rdkit.Chem.Draw.rdMolDraw2D module

Module containing a C++ implementation of 2D molecule drawing

class rdkit.Chem.Draw.rdMolDraw2D.ContourParams(self)

Bases: object

Parameters for drawing contours

property colourMap

the color map to use when filling the grid

property contourColour

the color to use for drawing the contours

property contourWidth

line width of the contours

property coordScaleForQuantization

scaling factor used to convert coordinates to ints when forming the continuous lines

property dashNegative

use a dashed line for negative contours

property drawAsLines

draw the contours as continuous lines isntead of line segments

property extraGridPadding

extra space (in molecule coords) around the grid

property fillGrid

colors the grid in addition to drawing contours

property fillThreshold

magnitude threshold to determine if a grid point is filled

property fillThresholdIsFraction

if true, fillThreshold is a fraction of the range of the data

property gridResolution

set the resolution of the grid

property isovalScaleForQuantization

scaling factor used to convert isovalues to ints when forming the continuous lines

setColourMap(self, colours: object) → None

setContourColour(self, colour: tuple) → None

property setScale

set the scale of the drawing object (useful if you draw the grid/contours first)

property useFillThreshold

use a magnitude threshold to determine if a grid point is filled

class rdkit.Chem.Draw.rdMolDraw2D.DrawElement(*values)

Bases: IntEnum

ALL = 2147483647

ANNOTATIONS = 16

ATOMLABELS = 4

BONDS = 2

HIGHLIGHTS = 8

NONE = 0

POSTSHAPES = 64

PRESHAPES = 1

RADICALS = 32

class rdkit.Chem.Draw.rdMolDraw2D.IntStringMap

Bases: object

class rdkit.Chem.Draw.rdMolDraw2D.LegendPosition(*values)

Bases: Enum

Bottom = 0

Left = 2

Right = 3

Top = 1

class rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D

Bases: object

Drawer abstract base class

ClearDrawing(self) → None

clears the drawing by filling it with the background color

DrawArc(self, center: rdkit.Geometry.rdGeometry.Point2D, radius: float, angle1: float, angle2: float, rawCoords: bool = False) → None

draws an arc with the current drawing style. The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels. The angles are in degrees; angle2 should be > angle1.

DrawArrow(self, cds1: rdkit.Geometry.rdGeometry.Point2D, cds2: rdkit.Geometry.rdGeometry.Point2D, asPolygon: bool = False, frac: float = 0.05, angle: float = 0.5235987755982988, color: object | None = None, rawCoords: bool = False) → None

draws an arrow with the current drawing style. The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels. If asPolygon is true the head of the arrow will be drawn as a triangle, otherwise two lines are used. The fraction of the arrow length to use for the head is given by frac. The angle of the arrowhead (the angle between the main line and each arrowhead line) is given by angle. The color is a tuple of 3 floats (0-1) in red, green, blue (RGB) order.

DrawAttachmentLine(self, cds1: rdkit.Geometry.rdGeometry.Point2D, cds2: rdkit.Geometry.rdGeometry.Point2D, color: tuple, len: float = 1.0, nSegments: int = 16, rawCoords: bool = False) → None

draw a line indicating the presence of an attachment point (normally a squiggle line perpendicular to a bond). The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

DrawEllipse(self, cds1: rdkit.Geometry.rdGeometry.Point2D, cds2: rdkit.Geometry.rdGeometry.Point2D, rawCoords: bool = False) → None

draws a triangle with the current drawing style in the rectangle defined by the two points. The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

DrawLine(self, cds1: rdkit.Geometry.rdGeometry.Point2D, cds2: rdkit.Geometry.rdGeometry.Point2D, rawCoords: bool = False) → None

draws a line with the current drawing style. The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

DrawMolecule(self, mol: rdkit.Chem.rdchem.Mol, highlightAtoms: object | None = None, highlightAtomColors: object | None = None, highlightAtomRadii: dict | None = None, confId: int = -1, legend: str = '') → None

