schrodinger.ui.qt.structure2d module¶
2D structures drawing
- schrodinger.ui.qt.structure2d.get_qpicture_protected(renderer, chmmol, gen_coord=True)¶
Generate a QPicture for the given molecule. If the picture couldn’t be generated (e.g. the molecule is too large), then a QPicture will contain the failure message text.
- Parameters
renderer (Chm2DRenderer intance) – The renderer to use for generating the QPicture
chmmol (ChmMol instance.) – Structure to generate the picture for.
gen_coord (bool) – if True (default) generate new coordinates; if False, use existing 2D coordinates.
- Return type
QPicture
- Returns
The generated picture.
- schrodinger.ui.qt.structure2d.generate_qimage_from_chmmol(chmmol, width, height, renderer=None, bg_color=None, max_scale=None, gen_coord=True)¶
“Generate a 2D image in QImage format of a ChmMol molecule.”
- Parameters
chmmol (ChmMol instance.) – Structure to generate the picture for.
width (int) – width in pixels of the generated QImage.
height (int) – height in pixels of the generated QImage.
renderer (Chm2DRenderer intance or None) – The renderer to use for generating the QImage. If None, a new renderer will be created.
bg_color (PyQt5.QtGui.QColor or None) – background color filling the image around the scaled molecule.
max_scale (float or None) – maximum scaling of the structure image.
gen_coord (bool) – if True (default) generate new coordinates; if False, use existing 2D coordinates.
- Return type
QImage
- Returns
The generated QImage.
- schrodinger.ui.qt.structure2d.generate_qimage_from_structure(st, width, height, renderer=None, bg_color=None, max_scale=None, stereo_mode=StereoType.StereoFromAnnotationAndGeometry_Safe, gen_coord=True)¶
Generate a 2D image in QImage format of a schrodinger.structure.Structure. An intermediate ChmMol will be generated with stereochemstry deduced according to the stereo_mode parameter.
- Parameters
st (Structure instance.) – Structure to generate the picture for.
width (int) – width in pixels of the generated QImage.
height (int) – height in pixels of the generated QImage.
renderer (Chm2DRenderer intance or None) – The renderer to use for generating the QImage.
bg_color (PyQt5.QtGui.QColor or None) – background color filling the image around the scaled molecule.
max_scale (float or None) – maximum scaling of the structure image.
stereo_mode (schrodinger.infra._canvas2d.ChmMmctAdaptor.StereoType) – stereo source for internal transformation to ChmMol.
gen_coord (bool) – if True generate coordinates for chmmol.
- Return type
QImage
- Returns
The generated QImage.
- schrodinger.ui.qt.structure2d.get_qpicture_highlight(renderer, chmmol, atoms, bonds, color, gen_coord=False)¶
Generate a QPicture for the given molecule and highlight given atoms and bonds. If the picture couldn’t be generated (e.g. the molecule is too large), then a QPicture will contain the failure message text.
- Parameters
renderer (Chm2DRenderer intance) – The renderer to use for generating the QPicture
chmmol (ChmMol instance.) – Structure to generate the picture for.
atoms (list) – list of atoms that should be highlighted
bonds (list) – list of bonds that should be highlighted
color (
QtGui.QColor
) – color that is used to highlight atoms and bondsgen_coord (bool) – if True generate coordinates.
- Return type
QPicture
- Returns
The generated picture.
- schrodinger.ui.qt.structure2d.get_chmmol_bonds_from_atoms(chmmol, atoms)¶
This function returns a list of bonds that connect atoms in a given list.
- Parameters
chmmol (
canvas2d.ChmMol
) – molecule structureatoms (list) – list of atom indices
- schrodinger.ui.qt.structure2d.get_aligned_pictures(sts, renderer=None, atomTyping=11, core_color=None)¶
Calculate the maximum common substructure (MCS) between the given ligands, and generate 2D images, aligned by the core. If no MCS was detected, the images will be unaligned.
NOTE: This function becomes exponentioally slow with larger number of structures. Recommened maximum around 30 structures.
- Parameters
sts (Iterable of
structure.Structure
objects) – Structures to averagerenderer (Chm2DRenderer intance) – The renderer to use for generating the QPicture (optional)
atomTyping (int) – Atom typing scheme to use. Default is 11. For list of available schemes, see $SCHRODINGER/utilities/canvasMCS -h
highlight_color – Optional Color to highlight the common substructure.
