Script to extract ion names from CCD

[arose]

Should extend the existing cli/chem-comp-bonds/ script (renamed to chem-comp). Data should go to src\mol-model\structure\model\types\ions.ts. Include all chemical components with the word "ion" in their name. Will replace IonNames in src\mol-model\structure\model\types.ts.

Related: #63

[thetechnocrat-dev]

Is this still a good first issue?

[arose]

Is this still a good first issue?

Yes it is!

[thetechnocrat-dev]

I noticed there is a src/cli/lipid-params/index.ts file that does for lipids what this new function should do for ions.

I also noticed the current hardcoded IonNames have a comment above on how to extract all ions:

/**
 * TODO write script that read CCD and outputs list of ion names
 *
 * all chemical components with the word "ion" in their name, Sep 2016
 *
 * SET SESSION group_concat_max_len = 1000000;
 * SELECT GROUP_CONCAT(id_ ORDER BY id_ ASC SEPARATOR '", "') from
 * (
 *     SELECT count(obj_id) as c, id_
 *     FROM pdb.chem_comp WHERE name LIKE "% ION%"
 *     GROUP BY id_
 * ) AS t1;
 */
export var IonNames = new Set([
    '118', '119', '1AL', '1CU', '2FK', '2HP', '2OF', '3CO', ...

Lastly, I am able to run node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b to create the ccb.bcif locally. Where I'm stuck is what functions to use to query this file. Do you have any guidance to point me in the right direction?

[arose]

HI @McMenemy, if you reuse readCCD you can loop over all components like below. No need to create ccb.bcif here.

const ccd = await readCCD();
for (const k in ccd) {
    const { chem_comp } = ccd[k];
    if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
        // found ion, write out `chem_comp.id.value(0)`
    }
}

[thetechnocrat-dev]

@arose Thanks for the pointers to get started, exactly what I needed 💯 . Here is the the PR that goes with this issue.

[thetechnocrat-dev]

Should this issue get closed now?