DrawMolecule(self, mol: rdkit.Chem.rdchem.Mol, highlightAtoms: object, highlightBonds: object, highlightAtomColors: object | None = None, highlightBondColors: object | None = None, highlightAtomRadii: dict | None = None, confId: int = -1, legend: str = '') → None

renders a molecule

DrawMoleculeWithHighlights(self, mol: rdkit.Chem.rdchem.Mol, legend: str, highlight_atom_map: object, highlight_bond_map: object, highlight_radii: dict | None, highlight_linewidth_multipliers: object, confId: int = -1) → None

renders a molecule with multiple highlight colours

DrawMolecules(self, mols: object, highlightAtoms: object | None = None, highlightBonds: object | None = None, highlightAtomColors: object | None = None, highlightBondColors: object | None = None, highlightAtomRadii: object | None = None, confIds: object | None = None, legends: object | None = None) → None

renders multiple molecules

DrawPolygon(self, cds: object, rawCoords: bool = False) → None

draws a polygon with the current drawing style. The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

DrawReaction(self, rxn: rdkit.Chem.rdChemReactions.ChemicalReaction, highlightByReactant: bool = False, highlightColorsReactants: object | None = None, confIds: object | None = None) → None

renders a reaction

DrawRect(self, cds1: rdkit.Geometry.rdGeometry.Point2D, cds2: rdkit.Geometry.rdGeometry.Point2D, rawCoords: bool = False) → None

draws a rectangle with the current drawing style in the rectangle defined by the two points. The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

DrawString(self, string: str, pos: rdkit.Geometry.rdGeometry.Point2D, rawCoords: bool = False) → None

DrawString(self, string: str, pos: rdkit.Geometry.rdGeometry.Point2D, align: int, rawCoords: bool = False) → None

Overloaded function.

1. DrawString(self, string: str, pos: rdkit.Geometry.rdGeometry.Point2D, rawCoords: bool = False) -> None

add text to the canvas. The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

2. DrawString(self, string: str, pos: rdkit.Geometry.rdGeometry.Point2D, align: int, rawCoords: bool = False) -> None

add aligned text to the canvas. The align argument can be 0 (=MIDDLE), 1 (=START), or 2 (=END). The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

DrawTriangle(self, cds1: rdkit.Geometry.rdGeometry.Point2D, cds2: rdkit.Geometry.rdGeometry.Point2D, cds3: rdkit.Geometry.rdGeometry.Point2D, rawCoords: bool = False) → None

draws a triangle with the current drawing style. The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

DrawWavyLine(self, cds1: rdkit.Geometry.rdGeometry.Point2D, cds2: rdkit.Geometry.rdGeometry.Point2D, color1: tuple, color2: tuple, nSegments: int = 16, vertOffset: float = 0.05, rawCoords: bool = False) → None

draw a line indicating the presence of an attachment point (normally a squiggle line perpendicular to a bond). The coordinates are in the molecule frame unless rawCoords is true, in which case the coordinates are in pixels.

FillPolys(self) → bool

returns whether or not polygons are being filled

FlexiMode(self) → bool

returns whether or not FlexiMode is being used

FontSize(self) → float

get the default font size. The units are, roughly, pixels.

GetDrawCoords(self, point: rdkit.Geometry.rdGeometry.Point2D) → rdkit.Geometry.rdGeometry.Point2D

GetDrawCoords(self, atomIndex: int) → rdkit.Geometry.rdGeometry.Point2D

Overloaded function.

