rdkit.Chem.Draw.rdMolDraw2D module

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

rdkit.Chem.Draw.rdMolDraw2D.ContourAndDrawGaussians((MolDraw2D)drawer, (AtomPairsParameters)locs, (AtomPairsParameters)heights, (AtomPairsParameters)widths[, (int)nContours=10[, (AtomPairsParameters)levels=None[, (ContourParams)params=<rdkit.Chem.Draw.rdMolDraw2D.ContourParams object at 0x7500b4edab50>[, (AtomPairsParameters)mol=None]]]]) → None :

Generates and draws contours for a set of gaussians

• drawer: the MolDraw2D object to use

• locs: locations of the gaussians

• heights: the heights (or weights) of the gaussians

• widths: the standard deviations of the gaussians

• nContours: the number of contours to draw

• levels: the contours to use

• ps: additional parameters controlling the contouring.

• mol: molecule used to help set scale.

The values are calculated on a grid with spacing params.gridResolution. If params.setScale is set, the grid size will be calculated based on the locations of the gaussians and params.extraGridPadding. Otherwise the current size of the viewport will be used.

If the levels argument is empty, the contour levels will be determined automatically from the max and min values on the grid and levels will be updated to include the contour levels.

If params.fillGrid is set, the data on the grid will also be drawn using the color scheme in params.colourMap

If mol is not 0, uses the molecule to help set the scale, assuming that it will be drawn over the plot, so needs to fit on it.

*/

C++ signature :

void ContourAndDrawGaussians(RDKit::MolDraw2D {lvalue},boost::python::api::object,boost::python::api::object,boost::python::api::object [,unsigned int=10 [,boost::python::api::object=None [,RDKit::MolDraw2DUtils::ContourParams=<rdkit.Chem.Draw.rdMolDraw2D.ContourParams object at 0x7500b4edab50> [,boost::python::api::object=None]]]])

rdkit.Chem.Draw.rdMolDraw2D.ContourAndDrawGrid((MolDraw2D)drawer, (AtomPairsParameters)data, (AtomPairsParameters)xcoords, (AtomPairsParameters)ycoords[, (int)nContours=10[, (AtomPairsParameters)levels=None[, (ContourParams)params=<rdkit.Chem.Draw.rdMolDraw2D.ContourParams object at 0x7500b4eda190>[, (AtomPairsParameters)mol=None]]]]) → None :

Generates and draws contours for data on a grid

• drawer: the MolDraw2D object to use

• data: numpy array with the data to be contoured

• xcoords: the x coordinates of the grid

• ycoords: the y coordinates of the grid

• nContours: the number of contours to draw

• levels: the contours to use

• ps: additional parameters controlling the contouring

• mol: molecule used to help set scale.

The values are calculated on a grid with spacing params.gridResolution. If params.setScale is set, the grid size will be calculated based on the locations of the gaussians and params.extraGridPadding. Otherwise the current size of the viewport will be used.

If the levels argument is empty, the contour levels will be determined automatically from the max and min values on the grid and levels will be updated to include the contour levels.

If params.fillGrid is set, the data on the grid will also be drawn using the color scheme in params.colourMap

If mol is not 0, uses the molecule to help set the scale, assuming that it will be drawn over the plot, so needs to fit on it.

*/

C++ signature :

void ContourAndDrawGrid(RDKit::MolDraw2D {lvalue},boost::python::api::object {lvalue},boost::python::api::object {lvalue},boost::python::api::object {lvalue} [,unsigned int=10 [,boost::python::api::object {lvalue}=None [,RDKit::MolDraw2DUtils::ContourParams=<rdkit.Chem.Draw.rdMolDraw2D.ContourParams object at 0x7500b4eda190> [,boost::python::api::object=None]]]])

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

Bases: instance

Parameters for drawing contours

C++ signature :

void __init__(_object*)

