Moleco

Moleco stands for molecule to color. It generates unique color swatch for given substance based on its InChI notation. It can also generate color identification for mixture using MInChI notation.

How to run

moleco generate "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3" --print

That will generate a color swatch for caffeine.

Installation

For now you can only install it with help of cargo, rust package manager.

cargo install moleco

Support for mixtures

Of course in nature there is much more likely to see mixtures instead of single substances, so MInChI is supported as well. You can generate toothpaste:

moleco generate "MInChI=0.00.1S/C12H26O4S.Na/c1-2-3-4-5-6-7-8-9-10-11-12-16-17(13,14)15;/h2-12H2,1H3,(H,13,14,15);/q;+1/p-1&C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2&C7H5NO3S.Na/c9-7-5-3-1-2-4-6(5)12(10,11)8-7;/h1-4H,(H,8,9);/q;+1/p-1&Ca.H3O4P.2H2O/c;1-5(2,3)4;;/h;(H3,1,2,3,4);2*1H2/q+2;;;/p-2&FH2O3P.2Na/c1-5(2,3)4;;/h(H2,2,3,4);;/q;2*+1/p-2&H2O/h1H2/n{6&2&&5&3&4&1}/g{215wf-3&25wf-2&1wf-2&8wf-3&2wf-3&5wf-1&15wf-3}" --print

or dishwashing liquid:

moleco generate "MInChI=0.00.1S/C12H26O4S.Na/c1-2-3-4-5-6-7-8-9-10-11-12-16-17(13,14)15;/h2-12H2,1H3,(H,13,14,15);/q;+1/p-1&C18H30O3S.Na/c1-2-3-4-5-6-7-8-9-10-11-12-17-13-15-18(16-14-17)22(19,20)21;/h13-16H,2-12H2,1H3,(H,19,20,21);/q;+1/p-1&ClH.Na/h1H;/q;+1/p-1&H2O/h1H2/n{4&{2&4}&&{1&4}&3}/g{807wf-3&{6pp1&4pp1}117wf-3&1wf-2&{27pp0&73pp0}66wf-3&}" --print

or solution of 9-Borabicyclo[3.3.1]nonane in undefined amounts of hexanes:

moleco generate "MInChI=0.00.1S/C6H12/c1-6-4-2-3-5-6/h6H,2-5H2,1H3&C6H14/c1-3-5-6-4-2/h3-6H2,1-2H3&C6H14/c1-4-5-6(2)3/h6H,4-5H2,1-3H3&C6H14/c1-4-6(3)5-2/h6H,4-5H2,1-3H3&C8H15B/c1-3-7-5-2-6-8(4-1)9-7/h7-9H,1-6H2/n{5&{2&3&4&1}}/g{4mr-1&{&&&}}" --print

or, if you are fan, you can generate bechamel sauce:

moleco generate "MInChI=0.00.1S/C12H17N4OS.ClH/c1-8-11(3-4-17)18-7-16(8)6-10-5-14-9(2)15-12(10)13;/h5,7,17H,3-4,6H2,1-2H3,(H2,13,14,15);1H/q+1;/p-1&C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t11-,12+,14-/m0/s1&C19H19N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,8,12,21H,5-7H2,(H,24,29)(H,27,28)(H,31,32)(H3,20,22,25,26,30)/t12-/m0/s1&C20H30O/c1-16(8-6-9-17(2)13-15-21)11-12-19-18(3)10-7-14-20(19,4)5/h6,8-9,11-13,21H,7,10,14-15H2,1-5H3/b9-6+,12-11+,16-8+,17-13+&C27H44O/c1-19(2)8-6-9-21(4)25-15-16-26-22(10-7-17-27(25,26)5)12-13-23-18-24(28)14-11-20(23)3/h12-13,19,21,24-26,28H,3,6-11,14-18H2,1-2,4-5H3/b22-12+,23-13-/t21-,24+,25-,26+,27-/m1/s1&C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1&C6H5NO2/c8-6(9)5-2-1-3-7-4-5/h1-4H,(H,8,9)&C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)&C9H17NO5/c1-9(2,5-11)7(14)8(15)10-4-3-6(12)13/h7,11,14H,3-5H2,1-2H3,(H,10,15)(H,12,13)/t7-/m0/s1&Ca/q+2&Na/q+1/n{{{{&}&6&11&&4}&{{&}&&&1&2&7&9&8&3&}}&{{&}&6&11&&&4&5&10}}/g{{{{56wf-2&25wf-3}8wf-1&3wf-3&1wf-2&125wf-4&}466wf-3&{{56wf-4&168wf-3}725wf-3&187wf-4&137wf-3&447wf-8&215wf-8&6365wf-8&1008wf-8&341wf-8&49wf-8&9wf-3}534wf-3}1pp1&{{6wv-1&2wv-2}2wv-2&8wv-5&48wv-5&48wv-3&36wv-3&&&}9pp1}" --print

How mixture bar sizes are calculated

First of all - values at mixture bar (at the bottom for mixtures) are on logharitmic scale. This may be problematic, since if you consider two solutions of ethanol, one 40% and second 70% - its hard to see what is what:

Not really a difference.