- Return type
List of
QPicture
objects.- Returns
QPictures for the aligned 2D images.
- schrodinger.ui.qt.structure2d.get_ligand(st)¶
Return a substructure that can be rendered in a 2D image (the first ligand in
st
, unless it’s also has too many atoms).- Parameters
st (structure.Structure) – the structure
- Returns
the ligand structure or None if the structure has too many atoms
- Return type
structure.Structure or None
- class schrodinger.ui.qt.structure2d.StructurePicture(parent=None, layout=None, height=200, width=200, background='white', annotators=None)¶
Bases:
PyQt6.QtWidgets.QLabel
This is the label that normally stores the picture of the molecule. It can also store a text message.
We make sure that this stays the same size, no matter what data (if any) is stored in it.
- __init__(parent=None, layout=None, height=200, width=200, background='white', annotators=None)¶
- Parameters
parent (QWidget) – the widget that owns this widget
layout (QLayout) – The layout that this widget should be placed in
height (int) – the height of this label in pixels
width (int) – the width of this label in pixels
annotators (list) – Each item of the list should be a
canvas2d.ChemViewAnnotator
object that will be applied to thecanvas2d.ChmRender2DModel
when generating the image
- sizeHint(self) QSize ¶
- drawStructure(structure, StereoType=StereoType.StereoFromAnnotationAndGeometry_Safe, hydrogenTreatment=H.H_ExplicitOnly, wantProperties=True, wantMMStereoProps=True, readAtomBondProperties=True, allowRadicals=False)¶
Makes a 2-D rendering of the structure
- Parameters
structure (schrodinger.structure.Structure class object) – structure to be drawn on the canvas
StereoType (canvas2d.ChmMmctAdaptor.StereoType) – Stereochemistry option to use. Available options: # Does not include stereochemistry info: canvas2d.ChmMmctAdaptor.NoStereo # Ignores mmstereo annotations: canvas2d.ChmMmctAdaptor.StereoFromGeometry # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromGeometry_Safe # Ignores 3d geometry: canvas2d.ChmMmctAdaptor.StereoFromAnnotation # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromAnnotation_Safe # Uses mmstereo annotaions with 3D geometry as a backup: canvas2d.ChmMmctAdaptor.StereoFromAnnotationAndGeometry # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromAnnotationAndGeometry_Safe
hydrogenTreatment (canvas2d.ChmAtomOption.H) – Hydrogen treatment method. Available options: canvas2d.ChmAtomOption.H_Never canvas2d.ChmAtomOption.H_ExplicitOnly canvas2d.ChmAtomOption.H_Polar canvas2d.ChmAtomOption.H_ExplicitPolar canvas2d.ChmAtomOption.H_Chiral canvas2d.ChmAtomOption.H_ExplicitChiral canvas2d.ChmAtomOption.H_ExplicitPolarAndChiral canvas2d.ChmAtomOption.H_All
wantProperties (bool) – Whether properties should be copied.
wantMMStereoProps (bool) – Whether to copy mmstereo properties.
readAtomBondProperties (bool) – Whether to copy atom and bond-level properties.
allowRadicals (bool) – Whether to assume that valence deficiencies represent unpaired electrons.
- drawChmmol(chmmol, atoms=[], bonds=[], color=<PyQt6.QtGui.QColor object>, gen_coord=False)¶
Makes a 2-D rendering of the chmmol object with optional atoms and bonds highlighting.
- Parameters
chmmol (ChmMol instance.) – Structure to generate the picture for.
atoms (list) – list of atoms that should be highlighted
bonds (list) – list of bonds that should be highlighted
color (
QtGui.QColor
) – color that is used to highlight atoms and bondsgen_coord (bool) – if True generate coordinates.
- drawRDMol(mol)¶
Draws the given RDKit molecule.
- Parameters
mol (Chem.rdchem.Mol) – structure to be drawn
- setAnnotators(annotators)¶
This function allows to reset annotators between renderning 2-D structures.