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 gridResolution

set the resolution of the grid

property isovalScaleForQuantization

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

setColourMap((ContourParams)self, (AtomPairsParameters)colours) → None :

C++ signature :

void setColourMap(RDKit::MolDraw2DUtils::ContourParams {lvalue},boost::python::api::object)

setContourColour((ContourParams)self, (tuple)colour) → None :

C++ signature :

void setContourColour(RDKit::MolDraw2DUtils::ContourParams {lvalue},boost::python::tuple)

property setScale

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

rdkit.Chem.Draw.rdMolDraw2D.DrawMoleculeACS1996((MolDraw2D)drawer, (Mol)mol[, (str)legend=''[, (AtomPairsParameters)highlightAtoms=None[, (AtomPairsParameters)highlightBonds=None[, (AtomPairsParameters)highlightAtomColors=None[, (AtomPairsParameters)highlightBondColors=None[, (AtomPairsParameters)highlightAtomRadii=None[, (int)confId=-1]]]]]]]) → None :

Draws molecule in ACS 1996 mode.

C++ signature :

void DrawMoleculeACS1996(RDKit::MolDraw2D {lvalue},RDKit::ROMol [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,int=-1]]]]]]])

class rdkit.Chem.Draw.rdMolDraw2D.IntStringMap((object)arg1)

Bases: instance

C++ signature :

void __init__(_object*)

rdkit.Chem.Draw.rdMolDraw2D.MeanBondLength((Mol)mol[, (int)confId=-1]) → float :

Calculate the mean bond length for the molecule.

C++ signature :

double MeanBondLength(RDKit::ROMol [,int=-1])

class rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D

Bases: instance

Drawer abstract base class

Raises an exception This class cannot be instantiated from Python

ClearDrawing((MolDraw2D)self) → None :

clears the drawing by filling it with the background color

C++ signature :

void ClearDrawing(RDKit::MolDraw2D {lvalue})

DrawArc((MolDraw2D)self, (Point2D)center, (float)radius, (float)angle1, (float)angle2[, (bool)rawCoords=False]) → None :

draws an arc with the current drawing style. The coordinates are in the molecule frame, the angles are in degrees, angle2 should be > angle1.

C++ signature :

void DrawArc(RDKit::MolDraw2D {lvalue},RDGeom::Point2D,double,double,double [,bool=False])

DrawArrow((MolDraw2D)self, (Point2D)cds1, (Point2D)cds2[, (bool)asPolygon=False[, (float)frac=0.05[, (float)angle=0.5235987755982988[, (AtomPairsParameters)color=None[, (bool)rawCoords=False]]]]]) → None :

draws an arrow with the current drawing style. The coordinates are in the molecule frame. If asPolygon is true the head of the arrow will be drawn as a triangle, otherwise two lines are used.

C++ signature :

void DrawArrow(RDKit::MolDraw2D {lvalue},RDGeom::Point2D,RDGeom::Point2D [,bool=False [,double=0.05 [,double=0.5235987755982988 [,boost::python::api::object=None [,bool=False]]]]])

DrawAttachmentLine((MolDraw2D)self, (Point2D)cds1, (Point2D)cds2, (tuple)color[, (float)len=1.0[, (int)nSegments=16[, (bool)rawCoords=False]]]) → None :

draw a line indicating the presence of an attachment point (normally a squiggle line perpendicular to a bond)

C++ signature :

void DrawAttachmentLine(RDKit::MolDraw2D {lvalue},RDGeom::Point2D,RDGeom::Point2D,boost::python::tuple {lvalue} [,double=1.0 [,unsigned int=16 [,bool=False]]])

DrawEllipse((MolDraw2D)self, (Point2D)cds1, (Point2D)cds2[, (bool)rawCoords=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

C++ signature :

void DrawEllipse(RDKit::MolDraw2D {lvalue},RDGeom::Point2D,RDGeom::Point2D [,bool=False])