1. GetDrawCoords(self, point: rdkit.Geometry.rdGeometry.Point2D) -> rdkit.Geometry.rdGeometry.Point2D

get the coordinates in drawing space for a particular point in molecule space

2. GetDrawCoords(self, atomIndex: int) -> rdkit.Geometry.rdGeometry.Point2D

get the coordinates in drawing space for a particular atom

GetMolSize(self, mol: rdkit.Chem.rdchem.Mol, highlightAtoms: object | None = None, highlightBonds: object | None = None, highlightAtomColors: object | None = None, highlightBondColors: object | None = None, highlightAtomRadii: dict | None = None, confId: int = -1, legend: str = '') → tuple

returns the width and height required to draw a molecule at the current size

Height(self) → int

get the height of the drawing canvas

LineWidth(self) → float

returns the line width being used

Offset(self) → rdkit.Geometry.rdGeometry.Point2D

returns the offset (in drawing coordinates) for the drawing

SetColour(self, tpl: tuple) → None

set the color being used fr drawing and filling

SetDrawOptions(self, opts: rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions) → None

Copies the drawing options passed in over our drawing options

SetFillPolys(self, val: bool) → None

sets whether or not polygons are filled

SetFlexiMode(self, mode: bool) → None

when FlexiMode is set, molecules will always been drawn with the default values for bond length, font size, etc.

SetFontSize(self, new_size: float) → None

change the default font size. The units are, roughly, pixels.

SetLineWidth(self, width: float) → None

set the line width being used

SetOffset(self, x: int, y: int) → None

set the offset (in drawing coordinates) for the drawing

SetScale(self, width: int, height: int, minv: rdkit.Geometry.rdGeometry.Point2D, maxv: rdkit.Geometry.rdGeometry.Point2D, mol: object | None = None) → None

uses the values provided to set the drawing scaling

Width(self) → int

get the width of the drawing canvas

drawOptions(self) → rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions

Returns a modifiable version of the current drawing options

class rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DCairo(self, width: int, height: int, panelWidth: int = -1, panelHeight: int = -1, noFreetype: bool = False)

Bases: MolDraw2D

Cairo molecule drawer

FinishDrawing(self) → None

add the last bits to finish the drawing

GetDrawingText(self) → bytes

return the PNG data as a string

WriteDrawingText(self, fName: str) → None

write the PNG data to the named file

class rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG(self, width: int, height: int, panelWidth: int = -1, panelHeight: int = -1, noFreetype: bool = False)

Bases: MolDraw2D

SVG molecule drawer

AddMoleculeMetadata(self, mol: rdkit.Chem.rdchem.Mol, confId: int = -1) → None

add RDKit-specific information to the bottom of the drawing

FinishDrawing(self) → None

add the last bits of SVG to finish the drawing

GetDrawingText(self) → str

return the SVG

TagAtoms(self, mol: rdkit.Chem.rdchem.Mol, radius: float = 0.2, events: object | None = None) → None

allow atom selection in the SVG

class rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions(self)

Bases: object

Drawing options

property addAtomIndices

adds atom indices to drawings. Default False.

property addBondIndices

adds bond indices to drawings. Default False.

property addStereoAnnotation

adds R/S and E/Z to drawings. Default False.

property addStereoGroupAnnotation

Whether to add the enhanced stereo labels. Default is True.

property additionalAtomLabelPadding

additional padding to leave around atom labels. Expressed as a fraction of the font size.

property annotationColour

the annotation colour as an (R,G,B,A) tuple, values should be between 0 and 1

property annotationFontScale

Scale of font for atom and bond annotation relative to atom label font. Default=0.75.

property atomHighlightsAreCircles

forces atom highlights always to be circles. Default (false) is to put ellipses round longer labels.

property atomLabelDeuteriumTritium

labels deuterium as D and tritium as T

property atomLabels

maps indices to atom labels

property atomNoteColour

the atom note colour as an (R,G,B,A) tuple, values should be between 0 and 1

property atomRegions

regions to outline

property backgroundColour

the background colour as an (R,G,B,A) tuple, values should be between 0 and 1

property baseFontSize

relative size of font. Defaults to 0.6. -1 means use default.

property bondLineWidth

if positive, this overrides the default line width for bonds

property bondNoteColour

the bond note colour as an (R,G,B,A) tuple, values should be between 0 and 1

property bracketsAroundAtomLists

Whether to put brackets round atom lists in query atoms. Default is true.

