Depicting Molecule with Various Styles

Problem

You want to depict a molecule with various styles.

Table 1. Gallery of molecule depictions using different styles (click on any image below)

The examples below generate interactive .svg images These svg images should be included into and HTML page with the SVG MIME type.

<object data="<imagename>.svg" type="image/svg+xml"></object>

Table 2. Gallery of interactive molecule depictions in SVG (click on any image below)

Ingredients

OEChem TK - cheminformatics toolkit OEDepict TK - molecule depiction toolkit

Difficulty Level

Solution

Default

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-default.png", disp) Download code depiction-default.py

See also

• OE2DMolDisplayOptions class

• OE2DMolDisplay class

• OERenderMolecule function

Aromaticity Style

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetAromaticStyle(oedepict.OEAromaticStyle_Circle) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-aromatic-style.png", disp) Download code depiction-aromatic-style.py

See also

• OE2DMolDisplayOptions.SetAromaticStyle method

• OEAromaticStyle namespace

Atom Color Style

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetAtomColorStyle(oedepict.OEAtomColorStyle_BlackCPK) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-atom-color-style.png", disp) Download code depiction-atom-color-style.py

See also

• OE2DMolDisplayOptions.SetAtomColorStyle method

• OEAtomColorStyle namespace

Super Atom Style

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetSuperAtomStyle(oedepict.OESuperAtomStyle_All) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-super-atom-style.png", disp) Download code depiction-super-atom-style.py

See also

• OE2DMolDisplayOptions.SetSuperAtomStyle method

• OESuperAtomStyle namespace

Atom Stereo Style

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) stereostyle = oedepict.OEAtomStereoStyle_Display_All stereostyle |= oedepict.OEAtomStereoStyle_HashWedgeStyle_Standard opts.SetAtomStereoStyle(stereostyle) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-atom-stereo-style.png", disp) Download code depiction-atom-stereo-style.py

See also

• OE2DMolDisplayOptions.SetAtomStereoStyle method

• OEAtomStereoStyle namespace

Bond Stereo Style

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetBondStereoStyle(oedepict.OEBondStereoStyle_Display_All) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-bond-stereo-style.png", disp) Download code depiction-bond-stereo-style.py

See also

• OE2DMolDisplayOptions.SetBondStereoStyle method

• OEBondStereoStyle namespace

Title Style

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetTitleLocation(oedepict.OETitleLocation_Bottom) fonttype = oedepict.OEFontFamily_Default fontstyle = oedepict.OEFontStyle_Bold | oedepict.OEFontStyle_Italic fontalign = oedepict.OEAlignment_Center fontsize = 10 font = oedepict.OEFont(fonttype, fontstyle, fontsize, fontalign, oechem.OERoyalBlue) opts.SetTitleFont(font) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-title.png", disp) Download code depiction-title.py

See also

• OE2DMolDisplayOptions.SetTitleLocation method

• OETitleLocation namespace

• OEFont class

• OE2DMolDisplayOptions.SetTitleFont method

Border Style

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) disp = oedepict.OE2DMolDisplay(mol, opts) layer = disp.GetLayer(oedepict.OELayerPosition_Below) lightred = oechem.OEColor(255, 235, 235) # R, G, B mediumred = oechem.OEColor(225, 55, 55) # R, G, B linewidth = 6.0 pen = oedepict.OEPen(lightred, mediumred, oedepict.OEFill_On, linewidth) cornersize = 30 oedepict.OEDrawCurvedBorder(layer, pen, cornersize) oedepict.OERenderMolecule("depiction-border.png", disp) Download code depiction-border.py

See also

• OE2DMolDisplay.GetLayer method

• OELayerPosition namespace

• OEPen class

• OEDrawCurvedBorder method

Display Atom Index

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetAtomPropertyFunctor(oedepict.OEDisplayAtomIdx()) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-atom-idx.png", disp) Download code depiction-atom-idx.py

See also

• OE2DMolDisplayOptions.SetAtomPropertyFunctor method

• OEDisplayAtomIdx class

• OEDisplayAtomPropBase base class

Display Bond Index

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetBondPropertyFunctor(oedepict.OEDisplayBondIdx()) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-bond-idx.png", disp) Download code depiction-bond-idx.py

See also

• OE2DMolDisplayOptions.SetBondPropertyFunctor method

• OEDisplayBondIdx class

• OEDisplayBondPropBase base class

Display Atom Property

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict class LabelAtomTopology(oedepict.OEDisplayAtomPropBase): def __init__(self): oedepict.OEDisplayAtomPropBase.__init__(self) def __call__(self, atom): if atom.IsInRing(): return "R" return "C" def CreateCopy(self): copy = LabelAtomTopology() return copy.__disown__() mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetAtomPropertyFunctor(LabelAtomTopology()) fonttype = oedepict.OEFontFamily_Default fontstyle = oedepict.OEFontStyle_Bold fontalign = oedepict.OEAlignment_Center fontsize = 10 font = oedepict.OEFont(fonttype, fontstyle, fontsize, fontalign, oechem.OEDarkRed) opts.SetAtomPropLabelFont(font) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-atom-prop.png", disp) Download code depiction-atom-prop.py

