Integrate MolQL transpilers in Mol*

[ptourlas]

Greetings!

I have seen the examples offered at http://molql.org/explorer.html and I would like to integrate the PyMol and VMD transpilers in a Molstar fork that I have. My goal is to allow selections from any language the user prefers, just like in the MolQL explorer. From what I understand, the transpilers produce something pretty close to what Molstar "speaks". For example,
StructureSelectionQueries.water.expression() (see https://github.com/molstar/molstar/blob/704a9a111dff82e3566276068b1c33505570ccb7/src/mol-plugin-state/helpers/structure-selection-query.ts#L276)
returns:

{
    head: {
      name: "structure-query.modifier.union",
    },
    args: [
      {
        head: {
          name: "structure-query.generator.atom-groups",
        },
        args: {
          "entity-test": {
            head: {
              name: "core.rel.eq",
            },
            args: [
              {
                head: {
                  name: "structure-query.atom-property.macromolecular.entity-type",
                },
              },
              "water",
            ],
          },
        },
      },
    ],
  }

which I can use to add a representation for the waters in a given structure.

On the other hand, water selection in the MolQL explorer yields:

{
  "source": "molql-explorer",
  "version": "0.1.0",
  "expression": {
    "head": "structure.generator.atom-groups",
    "args": {
      "residue-test": {
        "head": "core.set.has",
        "args": [
          {
            "head": "core.type.set",
            "args": [
              "H2O",
              "HH0",
              "OHH",
              "HOH",
              "OH2",
              "SOL",
              "WAT",
              "TIP",
              "TIP2",
              "TIP3",
              "TIP4"
            ]
          },
          {
            "head": "structure.atom-property.macromolecular.label_comp_id"
          }
        ]
      }
    }
  }
}

I tried to substitute the first query with the expression part of the second, but Molstar greeted me with an Error: Can only apply symbols message.
Any hints on how to approach this?

[dsehnal]

Hi, this should be possible without too many changes. The example you provided is "broken" because the structure namespace has been renamed to structure-query in Mol*, but mostly the language is the same.

Just getting the source from https://github.com/MolQL/molql/tree/master/src/transpilers/pymol and vmd folders and placing it in https://github.com/molstar/molstar/tree/master/src/mol-script should get you most of the way.

Notable replacements are parsimmon => mol-util/monadic-parser and /molql/builder => mol-script/language/builder's MolScriptBuilder.

Would you be willing to make a PR to the Mol* repository with this and we can make it work there? I am sure other people would appreciate this as well!

[ptourlas]

As a handy reference to anyone interested, the relevant PR is molstar/molstar#325