DrawLine((MolDraw2D)self, (Point2D)cds1, (Point2D)cds2[, (bool)rawCoords=False]) → None :

draws a line with the current drawing style. The coordinates are in the molecule frame

C++ signature :

void DrawLine(RDKit::MolDraw2D {lvalue},RDGeom::Point2D,RDGeom::Point2D [,bool=False])

DrawMolecule((MolDraw2D)self, (Mol)mol[, (AtomPairsParameters)highlightAtoms=None[, (AtomPairsParameters)highlightAtomColors=None[, (AtomPairsParameters)highlightAtomRadii=None[, (int)confId=-1[, (str)legend='']]]]]) → None :

renders a molecule

C++ signature :

void DrawMolecule(RDKit::MolDraw2D {lvalue},RDKit::ROMol [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,int=-1 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’]]]]])

DrawMolecule( (MolDraw2D)self, (Mol)mol, (AtomPairsParameters)highlightAtoms, (AtomPairsParameters)highlightBonds [, (AtomPairsParameters)highlightAtomColors=None [, (AtomPairsParameters)highlightBondColors=None [, (AtomPairsParameters)highlightAtomRadii=None [, (int)confId=-1 [, (str)legend=’’]]]]]) -> None :

renders a molecule

C++ signature :

void DrawMolecule(RDKit::MolDraw2D {lvalue},RDKit::ROMol,boost::python::api::object,boost::python::api::object [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,int=-1 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’]]]]])

DrawMoleculeWithHighlights((MolDraw2D)self, (Mol)mol, (str)legend, (AtomPairsParameters)highlight_atom_map, (AtomPairsParameters)highlight_bond_map, (AtomPairsParameters)highlight_radii, (AtomPairsParameters)highlight_linewidth_multipliers[, (int)confId=-1]) → None :

renders a molecule with multiple highlight colours

C++ signature :

void DrawMoleculeWithHighlights(RDKit::MolDraw2D {lvalue},RDKit::ROMol,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,boost::python::api::object,boost::python::api::object,boost::python::api::object,boost::python::api::object [,int=-1])

DrawMolecules((MolDraw2D)self, (AtomPairsParameters)mols[, (AtomPairsParameters)highlightAtoms=None[, (AtomPairsParameters)highlightBonds=None[, (AtomPairsParameters)highlightAtomColors=None[, (AtomPairsParameters)highlightBondColors=None[, (AtomPairsParameters)highlightAtomRadii=None[, (AtomPairsParameters)confIds=None[, (AtomPairsParameters)legends=None]]]]]]]) → None :

renders multiple molecules

C++ signature :

void DrawMolecules(RDKit::MolDraw2D {lvalue},boost::python::api::object [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None]]]]]]])

DrawPolygon((MolDraw2D)self, (AtomPairsParameters)cds[, (bool)rawCoords=False]) → None :

draws a polygon with the current drawing style. The coordinates are in the molecule frame

C++ signature :

void DrawPolygon(RDKit::MolDraw2D {lvalue},boost::python::api::object [,bool=False])

DrawReaction((MolDraw2D)self, (ChemicalReaction)rxn[, (bool)highlightByReactant=False[, (AtomPairsParameters)highlightColorsReactants=None[, (AtomPairsParameters)confIds=None]]]) → None :

renders a reaction

C++ signature :

void DrawReaction(RDKit::MolDraw2D {lvalue},RDKit::ChemicalReaction [,bool=False [,boost::python::api::object=None [,boost::python::api::object=None]]])

DrawRect((MolDraw2D)self, (Point2D)cds1, (Point2D)cds2[, (bool)rawCoords=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

C++ signature :

void DrawRect(RDKit::MolDraw2D {lvalue},RDGeom::Point2D,RDGeom::Point2D [,bool=False])

DrawString((MolDraw2D)self, (str)string, (Point2D)pos[, (bool)rawCoords=False]) → None :

add text to the canvas

C++ signature :

void DrawString(RDKit::MolDraw2D {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,RDGeom::Point2D [,bool=False])