- Parameters
annotators (list) – Each item of the list should be a
canvas2d.ChemViewAnnotator
object that will be applied to thecanvas2d.ChmRender2DModel
when generating the image
- class schrodinger.ui.qt.structure2d.StructureToolTip(structure=None, offset=(10, 10), global_position=None, height=200, width=200, **kwargs)¶
Bases:
schrodinger.ui.qt.structure2d.StructurePicture
A tooltip that shows a chemical structure
- __init__(structure=None, offset=(10, 10), global_position=None, height=200, width=200, **kwargs)¶
- Parameters
structure (structure object that canvas2d.ChmMmctAdaptor.create() accepts.) – the structure to draw in the cell. This can be given at instantiation time if the structure will always be the same, or it can be given a show time if the structure will change dynamically.
offset (tuple(int, int)) – x and y pixel offset from the mouse pointer position to draw the upper left corner of the tooltip window
global_position (tuple(int, int)) – global position relative to the screen to to draw the upper left corner of the tooltip window. This parameter overrides the offset parameter.
height (int) – the height of this tooltip in pixels
width (int) – the width of this tooltip in pixels
This class is designed to be created once and shown/hidden as often as needed. However, there seems to be an issue with PyQt that eventually (in an unreproducible fashion) the tooltip window may simply showing up. It will claim to be visible with self.isVisible() and return the full window size using self.visibleRegion(), but it won’t be visible. Therefore it is probably best to create a new instance each time. Instances of this class are lightweight, quick to create, and garbage collect without any apparent memory leaks.
- protein_present_image = None¶
- paintEvent(event)¶
Reimplmented the paint event to draw text on top of the image, using the value of self.top_left_text
- setOffset(offset)¶
Sets the x and y offset in pixels of the tooltip from the mouse pointer
- Parameters
offset (tuple(int, int)) – x and y pixel offset from the mouse pointer position to draw the upper left corner of the tooltip window
- setGlobalPosition(global_position)¶
Sets the x and y global position relative to the screen at which to draw the top left corner of the tooltip window.
- Parameters
global_position (tuple(int, int)) – global position relative to the screen to draw the upper left corner of the tooltip window. This parameter overrides the offset parameter.
- show(structure=None, pic=None, top_left_text=None)¶
Show the tooltip
- Parameters
structure (structure object that canvas2d.ChmMmctAdaptor.create() accepts.) – the structure to draw in the cell. This can be given at instantiation time if the structure will always be the same, or it can be given a show time if the structure will change dynamically.
- finish()¶
Hide ourselves. This slot should be connected to a signal that is emitted when the parent widget receives a leaveEvent, or called directly from the widget’s leaveEvent routine.
Don’t destroy ourselves here even if we are being used in one-time use mode, because bus errors can result if we are created/destroyed in too short a timeframe - as can happen with tooltips.
- class schrodinger.ui.qt.structure2d.LabeledStructureToolTip(structure=None, offset=(2, 16), global_position=None, height=200, width=200, **kwargs)¶
Bases:
PyQt6.QtWidgets.QFrame
Class that creates a tooltip with a 2d structure picture. An arbitrary number of labels can be added that will be displayed beneath the picture.
- __init__(structure=None, offset=(2, 16), global_position=None, height=200, width=200, **kwargs)¶
- Parameters
structure (
structure.Structure
,Chem.rdchem.Mol
, orcanvas2d.ChmMol
) – the structure to draw in the cell. This can be given at instantiation time if the structure will always be the same, or it can be given a show time if the structure will change dynamically.offset (tuple of 2 ints) – x and y pixel offset from the mouse pointer position to draw the upper left corner of the tooltip window
global_position (tuple of 2 ints) – global position relative to the screen to to draw the upper left corner of the tooltip window. This parameter overrides the offset parameter.
height (int) – the height of this tooltip in pixels
width (int) – the width of this tooltip in pixels
- draw2DPicture(structure)¶
Draws 2D picture of the structure.
- Parameters
structure (
structure.Structure
,Chem.rdchem.Mol
, orcanvas2d.ChmMol
) – Structure to draw
- setGlobalPosition(global_position)¶
Sets the x and y global position relative to the screen at which to draw the top left corner of the tooltip window.
- Parameters
global_position (tuple(int, int)) – global position relative to the screen to draw the upper left corner of the tooltip window. This parameter overrides the offset parameter.
