColor(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.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(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.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: rdkit.Chem.rdchem.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: schrodinger.protein.helm._helm_parser.PolymerType, is_branch: bool, is_smiles: bool, position: PyQt6.QtCore.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: PyQt6.QtGui.QFont.Weight = Weight.Normal, color: schrodinger.protein.helm.helm_renderer.HexColor = HexColor.Black, parent=None)¶
Bases:
PyQt6.QtWidgets.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: PyQt6.QtGui.QFont.Weight = Weight.Normal, color: schrodinger.protein.helm.helm_renderer.HexColor = HexColor.Black, parent=None)¶
- class schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin(monomer: schrodinger.protein.helm.helm_renderer.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: schrodinger.protein.helm.helm_renderer.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: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin
,PyQt6.QtWidgets.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: QPainter, option: QStyleOptionGraphicsItem, widget: Optional[QWidget] = None)¶
- class schrodinger.protein.helm.helm_renderer.StandardAminoAcidMonomerItem(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.AminoAcidMonomerBase
- class schrodinger.protein.helm.helm_renderer.DAminoAcidMonomerItem(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.AminoAcidMonomerBase
- DEFAULT_X_RADIUS = 16.0¶
- class schrodinger.protein.helm.helm_renderer.OtherAminoAcidMonomerItem(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.AminoAcidMonomerBase
- class schrodinger.protein.helm.helm_renderer.BBPhosphateMonomerBase(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin
,PyQt6.QtWidgets.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: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.BBPhosphateMonomerBase
- class schrodinger.protein.helm.helm_renderer.BBModifiedPhosphateMonomerItem(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.BBPhosphateMonomerBase
- class schrodinger.protein.helm.helm_renderer.BBSugarMonomerBase(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin
,PyQt6.QtWidgets.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: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.BBSugarMonomerBase
- class schrodinger.protein.helm.helm_renderer.BBModifiedSugarMonomerItem(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.BBSugarMonomerBase
- class schrodinger.protein.helm.helm_renderer.NABaseMonomerBase(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin
,PyQt6.QtWidgets.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[PyQt6.QtCore.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: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.NABaseMonomerBase
- class schrodinger.protein.helm.helm_renderer.NAUnnaturalBaseMonomerItem(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.NABaseMonomerBase
- class schrodinger.protein.helm.helm_renderer.ChemMonomerItem(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomer)¶
Bases:
schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin
,PyQt6.QtWidgets.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: schrodinger.protein.helm.helm_renderer.HelmMonomer) schrodinger.protein.helm.helm_renderer.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: schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin, end: schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin, is_cyclic: bool = True)¶
Bases:
object
- is_cyclic: bool = True¶
- getMonomers() Tuple[schrodinger.protein.helm.helm_renderer.HelmMonomer, schrodinger.protein.helm.helm_renderer.HelmMonomer] ¶
Convenience function returning a 2-tuple of the (start, end) monomer definitions.
- getMonomerTypes() Tuple[schrodinger.protein.helm._helm_parser.PolymerType, schrodinger.protein.helm._helm_parser.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: schrodinger.protein.helm._helm_parser.PolymerType¶
Determine the
PolymerType
of the connector, based on thePolymerType
of the two monomers it connects.
- __init__(start: schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin, end: schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin, is_cyclic: bool = True) None ¶
- class schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
object
Base class for all connectors.
- __init__(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
- getStartPos() PyQt6.QtCore.QPointF ¶
- getEndPos() PyQt6.QtCore.QPointF ¶
- setup() None ¶
- class schrodinger.protein.helm.helm_renderer.LineHelmConnectorItem(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin
,PyQt6.QtWidgets.QGraphicsLineItem
Base class for all connectors rendered as a straight line.
- setup() None ¶
- class schrodinger.protein.helm.helm_renderer.PolylineHelmConnectorItem(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.HelmConnectorItemMixin
,PyQt6.QtWidgets.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: PyQt6.QtCore.QPointF) PyQt6.QtWidgets.QAbstractGraphicsShapeItem ¶
- getArrowheadPos(monomer: schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin, other_monomer: schrodinger.protein.helm.helm_renderer.HelmMonomerItemMixin) PyQt6.QtCore.QPointF ¶
Logic for determining where the arrowhead should be attached to
monomer
, given that the other end of the connector is attached toother_monomer
. Returns a position in the global QGraphicsScene coordinate system.
