Draw a cartoon

With HELMshaker, you can visualize an oligonucleotide and customize the cartoon. For ASOs, a single strand is drawn. For siRNAs, the cartoon is based on the hydrogen pairings in the molecule. These pairings need to be available for siRNA cartoon visualizations.

Customization Options

1. title: Title of the plot
2. start_polymer: Optional, the strand which is drawn first from left to right (will be on top)
3. show_position: Shows the numbering of nucleotide positions
4. show_direction: Annotates 5' and 3' ends
5. show_legend: Shows the color legend
6. show_base: Annotates bases
7. color_map: Custom color map (if desired)
8. show_phosphate: Shows specific phosphate linkers
9. show_conjugate: Annotates the conjugate names
10. font_size: Font size, scaling up all fonts in the cartoon

Examples

The examples below all draw the same siRNA. Load it once, against a library you have already loaded. HELMshaker ships no monomers, so see Monomer Libraries for how to get one.

from helmshaker import Molecule, MonomerLibrary

library = MonomerLibrary()
library.load_from_file("monomers.json")  # your dictionary, or one pulled from TMR

sirna = "CHEM1{[Ahx]}|CHEM2{[PEG4]}|RNA1{[fl2r](U)[sp].[m](C)[sp].[fl2r](U)p.[m](C)p.[fl2r](G)p.[m](U)p.[fl2r](G)p.[m](G)p.[fl2r](C)p.[m](C)p.[fl2r](U)p.[m](U)p.[fl2r](A)p.[m](A)p.[fl2r](U)p.[m](G)p.[fl2r](A)p.[m](A)[sp].[fl2r](A)[sp].[fl2r](T)}|RNA2{[fl2r](U)[sp].[fl2r](U)p.[fl2r](U)p.[fl2r](C)p.[fl2r](A)p.[fl2r](U)p.[fl2r](U)p.[fl2r](A)p.[fl2r](A)p.[fl2r](G)p.[fl2r](G)p.[fl2r](C)p.[fl2r](C)p.[fl2r](A)p.[fl2r](C)p.[fl2r](G)p.[fl2r](A)p.[fl2r](G)p.[fl2r](A)p.[fl2r](U)[sp].[fl2r](U)}$RNA1,CHEM1,61:R2-1:R1|CHEM1,CHEM2,1:R2-1:R1|RNA1,RNA2,2:pair-56:pair|RNA1,RNA2,56:pair-2:pair$$$V2.0"

molecule = Molecule.from_helm(sirna, monomer_library=library)

A simple cartoon of a naked siRNA:

fig, ax = molecule.visualize_cartoon(
    show_position=False,
    show_conjugate=False,
    show_direction=False
)
fig.savefig('sample.png')

Add positions and conjugates:

fig, ax = molecule.visualize_cartoon(
    show_position=True,
    show_conjugate=True,
    show_direction=True
)
fig.savefig('sample.png')

Add specific phosphate linkers:

fig, ax = molecule.visualize_cartoon(
    show_base=False,
    show_direction=True,
    show_position=True,
    show_phosphate=True,
    show_legend=True,
    show_conjugate=True
)
fig.savefig('sample.png')

Add bases:

fig, ax = molecule.visualize_cartoon(
    show_position=True,
    show_base=True,
    show_conjugate=True,
    show_direction=True
)
fig.savefig('sample.png')

Full Example

from helmshaker import Molecule

sirna = "CHEM1{[Ahx]}|CHEM2{[PEG4]}|RNA1{[fl2r](U)[sp].[m](C)[sp].[fl2r](U)p.[m](C)p.[fl2r](G)p.[m](U)p.[fl2r](G)p.[m](G)p.[fl2r](C)p.[m](C)p.[fl2r](U)p.[m](U)p.[fl2r](A)p.[m](A)p.[fl2r](U)p.[m](G)p.[fl2r](A)p.[m](A)[sp].[fl2r](A)[sp].[fl2r](T)}|RNA2{[fl2r](U)[sp].[fl2r](U)p.[fl2r](U)p.[fl2r](C)p.[fl2r](A)p.[fl2r](U)p.[fl2r](U)p.[fl2r](A)p.[fl2r](A)p.[fl2r](G)p.[fl2r](G)p.[fl2r](C)p.[fl2r](C)p.[fl2r](A)p.[fl2r](C)p.[fl2r](G)p.[fl2r](A)p.[fl2r](G)p.[fl2r](A)p.[fl2r](U)[sp].[fl2r](U)}$RNA1,CHEM1,61:R2-1:R1|CHEM1,CHEM2,1:R2-1:R1|RNA1,RNA2,2:pair-56:pair|RNA1,RNA2,56:pair-2:pair$$$V2.0"

molecule = Molecule.from_helm(sirna, monomer_library=library)

fig, ax = molecule.visualize_cartoon(
    title="siRNA Visualization",
    start_polymer="RNA2",  # polymer to start drawing from, this will be on top
    show_base=True,        # annotates bases
    show_direction=True,   # annotates 5' and 3' ends
    show_position=True,    # annotates each nucleotide position
    show_phosphate=True,   # color the phosphate linkers
    show_conjugate=True,
    show_legend=True,      # shows color legend
    font_size=12           # font size
)

fig.savefig("sample.png")

Working with the Figure and Axes

The visualize_cartoon() method returns a tuple of (Figure, Axes) for further customization:

fig, ax = molecule.visualize_cartoon(show_position=False)

# Further customize with matplotlib
ax.set_title("Custom Title", fontsize=16)
fig.tight_layout()
fig.savefig('sample.png', dpi=300)

ASO Cartoon

The ASO cartoon has the same customization options:

aso = "CHEM1{[Ahx]}|CHEM2{[PEG4]}|CHEM3{[OVal]}|RNA1{p.[d](C)p.[d](A)p.[lna](G)[sp].[lna](A)[sp].[lna](G)[sp].[d](T)[sp].[d](T)[sp].[d](A)[sp].[d](C)[sp].[d](T)[sp].[d](T)[sp].[d](G)[sp].[d](C)[sp].[d](C)[sp].[d](A)[sp].[lna](A)[sp].[lna]([m5C])[sp].[lna](T)[sp]}$CHEM1,RNA1,1:R2-1:R1|RNA1,CHEM2,55:R2-1:R1|CHEM2,CHEM3,1:R2-1:R1$$$V2.0"

molecule = Molecule.from_helm(aso, monomer_library=library)

fig, ax = molecule.visualize_cartoon(
    show_phosphate=True,
    show_base=True
)
fig.savefig("aso.png")