- show(structure=None)¶
Show the tooltip
- Parameters
structure (
structure.Structure
,Chem.rdchem.Mol
, orcanvas2d.ChmMol
) – the structure to draw in the cell. This can be given at instantiation time if the structure will always be the same, or it can be given a show time if the structure will change dynamically.
- addLabel(text)¶
Add a label containing the specified text underneath the structure picture.
- Parameters
text (str) – Text to be included in the label
- class schrodinger.ui.qt.structure2d.structure_scene¶
Bases:
PyQt6.QtWidgets.QGraphicsScene
Scene which holds the structure_view object
- class schrodinger.ui.qt.structure2d.structure_view(scene)¶
Bases:
PyQt6.QtWidgets.QGraphicsView
View which holds a structure_item object
- atom_clicked¶
pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL
types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.
- bond_clicked¶
pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL
types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.
- __init__(scene)¶
- wheelEvent(self, event: QWheelEvent)¶
- resizeEvent(self, event: QResizeEvent)¶
- class schrodinger.ui.qt.structure2d.structure_item(rect=None)¶
Bases:
PyQt6.QtWidgets.QGraphicsItem
- __init__(rect=None)¶
- Parameters
rect (QRectF) – Size of the rect of the bounding box.
- boundingRect(self) QRectF ¶
- clear()¶
Clear picture from item.
- generate_picture(gen_coord=True)¶
Generates a QPicture of the structure. This should be called after setting the structure and the accompaning annotators.
- Parameters
gen_coord (bool) – if True generate coordinates.
- paint(painter, option, widget=0)¶
Overrides the paint function to draw the picture that has already been generated. This should never be called manually.
- set_colormap(colormap)¶
Sets the colormap for the atom and bond coloring. Otherwise, the coloring used will be that coming from the ct and/or chmmol.
- set_structure(struct, StereoType=StereoType.StereoFromAnnotationAndGeometry_Safe, hydrogenTreatment=H.H_ExplicitOnly, wantProperties=True, wantMMStereoProps=True, readAtomBondProperties=True, allowRadicals=False)¶
Set the structure to the given Structure object.
- Parameters
struct (schrodinger.structure.Structure class object) – structure to be drawn on the canvas
StereoType (ChmMmctAdaptor.StereoType) – Stereochemistry option to use. Avialable options: # Does not include stereochemistry info: canvas2d.ChmMmctAdaptor.NoStereo # Ignores mmstereo annotations: canvas2d.ChmMmctAdaptor.StereoFromGeometry # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromGeometry_Safe # Ignores 3d geometry: canvas2d.ChmMmctAdaptor.StereoFromAnnotation # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromAnnotation_Safe # Uses mmstereo annotaions with 3D geometry as a backup: canvas2d.ChmMmctAdaptor.StereoFromAnnotationAndGeometry # Silently ignores stereo information that Canvas doesn’t agree with: canvas2d.ChmMmctAdaptor.StereoFromAnnotationAndGeometry_Safe
hydrogenTreatment (canvas2d.ChmAtomOption.H) – Hydrogen treatment method. canvas2d.ChmAtomOption.H_Never canvas2d.ChmAtomOption.H_ExplicitOnly canvas2d.ChmAtomOption.H_Polar canvas2d.ChmAtomOption.H_ExplicitPolar canvas2d.ChmAtomOption.H_Chiral canvas2d.ChmAtomOption.H_ExplicitChiral canvas2d.ChmAtomOption.H_ExplicitPolarAndChiral canvas2d.ChmAtomOption.H_All
wantProperties (bool) – Whether properties should be copied.
wantMMStereoProps (bool) – Whether to copy mmstereo properties.
readAtomBondProperties (bool) – Whether to copy atom and bond-level properties.
allowRadicals (bool) – Whether to assume that valence deficiencies represent unpaired electrons.
- set_rect(rect)¶
- Parameters
rect (QRect) – size of bounding box
- set_text(text, alignment=None)¶
Sets text in the view. This is useful if you display text in place of a structure, in places where no structure is available.
