passing variable as SMILES string

[dpfelse]

What happened?

I have no problem passing a SMILES string to CHEM as suggested in in the online information:

: ```smiles

: CCC=O

: ```

(":" added to allow this to format correctly.)

Is correctly rendered. However, I would like to pass a variable (from a table in the front matter). This would look something like this:

: ```smiles

: = this.compound_properties["ABCD-XXXXXXXX"].SMILES

: ``` Where the table in the front matter includes the following: compound_properties: ABCD-XXXXXXXX: {ABCD#: "ABCD-XXXXXXXX", SMILES: "CCC=)"}

If I use the expression ("=this.compound_properties["ABCD-XXXXXXXX"].SMILES") by itself in Obsidian, the correct SMILES string is returned. However, in the context of the CHEM code, it gives an error.

What did you expect to happen?

I expected the structure to be rendered according to the SMILES string in my front matter table ("CCC=O" in this example)

How can we reproduce it (as minimally and precisely as possible)?

you would need to create a document with a parameter in the front matter.

Anything else we need to know?

Perhaps I have missed something obvious. I am fairly new to Obsidian.

Plugin version

0.2.1

Obsidian version

1.4.16

[dpfelse]

A small update - someone on the Obsidian forum has suggested that this may be an issue with the race conditions - the value of the SMILES string is not solved from the dataview dynamic variant ("=this.compound_properties["ABCD-XXXXXXXX"].SMILES") before it is accessed by Chem. I am not sure if there is a way to address this. For instance, can I call Chem from within dataviewjs (is there an API for Chem)? Otherwise, if Chem only accepts a string, I may be out of luck.

[Acylation]

Hi could you please refer the forum link here? Thanks for posting your use case and I will need more investigation to determine if this syntax can be supported. If this is technically applicable I would certainly like to implement it.

[dpfelse]

Hi, Thanks for your reply. I appreciate your considering this - it would be very useful to me (and I suspect others)!

The link to my original post on the Obsidian forum is here: https://forum.obsidian.md/t/passing-a-string-to-a-plugin/71973?u=dpfels

Best, Dan

[dpfelse]

Hi, Was there any progress on this? I am still interested in this feature. Thanks, Dan

[Acylation]

I've been busy these weeks but will soon be back to keyboard. Thanks for your patience and kind following up!

[Alicecomma]

Unrelated to this plugin, problem is in navigating the yaml with dataview rather than dataviewjs.

With minor changes to the yaml this works for me (list index moved into compound:, SMILES fixed because CCC=) is not valid, while CCC is):

---
compound_properties:
 - {compound: ABCD-XXXXXXXX, ABCD#: "ABCD-XXXXXXXX", SMILES: "CCC"
---

`$= "~~~ smiles\n"+dv.current().compound_properties[0].SMILES+"\n~~~"`

I don't know why you'd want individual list items to be indexed by their name, but that makes your yaml hard to work with in dataviewjs.

Regardless you cannot pass this (= runs dataview) into a codeblock and let it be rendered. You have to pass dv.current() into dataviewjs ($= runs dataviewjs; enable in-line in settings). Then for some reason ~~~smiles defines the codeblock. You use \n to simulate newlines. There may be a way to do .where(x=>x.compound==ABCD-XXXXXXXX) but I can't get this method to recognize .where().

[dpfelse]

Thanks! A couple of comments. First, "CCC=)" was (obviously) a typo. I was attempting to mask the original data from my compound list and mis-typed.

Your method works on my end. However, I was originally doing this to create a look-up table in YAML with critical compound data (including SMILES and other information) so I can pull this into notes on the fly using the "ABCD-XXXXXXX" ID# as an index. I am constantly taking notes that reference the ID#, which is not as useful as the actual structure for reminding me what is being described.

I will see if I can get ".where()" to work. However, given my limited skills, I appreciate any other suggestions you can offer. (Otherwise, I will post here if I come up with a solution of my own.)

Thanks again! Dan

[Acylation]

Thank you so much @Alicecomma !

@dpfelse I've got some references on inline queries from the forum. It seems that in a code block the inline DQL won't be supported and you have to use DataviewJS currently. Same conclusion and solution.

• https://forum.obsidian.md/t/dataview-inline-query-inside-of-a-code-block/61151
• https://forum.obsidian.md/t/dont-execute-dataview-in-code-block/58261

I'm working on incluing Dataview api to support the inline DQLs in smiles block. Hope that won't be too complicated.

[Acylation]

Hi! In the latest 0.3.0 version your proposed syntax is implemented! You can now passing a SMILES string more easily. Thanks for the patience and the request!

```smiles
= this.compound_properties["ABCD-XXXXXXXX"].SMILES
\```

[craldaz]

Hello, i joined this conversation late. Thanks for doing this. I'm reading through the convo now and trying it out. I am getting it to work a little

| Name | MR | SMILES |
| ---- | ---- | ---- |
| Propane | 44 | `$= "~~~ smiles\n"+dv.current().compound_properties[0].SMILES+"\n~~~"` |

Is that the best syntax?

[craldaz]

Cool, it also works with files outside the current note:

```dataviewjs
const files = dv.pages('"compounds"');
dv.table(
  ["File", "Name", "MR", "Structure"],
  files.map(file => {
    const name = file.name;
    const mr = file.MR;
    const smiles = file.SMILES;
    const smilesRendered = smiles ? `~~~smiles\n${smiles}\n~~~` : "N/A";
    return [file.link, name, mr, smilesRendered];
  })
);

[Alicecomma]

Update for the programmatic approach: $="~~~smiles\n"+dv.current().SMILES+"\n~~~"-type syntax only works in reading mode and in table cells for whatever reason. I've found the following to however work:

```dataviewjs
dv.paragraph("`$smiles="+dv.current().SMILES+"`");
\```

(\ before last ``` is to allow rendering in comment)

The in-line version of this sadly doesn't work for me, also not with ~ to replace `

$=dv.paragraph("`$smiles="+dv.current().SMILES+"`")
$=dv.paragraph("~$smiles="+dv.current().SMILES+"~")

Since I've used the in-line method everywhere, I replaced everything instead with a dv.view() .js script that should be able to handle changes to the Chem plugin and allow me to change the program flow across several pages. The snippet:

// Assuming the input is stored in a variable called input
function display(SMILES) {
    dv.paragraph("`$smiles="+SMILES+"`")
}

const current = dv.current();

if (input) {
    let {SMILES = null, chemical = null} = input;
    if (SMILES) {
        display(SMILES);
        return;
    }
    if (chemical && dv.page(chemical)?.SMILES) {
        display(dv.page(chemical).SMILES);
        return;
    }
}

var SMILES_c = current.SMILES;
if (current.Chemical && dv.page(current.Chemical).SMILES) {
    SMILES_c = dv.page(current.Chemical).SMILES;
}

if (SMILES_c) {
    display(SMILES_c);
    return;
}

dv.paragraph("Couldn't find SMILES from input="+str(input)+", dv.current().SMILES="+str(current.SMILES)+", dv.current().Chemical="+str(current.Chemical));

I saved it as js/displayer.js in the vault and it can be called in a dataviewjs codeblock as await dv.view("js/displayer") on the note of interest. There are optional arguments as await dv.view("js/displayer", {chemical="Butane", SMILES="CCCC"}) where the SMILES arg takes precedent over the chemical arg. The in-line version doesn't work for me in live mode, again, as it returns - or <Promise> depending on presence or absence of await.