DrawString( (MolDraw2D)self, (str)string, (Point2D)pos, (int)align [, (bool)rawCoords=False]) -> None :

add aligned text to the canvas. The align argument can be 0 (=MIDDLE), 1 (=START), or 2 (=END)

C++ signature :

void DrawString(RDKit::MolDraw2D {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >,RDGeom::Point2D,int [,bool=False])

DrawTriangle((MolDraw2D)self, (Point2D)cds1, (Point2D)cds2, (Point2D)cds3[, (bool)rawCoords=False]) → None :

draws a triangle with the current drawing style. The coordinates are in the molecule frame

C++ signature :

void DrawTriangle(RDKit::MolDraw2D {lvalue},RDGeom::Point2D,RDGeom::Point2D,RDGeom::Point2D [,bool=False])

DrawWavyLine((MolDraw2D)self, (Point2D)cds1, (Point2D)cds2, (tuple)color1, (tuple)color2[, (int)nSegments=16[, (float)vertOffset=0.05[, (bool)rawCoords=False]]]) → None :

draw a line indicating the presence of an attachment point (normally a squiggle line perpendicular to a bond)

C++ signature :

void DrawWavyLine(RDKit::MolDraw2D {lvalue},RDGeom::Point2D,RDGeom::Point2D,boost::python::tuple {lvalue},boost::python::tuple {lvalue} [,unsigned int=16 [,double=0.05 [,bool=False]]])

FillPolys((MolDraw2D)self) → bool :

returns whether or not polygons are being filled

C++ signature :

bool FillPolys(RDKit::MolDraw2D {lvalue})

FlexiMode((MolDraw2D)self) → bool :

returns whether or not FlexiMode is being used

C++ signature :

bool FlexiMode(RDKit::MolDraw2D {lvalue})

FontSize((MolDraw2D)self) → float :

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

C++ signature :

double FontSize(RDKit::MolDraw2D {lvalue})

GetDrawCoords((MolDraw2D)self, (Point2D)point) → Point2D :

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

C++ signature :

RDGeom::Point2D GetDrawCoords(RDKit::MolDraw2D {lvalue},RDGeom::Point2D)

GetDrawCoords( (MolDraw2D)self, (int)atomIndex) -> Point2D :

get the coordinates in drawing space for a particular atom

C++ signature :

RDGeom::Point2D GetDrawCoords(RDKit::MolDraw2D {lvalue},int)

GetMolSize((MolDraw2D)self, (Mol)mol[, (AtomPairsParameters)highlightAtoms=None[, (AtomPairsParameters)highlightBonds=None[, (AtomPairsParameters)highlightAtomColors=None[, (AtomPairsParameters)highlightBondColors=None[, (AtomPairsParameters)highlightAtomRadii=None[, (int)confId=-1[, (str)legend='']]]]]]]) → tuple :

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

C++ signature :

boost::python::tuple GetMolSize(RDKit::MolDraw2D {lvalue},RDKit::ROMol [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,int=-1 [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’]]]]]]])

Height((MolDraw2D)self) → int :

get the height of the drawing canvas

C++ signature :

int Height(RDKit::MolDraw2D {lvalue})

LineWidth((MolDraw2D)self) → float :

returns the line width being used

C++ signature :

double LineWidth(RDKit::MolDraw2D {lvalue})

Offset((MolDraw2D)self) → Point2D :

returns the offset (in drawing coordinates) for the drawing

C++ signature :

RDGeom::Point2D Offset(RDKit::MolDraw2D {lvalue})

SetColour((MolDraw2D)self, (tuple)tpl) → None :

set the color being used fr drawing and filling

C++ signature :

void SetColour(RDKit::MolDraw2D {lvalue},boost::python::tuple)

SetDrawOptions((MolDraw2D)self, (MolDrawOptions)opts) → None :