- Parameters
text (string) – text to be displayed
alignment (Qt.AlignmentFlags) – alignment flags of text, defaults to QtCore.Qt.AlignVCenter|QtCore.Qt.AlignCenter
- add_annotator(annotator)¶
Adds annotator to stack. The order that these functions get added is the order that they will be applied to the picture.
- Parameters
annotator (schrodinger.infra.canvas2d.ChemViewAnnotator) – Annotator which draws on top an image
- add_annotator_function_return(function)¶
Add functions that need to get returned after the structure is rendered on the screen. An example of this would be a function that returns drawmol coordinates.
- clear_annotators()¶
Clears all annotators
- mousePressEvent(event)¶
Emit a signal if the user left-clicked on an atom or a bond
- getBondAtLocation(pos)¶
Return the bond at the specified coordinates
- Parameters
pos (
PyQt5.QtCore.QPoint
) – The specified coordinates- Returns
If there is a bond at the specified coordinates, return a list of the chmmol atom indices for the two bound atoms. (Note that the chmmol atom indices are zero-indexed, so you should add one to each index if you want the
schrodinger.structure.Structure
atom indices). If there is no bond at the specified coordinates, return an empty list.- Return type
list
- class schrodinger.ui.qt.structure2d.ColoredArrowAnnotator(mol, bond_info=None, draw_arrowhead=True)¶
Bases:
schrodinger.infra._canvas2d.ChemViewAnnotator
This annotator allows you to add colored arrows to bonds in 2d renderings.
This is a slightly less terrible port from C++. Most of the logic still keeps C++-style syntax, simply because rewriting it is not worth the effort. The interface is now more pythonic, at least.
- __init__(mol, bond_info=None, draw_arrowhead=True)¶
- Parameters
mol – is a chmmol
bond_info – is a list containing individual lists of: (atom1, atom2, outlined, QColor)
These lists are composed of:
atom1 is a ct-atom index
atom2 is a ct-atom index
outlined (0/1) is whether you want the arrow to have a black outline
qc is a qcolor for the bond
- add_bond_arrow(atom1, atom2, outlined, qc)¶
atom1 is a ct-atom index atom2 is a ct-atom index outlined (0/1) is whether you want the arrow to have a black outline qc is the qcolor of the bond
- clear_bond_arrows()¶
Clear all bond markers in this annotator
- annotate(view, dm)¶
This function annotates the specified arrows.
- class schrodinger.ui.qt.structure2d.CgCoreAnnotator(bond_info, colors, atoms, atomColors, mol)¶
Bases:
schrodinger.ui.qt.structure2d.ColoredArrowAnnotator
This is the original ColoredArrowAnnotator class name. When that class had the format of its input changed, it became incompatible with the original class.
This class will remain to preserve backwards compatability.
- __init__(bond_info, colors, atoms, atomColors, mol)¶
bond_info is a list of size 3N, (atom1 idx, a2 idx, outline) colors is a list of size 3N (R, G, B) atoms/atomColors are deprecated mol is a chmmol
- class schrodinger.ui.qt.structure2d.BaseSquareAnnotator¶
Bases:
schrodinger.infra._canvas2d.ChemViewAnnotator
Base class for annotators that draw a square around atoms
- annotate(view, dm)¶
Add this sphere to the list of things in the picture
- Parameters
view (Chemview) – the View this item goes in
dm (ChmDrawMol) – object that contains the list of atom and bond graphics
- class schrodinger.ui.qt.structure2d.RedSquareAnnotator(atom=None, size=100, color=GlobalColor.red)¶
Bases:
schrodinger.ui.qt.structure2d.BaseSquareAnnotator
Create a square around the specified atom.
- __init__(atom=None, size=100, color=GlobalColor.red)¶
Instantiate a RedSquareAnnotator instance.
- Parameters
atom (int) – the atom number to which square applies. Note that this expects the first atom to be atom 1, not 0.
size (float) – the size of one side of the square in pixels.
color (QColor) – the color used to draw annotator. Default is red.
- setAtom(atom, color=None)¶
Set the atom number to which the square applies
- Parameters
atom (int) – the atom number to which square applies. Note that this expects the first atom to be atom 1, not 0. If 0 is passed in, no atom will be annotated.
color (QColor) – the color used to draw annotator. If not given, the previously set color for this annotator will be used.
