Loading in PDB from JSON

[Dave-Montgomery]

I have a database of over 160,000 entries with small pdb files that are returned as a part of a JSON object. Is there any way to feed the pdb file in from the JSON object without making a file first?

[dsehnal]

Yes. Make a transform that parses the JSON from the downloaded string and returns the string with the PDB data. You can even make it “parametric” if a single Json contains more pdb structures. Similar to https://github.com/dsehnal/LiteMol/blob/master/src/Viewer/PDBe/Validation.ts#L184

The rest is just using the same transforms you would use with downloading, similar to say https://github.com/dsehnal/LiteMol/blob/master/examples/Channels/src/State.ts#L48

If you need more help let me know.

[gitoliver]

Hi David, We need more help on this. Dave would have to modify the LiteMol code to do this right? So you are proposing we use the loadData function as a template and modify it? I don't see how to do this without writing further code.

We'd need something like this:

export function loadData(plugin: Plugin.Controller, pdbId: string, pdbFileAsString: string) { return new Promise((res, rej) => { plugin.clear();

        let model = plugin.createTransform()
            .add(plugin.root, Transformer.Data.Download, { file: $pdbFileAsString, type: 'String', id: pdbId })
            .then(Transformer.Molecule.CreateFromData, { format: Core.Formats.Molecule.SupportedFormats.PDB }, { isBinding: true })

// What does the isBinding doing? .then(Transformer.Molecule.CreateModel, { modelIndex: 0 }) .then(Transformer.Molecule.CreateMacromoleculeVisual, { polymer: true, polymerRef: 'polymer-visual', het: true })

[dsehnal]

Right, you already have the JSON parsed.

Then just replace the Download transform with this FromData one and it will work https://github.com/dsehnal/LiteMol/blob/master/src/lib/Bootstrap/Entity/Transformer/Data.ts#L126

Btw isBinding is a UI thing meaning the parent node will be hidden in the tree.

David

[Dave-Montgomery]

Thank you! Worked like a charm.