Copies the drawing options passed in over our drawing options

C++ signature :

void SetDrawOptions(RDKit::MolDraw2D {lvalue},RDKit::MolDrawOptions)

SetFillPolys((MolDraw2D)self, (bool)val) → None :

sets whether or not polygons are filled

C++ signature :

void SetFillPolys(RDKit::MolDraw2D {lvalue},bool)

SetFlexiMode((MolDraw2D)self, (bool)mode) → None :

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

C++ signature :

void SetFlexiMode(RDKit::MolDraw2D {lvalue},bool)

SetFontSize((MolDraw2D)self, (float)new_size) → None :

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

C++ signature :

void SetFontSize(RDKit::MolDraw2D {lvalue},double)

SetLineWidth((MolDraw2D)self, (float)width) → None :

set the line width being used

C++ signature :

void SetLineWidth(RDKit::MolDraw2D {lvalue},double)

SetOffset((MolDraw2D)self, (int)x, (int)y) → None :

set the offset (in drawing coordinates) for the drawing

C++ signature :

void SetOffset(RDKit::MolDraw2D {lvalue},int,int)

SetScale((MolDraw2D)self, (int)width, (int)height, (Point2D)minv, (Point2D)maxv[, (AtomPairsParameters)mol=None]) → None :

uses the values provided to set the drawing scaling

C++ signature :

void SetScale(RDKit::MolDraw2D {lvalue},int,int,RDGeom::Point2D,RDGeom::Point2D [,boost::python::api::object=None])

Width((MolDraw2D)self) → int :

get the width of the drawing canvas

C++ signature :

int Width(RDKit::MolDraw2D {lvalue})

drawOptions((MolDraw2D)self) → MolDrawOptions :

Returns a modifiable version of the current drawing options

C++ signature :

RDKit::MolDrawOptions {lvalue} drawOptions(RDKit::MolDraw2D {lvalue})

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

Bases: MolDraw2D

Cairo molecule drawer

C++ signature :

void __init__(_object*,int,int [,int=-1 [,int=-1 [,bool=False]]])

FinishDrawing((MolDraw2DCairo)self) → None :

add the last bits to finish the drawing

C++ signature :

void FinishDrawing(RDKit::MolDraw2DCairo {lvalue})

GetDrawingText((MolDraw2DCairo)self) → object :

return the PNG data as a string

C++ signature :

boost::python::api::object GetDrawingText(RDKit::MolDraw2DCairo)

WriteDrawingText((MolDraw2DCairo)self, (str)fName) → None :

write the PNG data to the named file

C++ signature :

void WriteDrawingText(RDKit::MolDraw2DCairo {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

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

Bases: MolDraw2D

SVG molecule drawer

C++ signature :

void __init__(_object*,int,int [,int=-1 [,int=-1 [,bool=False]]])

AddMoleculeMetadata((MolDraw2DSVG)self, (Mol)mol[, (int)confId=-1]) → None :

add RDKit-specific information to the bottom of the drawing

C++ signature :

void AddMoleculeMetadata(RDKit::MolDraw2DSVG {lvalue},RDKit::ROMol [,int=-1])

FinishDrawing((MolDraw2DSVG)self) → None :

add the last bits of SVG to finish the drawing

C++ signature :

void FinishDrawing(RDKit::MolDraw2DSVG {lvalue})

GetDrawingText((MolDraw2DSVG)self) → str :

return the SVG

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > GetDrawingText(RDKit::MolDraw2DSVG {lvalue})

TagAtoms((MolDraw2DSVG)self, (Mol)mol[, (float)radius=0.2[, (AtomPairsParameters)events=None]]) → None :

allow atom selection in the SVG

C++ signature :

void TagAtoms(RDKit::MolDraw2DSVG {lvalue},RDKit::ROMol [,double=0.2 [,boost::python::api::object=None]])

class rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions((object)arg1)