- clearAtom()¶
Remove the current atom so no atoms are annotated
- getAtom()¶
Return the atom index current annotated
- Return type
int or None
- Returns
The index (1-based) of the atom annotated, or None if no atoms are annotated
- setColor(color)¶
Set the color of the square
- Parameters
color (QColor) – the color used to draw annotator.
- class schrodinger.ui.qt.structure2d.MultiSquareAnnotator(atom_dict, size=100)¶
Bases:
schrodinger.ui.qt.structure2d.BaseSquareAnnotator
Create a square around each specified atom.
- __init__(atom_dict, size=100)¶
Instantiate a MultiSquareAnnotator instance.
- Parameters
atom_dict (dict) – A dictionary of {atom number: QColor} specifying the appropriate color for each atom
size (float) – The size of one side of the square in pixels. Defaults to 100 pixels.
- class schrodinger.ui.qt.structure2d.AtomNumberAnnotator¶
Bases:
schrodinger.infra._canvas2d.ChemViewAnnotator
Show the atom number of each atom rather than a vertex or atomic symbol
- annotate(view, dm)¶
Add atom number to each atom
- Parameters
view (Chemview) – the View this item goes in
dm (ChmDrawMol) – object that contains the list of atom and bond graphics
- class schrodinger.ui.qt.structure2d.AtomLabelAnnotator(atom_labels)¶
Bases:
schrodinger.infra._canvas2d.ChemViewAnnotator
Changes the label displayed for an atom. The label can have subscripts.
- __init__(atom_labels)¶
Instantiate a AtomLabelAnnotator instance.
- Parameters
atom_labels (dict) – A dictionary of {atom number: label} specifying the label for each atom to be custom labeled. Each label may either be a string or a (str, str) tuple. In the latter case, the first string is the main label and the second string is the subscript. Note the atom numbers used here should be 1-based (first atom number = 1)
- annotate(view, drawmol)¶
Add a label to each atom specified in the atom_labels property
- Parameters
view (Chemview) – the View this item goes in
drawmol (ChmDrawMol) – object that contains the list of atom and bond graphics
- class schrodinger.ui.qt.structure2d.CircleAnnotator(atom=None, radius=75.0, color=GlobalColor.green, gradient=False, fill=False, width=4)¶
Bases:
schrodinger.infra._canvas2d.ChemViewAnnotator
Creates a circle behind one or more atoms.
- __init__(atom=None, radius=75.0, color=GlobalColor.green, gradient=False, fill=False, width=4)¶
Instantiate a ColorCircleAnnotator instance.
- Parameters
atom (int) – the atom number to which radius applies. Note that this expects the first atom to be atom 1, not 0.
radius (float) – the radius of the sphere in pixels. Default is 75.
color (QColor) – The color of the circle fill
gradient (bool) – If True, the circle is filled with a gradient that goes from white at the center to the defined color. gradient is exclusive with fill.
fill (bool) – If True, the circle is given a constant fill. fill is exclusive with gradient.
width (int) – The width of the pen if fill and gradient are both False. Default is 4.
- addAtom(atom_num, radius=None, color=None)¶
Add another sphere to this annotator
- Parameters
atom_num (int) – the atom number to which radius applies. Note that this expects the first atom to be atom 1, not 0.
radius (float) – the radius of the sphere in pixels. If not given, the radius given at the time of instance creation is used.
color (QColor) – The color of the circle fill. If not given, the color given at the time of instance creation is used.
- removeAtom(atom_num)¶
Remove an atom from the annotator
- Parameters
atom_num (int) – the atom number to which radius applies. Note that this expects the first atom to be atom 1, not 0.
- clearAtoms()¶
Remove all atoms from the annotator
- setColor(color, reset_colors=False)¶
Set the default color for this annotator
- Parameters
color (QColor) – The color of the circle fill.
reset_colors (bool) – If True, all existing circles will have their color reset to this value
- setRadius(radius, reset_radii=False)¶
Set the default radius for this annotator
- Parameters
radius (float) – The radius of the circle
reset_radii (bool) – If True, all existing circles will have their radius reset to this value
- annotate(view, dm)¶
Add this sphere to the list of things in the picture
- Parameters
view (Chemview) – the View this item goes in
dm (ChmDrawMol) – object that contains the list of atom and bond graphics