- class schrodinger.protein.helm.helm_renderer.AALinearConnectorItem(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.LineHelmConnectorItem
Graphics Item representing a non-branching connector between two amino acids.
- class schrodinger.protein.helm.helm_renderer.AABranchingConnectorItem(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.ArrowheadConnectorMixin
,schrodinger.protein.helm.helm_renderer.LineHelmConnectorItem
Graphics Item representing a branching connector between two amino acids.
- __init__(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
- getStartPos() PyQt6.QtCore.QPointF ¶
- getEndPos() PyQt6.QtCore.QPointF ¶
- class schrodinger.protein.helm.helm_renderer.DisulfideConnectorMixin(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.ArrowheadConnectorMixin
Mixin for representing disulfide bridges.
- __init__(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
- getStartPos() PyQt6.QtCore.QPointF ¶
- getEndPos() PyQt6.QtCore.QPointF ¶
- class schrodinger.protein.helm.helm_renderer.DisulfideLinearConnectorItem(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.DisulfideConnectorMixin
,schrodinger.protein.helm.helm_renderer.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: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.DisulfideConnectorMixin
,schrodinger.protein.helm.helm_renderer.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: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.LineHelmConnectorItem
Graphics Item representing backbone connections between nucleotides.
- class schrodinger.protein.helm.helm_renderer.NABackboneBaseConnectorItem(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.LineHelmConnectorItem
Graphics Item representing a connection between a nucleotide backbone and base.
- class schrodinger.protein.helm.helm_renderer.NABaseConnectorItem(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.LineHelmConnectorItem
Graphics Item representing a connection between two base pairs.
- class schrodinger.protein.helm.helm_renderer.ChemConnectorItem(connector: schrodinger.protein.helm.helm_renderer.HelmConnector, parent=None)¶
Bases:
schrodinger.protein.helm.helm_renderer.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: schrodinger.protein.helm.helm_renderer.HelmConnector) PyQt6.QtWidgets.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.HelmFallbackImage(entity_class: schrodinger.livedesign.entity_type.EntityClass)¶
Bases:
PyQt6.QtSvgWidgets.QGraphicsSvgItem
GraphicsItem for the stock image (in .svg format) shown when the input polymer is too complex to display in detail, as measured by N_MONOMER_MAX
- __init__(entity_class: schrodinger.livedesign.entity_type.EntityClass)¶
- class schrodinger.protein.helm.helm_renderer.HelmScene¶
Bases:
PyQt6.QtWidgets.QGraphicsScene
Scene object for rendering a helm molecule
- __init__()¶
- setHelmMolecule(helm_mol: rdkit.Chem.rdchem.Mol, fallback_entity: Optional[schrodinger.livedesign.entity_type.EntityClass])¶
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: rdkit.Chem.rdchem.Atom) Tuple[int, schrodinger.protein.helm.helm_renderer.HelmMonomer] ¶
Compute the properties of
monomer
needed for the logic that determines its graphical representation: theHelmMonomerItemMixin
child class thatmonomer_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: rdkit.Chem.rdchem.Bond, monomer_lookup: dict) schrodinger.protein.helm.helm_renderer.HelmConnector ¶
Compute the properties of
bond
needed for the logic that determines its graphical representation: theHelmConnectorItemMixin
child class thatconnector_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[rdkit.Chem.rdchem.Mol] = None, fallback_entity: Optional[schrodinger.livedesign.entity_type.EntityClass] = None, *args, **kwargs)¶
Bases:
PyQt6.QtWidgets.QWidget
A widget which creates a visual representation of a coarse-grained 2D helm molecule
- __init__(helm_mol: Optional[rdkit.Chem.rdchem.Mol] = None, fallback_entity: Optional[schrodinger.livedesign.entity_type.EntityClass] = 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: PyQt6.QtCore.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