Add formal charge label to representation

Greetings!

Is there a quick and painless way to add a label displaying the formal charge (M CHG 1 8 -1) to the nitrogen at position 8 ( 0.2451 -0.3881 -0.5673 N 5 5 0 0 0 2 0 0 0 0 0 0)

SMILES-CFFFSOON-SOOCFFF
     RDKit          3D

 15 14  0  0  0  0  0  0  0  0999 V2000
    2.4644   -0.6833    0.6783 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1589   -0.1223   -0.3545 F   0  0  0  0  0  0  0  0  0  0  0  0
    2.4354   -2.0263    0.4264 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.2334   -0.5214    1.7934 F   0  0  0  0  0  0  0  0  0  0  0  0
    0.7862    0.0206    0.8608 S   0  0  0  0  0  6  0  0  0  0  0  0
    0.9929    1.4434    1.1263 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1705   -0.7131    1.9690 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2451   -0.3881   -0.5673 N   5  5  0  0  0  2  0  0  0  0  0  0 <--------
   -1.0100    0.4366   -1.0736 S   0  0  0  0  0  6  0  0  0  0  0  0
   -1.6478   -0.2086   -2.2311 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7964    1.8705   -1.2847 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2304    0.2627    0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3428   -1.0280    0.7238 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9714    1.0394    1.3799 F   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4880    0.6179   -0.1175 F   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
  5  6  2  0
  5  7  2  0
  5  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  2  0
  9 12  1  0
 12 13  1  0
 12 14  1  0
 12 15  1  0
M  CHG  1   8  -1
M  END
$$$$

From what I understand, I could parse the file to get the charges and the atom ID’s and then add the labels manually with something similar to this:

styleProps = styleProps || { borderWidth: 0.1, borderColor: molstar.COLOR_NAMES.white };
            const atomExpression = this.expressions.atom;
            const structure = _structures[structureKey].data;
            const context = _plugin.managers.task.currentContext;

            Object.keys(atomLabels).forEach((atomId) => {
                const _atomId = parseInt(atomId)

                const query = molstar.StructureSelectionQuery('Query', atomExpression(_atomId));
                query.getSelection(_plugin, context, structure)
                    .then((selection) => {
                        const loci = molstar.StructureSelection.toLociWithSourceUnits(selection);

                        molstar.createTextRepresentation({ text: atomLabels[atomId], loci, size }, styleProps)
                            .then((label) => {
                                label.setState({ pickable: false });
                                _plugin.canvas3d.add(label);

                                if (!_representations[structureKey][representationKey]) {
                                    _representations[structureKey][representationKey] = [];
                                }
                                _representations[structureKey][representationKey].push(label);
                            });
                    });
            });

But I also saw this, https://github.com/molstar/molstar/blob/7a25699c2353c4142286c3403d3ab2416f48043c/src/mol-model/structure/model/properties/atomic/hierarchy.ts#L51 which made think that mol* is already aware of formal charges in some way.

Thanks in advance.

[ptourlas]

While you are at it, how about you add a formal-charge color theme similar to mol-theme/color/partial-charge.ts?

I am willing to work on this as well once I get the formal charge labels working. 👍

[ptourlas]

@ptourlas What would you like to do with that? The Loci/Location should get passed down automatically to the relevant parts of the code (e.g. when you are creating a label provider: https://github.com/molstar/molstar/blob/master/src/extensions/pdbe/structure-quality-report/behavior.ts#L27, there you can use StructureProperties.atom.pdbx_formal_charge(location); sorry if I created confusion about Loci vs Location; Loci is "multiple locations`` and you always need a single one to pass to the property getter).

This clarifies my use case. Since the relevant PR is also merged, I am closing the issue. Thanks!