property centreMoleculesBeforeDrawing

Moves the centre of the drawn molecule to (0,0). Default False.

property circleAtoms

(self) -> bool

property clearBackground

clear the background before drawing a molecule

property comicMode

simulate hand-drawn lines for bonds. When combined with a font like Comic-Sans or Comic-Neue, this gives xkcd-like drawings. Default is false.

property continuousHighlight

(self) -> bool

property drawMolsSameScale

when drawing multiple molecules with DrawMolecules, forces them to use the same scale. Default is true.

property drawingExtentsInclude

Drawing extents are computed taking into account only selected DrawElement items. Default=DrawElement.ALL

property dummiesAreAttachments

(self) -> bool

property dummyIsotopeLabels

adds isotope labels on dummy atoms. Default True.

property explicitMethyl

Draw terminal methyls explictly. Default is false.

property fillHighlights

(self) -> bool

property fixedBondLength

If > 0.0, fixes bond length to this number of pixels unless that would make it too big. Default -1.0 means no fix. If both set, fixedScale takes precedence.

property fixedFontSize

font size in pixels. default=-1 means not fixed. If set, always used irrespective of scale, minFontSize and maxFontSize.

property fixedScale

If > 0.0, fixes scale to that fraction of width of draw window unless that would make it too big. Default -1.0 means adjust scale to fit.

property flagCloseContactsDist

(self) -> int

property fontFile

Font file for use with FreeType text drawer. Can also be BuiltinTelexRegular (the default) or BuiltinRobotoRegular.

getAnnotationColour(self) → tuple

method returning the annotation colour

getAtomNoteColour(self) → tuple

method returning the atom note colour

getAtomPalette(self) → dict

returns the current atom palette as a dictionary mapping ints to 4-tuples

getBackgroundColour(self) → tuple

method returning the background colour

getBondNoteColour(self) → tuple

method returning the bond note colour

getHighlightColour(self) → tuple

method returning the highlight colour

getLegendColour(self) → tuple

method returning the legend colour

getQueryColour(self) → tuple

method returning the query colour

getSymbolColour(self) → tuple

method returning the symbol colour

getVariableAttachmentColour(self) → tuple

method for getting the colour of variable attachment points

property highlightBondWidthMultiplier

What to multiply default bond width by for highlighting bonds. Default-8.

property highlightColour

the highlight colour as an (R,G,B,A) tuple, values should be between 0 and 1

property highlightRadius

Default radius for highlight circles.

property includeAtomTags

include atom tags in output

property includeChiralFlagLabel

add a molecule annotation with “ABS” if the chiral flag is set. Default is false.

property includeMetadata

When possible, include metadata about molecules and reactions to allow them to be reconstructed. Default is true.

property includeRadicals

include radicals in the drawing (it can be useful to turn this off for reactions and queries). Default is true.

property isotopeLabels

adds isotope labels on non-dummy atoms. Default True.

property legendColour

the legend colour as an (R,G,B,A) tuple, values should be between 0 and 1

property legendFontSize

font size in pixels of the legend (if drawn)

property legendFraction

fraction of the draw panel to be used for the legend if present

property legendPosition

legend position enum. Default=Bottom. Values: LegendPosition.Bottom, LegendPosition.Top, LegendPosition.Left, LegendPosition.Right.

property legendVerticalText

when legend is Left or Right, draw text vertically (one char per line)

property maxFontSize

maximum font size in pixels. default=40, -1 means no maximum.

property minFontSize

minimum font size in pixels. default=6, -1 means no minimum.

property multiColourHighlightStyle

Either ‘CircleAndLine’ or ‘Lasso’, to control style of multi-coloured highlighting in DrawMoleculeWithHighlights. Default is CircleAndLine.

property multipleBondOffset

offset for the extra lines in a multiple bond as a fraction of mean bond length

property noAtomLabels

disables inclusion of atom labels in the rendering

property padding

Fraction of empty space to leave around molecule. Default=0.05.

