Chain-level operations

Hello! How can I copy, delete and transform chains programmatically? Should I do it after trajectory load? (our extension downloading mmCIF data)

    const trajectory = await builders.structure.parseTrajectory(data, 'mmcif');
    await applyTransformations(pdbtmDescriptor, trajectory);

pdbtmDescriptor contains our custom operations that transform the PDB coordinates at level of atoms. I am looking for functions to access and modifies atoms of specified chains with no low level array operations.

        let atomicConformationX = trajectory.data.representative.atomicConformation.x;
        let atomicConformationY = trajectory.data.representative.atomicConformation.y;
        let atomicConformationZ = trajectory.data.representative.atomicConformation.z;

        for (let i = 0; i < atomicConformationX.length; i++) {
            let coords = {
                x: atomicConformationX[i],
                y: atomicConformationY[i],
                z: atomicConformationZ[i]
            };
            coords = applyTransformationMatrix(coords, tmatrix);
            new_x.push(coords.x);
            new_y.push(coords.y);
            new_z.push(coords.z);
        }

I had to overwrite the xyz arrays with new arrays to apply the changes on the structure. Do you have any better or higher level way to achieve the same effect? Thank you.

[cycle20]

Thank you. I can exclude chains by hacking this function. It is just a hard-wired prototyping update, but it works. …and thank you for your patience in guiding me through this problem 😉

[dsehnal]

This is how the selector is built from the assembly records in mmCIF: https://github.com/molstar/molstar/blob/master/src/mol-model-formats/structure/property/assembly.ts#L62

You should be able to take that and just replace gen.asymIds with your chain names (maybe you will need to use auth_asym_id instead depending on which identifiers you require).

I know this is quite overwhelming as Mol* is a big library, but hopefully we will chew through that 😃