See also

• OEDisplayAtomPropBase base class

• OE2DMolDisplayOptions.SetAtomPropertyFunctor method

• OEFont class

• OE2DMolDisplayOptions.SetAtomPropLabelFont method

Display Bond Property

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict class LabelBondTopology(oedepict.OEDisplayBondPropBase): def __init__(self): oedepict.OEDisplayBondPropBase.__init__(self) def __call__(self, bond): if bond.IsAromatic(): return "a" return "" def CreateCopy(self): copy = LabelBondTopology() return copy.__disown__() mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetBondPropertyFunctor(LabelBondTopology()) fonttype = oedepict.OEFontFamily_Default fontstyle = oedepict.OEFontStyle_Bold fontalign = oedepict.OEAlignment_Center fontsize = 10 font = oedepict.OEFont(fonttype, fontstyle, fontsize, fontalign, oechem.OEDarkBlue) opts.SetBondPropLabelFont(font) disp = oedepict.OE2DMolDisplay(mol, opts) oedepict.OERenderMolecule("depiction-bond-prop.png", disp) Download code depiction-bond-prop.py

See also

• OEDisplayBondPropBase base class

• OE2DMolDisplayOptions.SetBondPropertyFunctor method

• OEFont class

• OE2DMolDisplayOptions.SetBondPropLabelFont method

Hover Atom Property

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetMargins(7.5) disp = oedepict.OE2DMolDisplay(mol, opts) family = oedepict.OEFontFamily_Default fstyle = oedepict.OEFontStyle_Default font = oedepict.OEFont(family, fstyle, 12, oedepict.OEAlignment_Center, oechem.OEDarkRed) for adisp in disp.GetAtomDisplays(): atom = adisp.GetAtom() hovertext = "atom idx=%s" % atom.GetIdx() oedepict.OEDrawSVGHoverText(disp, adisp, hovertext, font) oedepict.OERenderMolecule("depiction-hover-atom.svg", disp) Download code depiction-hover-atom.py

hover over any atoms

See also

• OEFont class

• OEDrawSVGHoverText function

Hover Bond Property

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetMargins(7.5) disp = oedepict.OE2DMolDisplay(mol, opts) family = oedepict.OEFontFamily_Default fstyle = oedepict.OEFontStyle_Default font = oedepict.OEFont(family, fstyle, 12, oedepict.OEAlignment_Center, oechem.OEDarkRed) for bdisp in disp.GetBondDisplays(): bond = bdisp.GetBond() hovertext = "bond idx=%s" % bond.GetIdx() oedepict.OEDrawSVGHoverText(disp, bdisp, hovertext, font) oedepict.OERenderMolecule("depiction-hover-bond.svg", disp) Download code depiction-hover-bond.py

hover over the middle of any bonds

See also

• OEFont class

• OEDrawSVGHoverText function

Toggle Atom Property

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetMargins(7.5) disp = oedepict.OE2DMolDisplay(mol, opts) family = oedepict.OEFontFamily_Default fstyle = oedepict.OEFontStyle_Default font = oedepict.OEFont(family, fstyle, 12, oedepict.OEAlignment_Center, oechem.OEDarkRed) for adisp in disp.GetAtomDisplays(): atom = adisp.GetAtom() toggletext = "atom idx=%s" % atom.GetIdx() oedepict.OEDrawSVGToggleText(disp, adisp, toggletext, font) oedepict.OERenderMolecule("depiction-toggle-atom.svg", disp) Download code depiction-toggle-atom.py

click on any atoms

See also

• OEFont class

• OEDrawSVGToggleText function

Toggle Bond Property

#!/usr/bin/env python3 from openeye import oechem from openeye import oedepict mol = oechem.OEGraphMol() oechem.OESmilesToMol(mol, "C/C=C\C1CCc2cc[nH]c2[C@@H]1C(=O)O molecule") oedepict.OEPrepareDepiction(mol) width, height, scale = 300, 200, oedepict.OEScale_AutoScale opts = oedepict.OE2DMolDisplayOptions(width, height, scale) opts.SetMargins(7.5) disp = oedepict.OE2DMolDisplay(mol, opts) family = oedepict.OEFontFamily_Default fstyle = oedepict.OEFontStyle_Default font = oedepict.OEFont(family, fstyle, 12, oedepict.OEAlignment_Center, oechem.OEDarkRed) for bdisp in disp.GetBondDisplays(): bond = bdisp.GetBond() toggletext = "bond idx=%s" % bond.GetIdx() oedepict.OEDrawSVGToggleText(disp, bdisp, toggletext, font) oedepict.OERenderMolecule("depiction-toggle-bond.svg", disp) Download code depiction-toggle-bond.py

click on middle of any bonds

See also

• OEFont class

• OEDrawSVGToggleText function

See also in OEChem TK manual

API

• OESmilesToMol function

See also in OEDepict TK manual

Theory

• Molecule Depiction chapter

• Generating Interactive SVG images chapter

API

• OE2DMolDisplay class

• OE2DMolDisplayOptions class

• OEPrepareDepiction function

• OERenderMolecule function