property prepareMolsBeforeDrawing

call prepareMolForDrawing() on each molecule passed to DrawMolecules()

property queryColour

the query colour as an (R,G,B,A) tuple, values should be between 0 and 1

property reagentPadding

Fraction of empty space to leave around each component of a reaction drawing. Default=0.0.

property rotate

Rotates molecule about centre by this number of degrees,

property scaleBondWidth

Scales the width of drawn bonds using image scaling.

property scaleHighlightBondWidth

Scales the width of drawn highlighted bonds using image scaling.

property scalingFactor

scaling factor for pixels->angstrom when auto scaling being used. Default is 20.

setAnnotationColour(self, tpl: tuple) → None

method for setting the annotation colour

setAtomNoteColour(self, tpl: tuple) → None

method for setting the atom note colour

setAtomPalette(self, cmap: object) → None

sets the palette for atoms and bonds from a dictionary mapping ints to 3-tuples

setBackgroundColour(self, tpl: tuple) → None

method for setting the background colour

setBondNoteColour(self, tpl: tuple) → None

method for setting the bond note colour

setHighlightColour(self, tpl: tuple) → None

method for setting the highlight colour

setLegendColour(self, tpl: tuple) → None

method for setting the legend colour

setQueryColour(self, tpl: tuple) → None

method for setting the query colour

setSymbolColour(self, tpl: tuple) → None

method for setting the symbol colour

setVariableAttachmentColour(self, tpl: tuple) → None

method for setting the colour of variable attachment points

property showAllCIPCodes

show all defined CIP codes (no hiding!). Default False.

property simplifiedStereoGroupLabel

if all specified stereocenters are in a single StereoGroup, show a molecule-level annotation instead of the individual labels. Default is false.

property singleColourBonds

if true all bonds are drawn using symbolColour rather than inheriting their colour from the atoms. Default is false.

property singleColourWedgeBonds

if true wedged and dashed bonds are drawn using symbolColour rather than inheriting their colour from the atoms. Default is false.

property splitBonds

(self) -> bool

property standardColoursForHighlightedAtoms

If true, highlighted hetero atoms are drawn in standard colours rather than black. Default=False

property stereoGroupAbsLabel

String to use for enhanced stereo ‘ABS’ groups. Default=’abs’.

property stereoGroupAndLabel

String to use for enhanced stereo ‘AND’ groups. Default=’and’.

property stereoGroupOrLabel

String to use for enhanced stereo ‘OR’ groups. Default=’or’.

property symbolColour

the symbol colour as an (R,G,B,A) tuple, values should be between 0 and 1

property unspecifiedStereoIsUnknown

if true, double bonds with unspecified stereo are drawn crossed, potential stereocenters with unspecified stereo are drawn with a wavy bond. Default is false.

updateAtomPalette(self, cmap: object) → None

updates the palette for atoms and bonds from a dictionary mapping ints to 3-tuples

useAvalonAtomPalette(self) → None

use the Avalon renderer palette for atoms and bonds

useBWAtomPalette(self) → None

use a black and white palette for atoms and bonds

useCDKAtomPalette(self) → None

use the CDK palette for atoms and bonds

property useComplexQueryAtomSymbols

replace any atom, any hetero, any halo queries with complex query symbols A, Q, X, M, optionally followed by H if hydrogen is included (except for AH, which stays *). Default is true

useDefaultAtomPalette(self) → None

use the default colour palette for atoms and bonds

property useMolBlockWedging

If the molecule came from a MolBlock, prefer the wedging information that provides. If false, use RDKit rules. Default false

property variableAtomRadius

radius value to use for atoms involved in variable attachment points.

property variableAttachmentColour

the variable attachment colour as an (R,G,B,A) tuple, values should be between 0 and 1

property variableBondWidthMultiplier

what to multiply standard bond width by for variable attachment points.

class rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle(*values)

Bases: Enum

CircleAndLine = 0

Lasso = 1