Bases: instance

Drawing options

C++ signature :

void __init__(_object*)

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 additionalAtomLabelPadding

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

property annotationFontScale

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

property atomHighlightsAreCircles

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

property atomLabelDeuteriumTritium

labels deuterium as D and tritium as T

property atomLabels

maps indices to atom labels

property atomRegions

regions to outline

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 centreMoleculesBeforeDrawing

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

property circleAtoms

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

property drawMolsSameScale

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

property dummiesAreAttachments

property dummyIsotopeLabels

adds isotope labels on dummy atoms. Default True.

property explicitMethyl

Draw terminal methyls explictly. Default is false.

property fillHighlights

property fixedBondLength

If > 0.0, fixes bond length to this number of pixelsunless that would make it too big. Default -1.0 meansno 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 ofdraw window. Default -1.0 means adjust scale to fit.

property flagCloseContactsDist

property fontFile

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

getAnnotationColour((MolDrawOptions)self) → object :

method returning the annotation colour

C++ signature :

boost::python::api::object getAnnotationColour(RDKit::MolDrawOptions)

getBackgroundColour((MolDrawOptions)self) → object :

method returning the background colour

C++ signature :

boost::python::api::object getBackgroundColour(RDKit::MolDrawOptions)

getHighlightColour((MolDrawOptions)self) → object :

method returning the highlight colour

C++ signature :

boost::python::api::object getHighlightColour(RDKit::MolDrawOptions)

getLegendColour((MolDrawOptions)self) → object :

method returning the legend colour

C++ signature :

boost::python::api::object getLegendColour(RDKit::MolDrawOptions)

getQueryColour((MolDrawOptions)self) → object :

method returning the query colour

C++ signature :

boost::python::api::object getQueryColour(RDKit::MolDrawOptions)

getSymbolColour((MolDrawOptions)self) → object :

method returning the symbol colour

C++ signature :

boost::python::api::object getSymbolColour(RDKit::MolDrawOptions)

getVariableAttachmentColour((MolDrawOptions)self) → object :

method for getting the colour of variable attachment points

C++ signature :

boost::python::api::object getVariableAttachmentColour(RDKit::MolDrawOptions)

property highlightBondWidthMultiplier

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

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 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 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 ofmulti-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

property prepareMolsBeforeDrawing

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

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 scalingbeing used. Default is 20.

setAnnotationColour((MolDrawOptions)self, (tuple)tpl) → None :

method for setting the annotation colour

C++ signature :

void setAnnotationColour(RDKit::MolDrawOptions {lvalue},boost::python::tuple)

setAtomPalette((MolDrawOptions)self, (AtomPairsParameters)cmap) → None :

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

C++ signature :

void setAtomPalette(RDKit::MolDrawOptions {lvalue},boost::python::api::object)

setBackgroundColour((MolDrawOptions)self, (tuple)tpl) → None :

method for setting the background colour

C++ signature :

void setBackgroundColour(RDKit::MolDrawOptions {lvalue},boost::python::tuple)

setHighlightColour((MolDrawOptions)self, (tuple)tpl) → None :

method for setting the highlight colour

C++ signature :

void setHighlightColour(RDKit::MolDrawOptions {lvalue},boost::python::tuple)

setLegendColour((MolDrawOptions)self, (tuple)tpl) → None :

method for setting the legend colour

C++ signature :

void setLegendColour(RDKit::MolDrawOptions {lvalue},boost::python::tuple)

setQueryColour((MolDrawOptions)self, (tuple)tpl) → None :

method for setting the query colour

C++ signature :

void setQueryColour(RDKit::MolDrawOptions {lvalue},boost::python::tuple)

setSymbolColour((MolDrawOptions)self, (tuple)tpl) → None :

method for setting the symbol colour

C++ signature :

void setSymbolColour(RDKit::MolDrawOptions {lvalue},boost::python::tuple)

setVariableAttachmentColour((MolDrawOptions)self, (tuple)tpl) → None :

method for setting the colour of variable attachment points

C++ signature :

void setVariableAttachmentColour(RDKit::MolDrawOptions {lvalue},boost::python::tuple)