But that was not the goal - the goal was to quickly differ between solutions with small amounts of potentially harmful chemicals. Consider again solution of ethanol - one 40% in water, second 40% of ethanol and 0.1% of bitrex (denatonium benzoate) in water.

Now its easy to make a difference even if there are trace amounts of extra substances.

Order of color swatches

Moleco will try to keep original order of substances in mixture - the one given in command (MInChi demo (see links below) have specific order for substances). It may happen though that one of substances in middle of notation has missing or unestimated concentration - in such case its swatch will be moved to the end of the bar, so primary colors of substances will be visibly matching to bar colors.

Good example of such behavior is image of dishwashing liquid - if you decipher notation you will see that third substance (sodium chloride) has missing concentration, so it is moved to the end of the bar, behind water swatch.

Unknown and unestimated capacity

Sometimes you will not pass all the concentration in mixture, like in this 37% solution of formaldehyde in water:

moleco generate "MInChI=0.00.1S/CH2O/c1-2/h1H2&H2O/h1H2/n{1&2}/g{37wf-2&}" --print

It is easy to calculate remaining amount of water (not in molar sense, but since sizes are logarithmic, it does not matter) - it is 63%. But what if there are two solvants like water and methanol without giving their concentrations - then it is possible to estimate remaining amount, but not exact amount of each solvent. In such case the remaining compound is marked as unknown.

moleco generate "MInChI=0.00.1S/CH2O/c1-2/h1H2&CH4O/c1-2/h2H,1H3 &H2O/h1H2/n{1&3&2}/g{37wf-2&&}" --print

Furthermore, if you use ratio (VP) in notation and you wont pass concentration of at least one ingredient, then the remaining amount is marked as unestimated.

moleco generate "MInChI=0.00.1S/CH2O/c1-2/h1H2&H2O/h1H2/n{1&2}/g{37vp0&}" --print

Similar is with molar per liter/kilogram notions - MB and MR - if you use them at all the bar will show extra unestimated and unknown compound. It is becauce moleco is not calculating molar mass and volumes (it doesn't contain any internal database for substances), so it assumes that there is something extra as the result.

moleco generate "MInChI=0.00.1S/CH2O/c1-2/h1H2&H2O/h1H2/n{1&2}/g{37mb0&63mb0}" --print

Extra concentration notes

In case of range notation, like "10:20" only higher amount will be taken into account. This is due to fact that moleco is trying to estimate unknown/unestimated substances and if max possible solution is exceeding potential capacity - it is assumed user knows what he is doing. If you want to show extra substance, because you know there is some, you can always add it as separate, unmarked substance. See exambles below - second one is showing extra substance because one extra group is added to indexation and concentration notation.

moleco generate "MInChI=0.00.1S/C2H6O/c1-2-3/h3H,2H2,1H3&H2O/h1H2/n{1&2}/g{4vp1&6vp1}" --print-only

vs

moleco generate "MInChI=0.00.1S/C2H6O/c1-2-3/h3H,2H2,1H3&H2O/h1H2/n{1&2&}/g{4vp1&6vp1&}" --print-only

results look like

Motivation

TODO

Questions

Why no support for molar mass and volume?

That would require incorporating some database of substances and their properties. This is way above the initial scope of this project, but could be considered in future.

Are there collisions?

TODO

Why no support for InChIKey?

TODO

Why the shape?

Diamond divided into four parts was initial idea, usually when creating color swatch you will get 4 or 5 colors, but to have nice complement hue - 4 is easy to generate and diamond shape looks nice. To avoid confusion with NFPA 704 marking - cutouts were introduced - therefore this "flower" shape.

Orientation mark is introduced as well to not be confused in case if single compound mark.

How to recognize the substance?

It may be challenging to recognize the substance based on the color swatch after some time, so be sure to keep the name of substance or InChI notation somewhere close if you are using just the swatch. If you have original image file though - original substance will be saved in EXIF metadata.

References

IhChI and MInChI

• https://jcheminf.biomedcentral.com/articles/10.1186/s13321-015-0068-4
• https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0357-4
• http://molmatinf.com/minchidemo/
• https://github.com/IUPAC/MInChI_demo

Color spaces

• https://paletton.com/
• https://ericportis.com/posts/2024/okay-color-spaces/

PubChem resources

• https://pubchem.ncbi.nlm.nih.gov/
• https://pubchem.ncbi.nlm.nih.gov/docs/compound-vs-substance