Visualization of Molecular Chemical Structures by SMILES Notation

Snow Flower Text supports visualization of molecular chemical structures. You can embed molecular structure diagrams in your AsciiDoc documents by simply writing text in SMILES format. No additional installation is required. There is no need to use a dedicated editor for drawing molecular chemical structures.

Vitamin C
SMILES (simplified molecular input line entry system) is a line notation format for describing the chemical structure of molecules using ASCII strings. AsciiDoc’s smiles block is a proprietary extension of Snow Flower Text.

How to use the smiles block

You can embed SMILES format strings in AsciiDoc’s [smiles] block to create visualization diagrams of molecular chemical structures in your documents.

  1. Select AsciiDoc for syntax.

  2. Use the smiles block.

The following is an example for Caffeine.

[smiles]
-----
CN1C=NC2=C1C(=O)N(C(=O)N2C)C
-----

This is rendered as follows

To learn more about the SMILES format, see Simplified molecular-input line-entry system.

Samples

Dinitrogen 
[smiles]
----------------------------------------
N#N
----------------------------------------
Dinitrogen
Methyl isocyanate (MIC) 
[smiles]
----------------------------------------
CN=C=O
----------------------------------------
Methyl isocyanate (MIC)
Vanillin 
[smiles]
----------------------------------------
O=Cc1ccc(O)c(OC)c1
----------------------------------------
Vanillin
Melatonin (C13H16N2O2) 
[smiles]
----------------------------------------
CC(=O)NCCC1=CNc2c1cc(OC)cc2
----------------------------------------
Melatonin (C13H16N2O2)
Flavopereirin (C17H15N2) 
[smiles]
----------------------------------------
CCc1c[n+]2ccc3c4ccccc4[nH]c3c2cc1
----------------------------------------
Flavopereirin (C17H15N2)
Nicotine (C10H14N2) 
[smiles]
----------------------------------------
CN1CCC[C@H]1c2cccnc2
----------------------------------------
Nicotine (C10H14N2)
Oenanthotoxin (C17H22O2) 
[smiles]
----------------------------------------
CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO
----------------------------------------
Oenanthotoxin (C17H22O2)
Pyrethrin II (C22H28O5) 
[smiles]
----------------------------------------
CC1=C(C(=O)C[C@@H]1OC(=O)[C@@H]2[C@H](C2(C)C)/C=C(\C)/C(=O)OC)C/C=C\C=C
----------------------------------------
Pyrethrin II (C22H28O5)
Aflatoxin B1 (C17H12O6) 
[smiles]
----------------------------------------
COC1=C2C3=C(C(=O)CC3)C(=O)OC2=C4[C@@H]5C=CO[C@@H]5OC4=C1
----------------------------------------
Aflatoxin B1 (C17H12O6)
Glucose (β-D-glucopyranose) (C6H12O6) 
[smiles]
----------------------------------------
OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)1
----------------------------------------
Glucose (β-D-glucopyranose) (C6H12O6)
Bergenin (cuscutin, a resin) (C14H16O9) 
[smiles]
----------------------------------------
OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2
----------------------------------------
Bergenin (cuscutin, a resin) (C14H16O9)
A pheromone of the Californian scale insect 
[smiles]
----------------------------------------
CC(=O)OCCC(/C)=C\C[C@H](C(C)=C)CCC=C
----------------------------------------
A pheromone of the Californian scale insect
(2S,5R)-Chalcogran: a pheromone of the bark beetle Pityogenes chalcographus 
[smiles]
----------------------------------------
CC[C@H](O1)CC[C@@]12CCCO2
----------------------------------------
(2S,5R)-Chalcogran: a pheromone of the bark beetle Pityogenes chalcographus
α-Thujone (C10H16O) 
[smiles]
----------------------------------------
CC(C)[C@@]12C[C@@H]1[C@@H](C)C(=O)C2
----------------------------------------
α-Thujone (C10H16O)
Thiamine (vitamin B1, C12H17N4OS+) 
[smiles]
----------------------------------------
OCCc1c(C)[n+](cs1)Cc2cnc(C)nc2N
----------------------------------------
Thiamine (vitamin B1, C12H17N4OS+)

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Reference