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 singleColourWedgeBonds

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

property splitBonds

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((MolDrawOptions)self, (AtomPairsParameters)cmap) → None :

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

C++ signature :

void updateAtomPalette(RDKit::MolDrawOptions {lvalue},boost::python::api::object)

useAvalonAtomPalette((MolDrawOptions)self) → None :

use the Avalon renderer palette for atoms and bonds

C++ signature :

void useAvalonAtomPalette(RDKit::MolDrawOptions {lvalue})

useBWAtomPalette((MolDrawOptions)self) → None :

use a black and white palette for atoms and bonds

C++ signature :

void useBWAtomPalette(RDKit::MolDrawOptions {lvalue})

useCDKAtomPalette((MolDrawOptions)self) → None :

use the CDK palette for atoms and bonds

C++ signature :

void useCDKAtomPalette(RDKit::MolDrawOptions {lvalue})

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((MolDrawOptions)self) → None :

use the default colour palette for atoms and bonds

C++ signature :

void useDefaultAtomPalette(RDKit::MolDrawOptions {lvalue})

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 variableBondWidthMultiplier

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

rdkit.Chem.Draw.rdMolDraw2D.MolToACS1996SVG((Mol)mol[, (str)legend=''[, (AtomPairsParameters)highlightAtoms=None[, (AtomPairsParameters)highlightBonds=None[, (AtomPairsParameters)highlightAtomColors=None[, (AtomPairsParameters)highlightBondColors=None[, (AtomPairsParameters)highlightAtomRadii=None[, (int)confId=-1]]]]]]]) → str :

Returns ACS 1996 mode svg for a molecule

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > MolToACS1996SVG(RDKit::ROMol [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,int=-1]]]]]]])

rdkit.Chem.Draw.rdMolDraw2D.MolToSVG((Mol)mol[, (int)width=300[, (int)height=300[, (AtomPairsParameters)highlightAtoms=None[, (bool)kekulize=True[, (int)lineWidthMult=1[, (bool)fontSize=12[, (int)includeAtomCircles=True]]]]]]]) → str :

Returns svg for a molecule

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > MolToSVG(RDKit::ROMol [,unsigned int=300 [,unsigned int=300 [,boost::python::api::object=None [,bool=True [,unsigned int=1 [,bool=12 [,int=True]]]]]]])

class rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle

Bases: enum

CircleAndLine = rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle.CircleAndLine

Lasso = rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle.Lasso

names = {'CircleAndLine': rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle.CircleAndLine, 'Lasso': rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle.Lasso}

values = {0: rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle.CircleAndLine, 1: rdkit.Chem.Draw.rdMolDraw2D.MultiColourHighlightStyle.Lasso}

rdkit.Chem.Draw.rdMolDraw2D.PrepareAndDrawMolecule((MolDraw2D)drawer, (Mol)mol[, (str)legend=''[, (AtomPairsParameters)highlightAtoms=None[, (AtomPairsParameters)highlightBonds=None[, (AtomPairsParameters)highlightAtomColors=None[, (AtomPairsParameters)highlightBondColors=None[, (AtomPairsParameters)highlightAtomRadii=None[, (int)confId=-1[, (bool)kekulize=True]]]]]]]]) → None :

Preps a molecule for drawing and actually draws it

C++ signature :

void PrepareAndDrawMolecule(RDKit::MolDraw2D {lvalue},RDKit::ROMol [,std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >=’’ [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,boost::python::api::object=None [,int=-1 [,bool=True]]]]]]]])

rdkit.Chem.Draw.rdMolDraw2D.PrepareMolForDrawing((Mol)mol[, (bool)kekulize=True[, (bool)addChiralHs=True[, (bool)wedgeBonds=True[, (bool)forceCoords=False[, (bool)wavyBonds=False]]]]]) → Mol :

Does some cleanup operations on the molecule to prepare it to draw nicely. The operations include: kekulization, addition of chiral Hs (so that we can draw wedges to them), wedging of bonds at chiral centers, and generation of a 2D conformation if the molecule does not already have a conformation

Returns a modified copy of the molecule.

C++ signature :

RDKit::ROMol* PrepareMolForDrawing(RDKit::ROMol const* [,bool=True [,bool=True [,bool=True [,bool=False [,bool=False]]]]])

rdkit.Chem.Draw.rdMolDraw2D.SetACS1996Mode((MolDrawOptions)drawOptions, (float)meanBondLength) → None :

Set the draw options to produce something as close as possible to the ACS 1996 guidelines as described at https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Chemistry/Structure_drawing

• MolDrawOptions opt - the options what will be changed

• float meanBondLength - mean bond length of the molecule

Works best if the MolDraw2D object is created with width and height -1 (a flexiCanvas). The mean bond length may be calculated with MeanBondLength. It is used to calculate the offset for the lines in multiple bonds.

Options changed are:

bondLineWidth = 0.6 scaleBondWidth = false scalingFactor = 14.4 / meanBondLen multipleBondOffset = 0.18 highlightBondWidthMultiplier = 32 setMonochromeMode - black and white fixedFontSize = 10 additionalAtomLabelPadding = 0.066 fontFile - if it isn’t set already, then if RDBASE is set and the file

exists, uses $RDBASE/Data/Fonts/FreeSans.ttf. Otherwise uses BuiltinRobotoRegular.

*/

C++ signature :

void SetACS1996Mode(RDKit::MolDrawOptions {lvalue},double)

rdkit.Chem.Draw.rdMolDraw2D.SetDarkMode((MolDrawOptions)d2d) → None :

set dark mode for a MolDrawOptions object

C++ signature :

void SetDarkMode(RDKit::MolDrawOptions {lvalue})

SetDarkMode( (MolDraw2D)d2d) -> None :

set dark mode for a MolDraw2D object

C++ signature :

void SetDarkMode(RDKit::MolDraw2D {lvalue})

rdkit.Chem.Draw.rdMolDraw2D.SetMonochromeMode((MolDrawOptions)options, (tuple)fgColour, (tuple)bgColour) → None :

set monochrome mode for a MolDrawOptions object

C++ signature :

void SetMonochromeMode(RDKit::MolDrawOptions {lvalue},boost::python::tuple,boost::python::tuple)

SetMonochromeMode( (MolDraw2D)drawer, (tuple)fgColour, (tuple)bgColour) -> None :

set monochrome mode for a MolDraw2D object

C++ signature :

void SetMonochromeMode(RDKit::MolDraw2D {lvalue},boost::python::tuple,boost::python::tuple)

rdkit.Chem.Draw.rdMolDraw2D.UpdateDrawerParamsFromJSON((MolDraw2D)drawer, (str)json) → None :

C++ signature :

void UpdateDrawerParamsFromJSON(RDKit::MolDraw2D {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

rdkit.Chem.Draw.rdMolDraw2D.UpdateMolDrawOptionsFromJSON((MolDrawOptions)opts, (str)json) → None :

C++ signature :

void UpdateMolDrawOptionsFromJSON(RDKit::MolDrawOptions {lvalue},std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)

class rdkit.Chem.Draw.rdMolDraw2D.map_indexing_suite_IntStringMap_entry((object)arg1)

Bases: instance

C++ signature :

void __init__(_object*)

data((map_indexing_suite_IntStringMap_entry)arg1) → str :

C++ signature :

std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > data(std::pair<int const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > {lvalue})

key((map_indexing_suite_IntStringMap_entry)arg1) → int :

C++ signature :

int key(std::pair<int const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > {lvalue})