Run NGL.autoLoad on whole PDB (usuing local mirror)

gistfile1.txt

/**
 * Quick script to check cif parsing in NGL by attempting to 
 * autoLoad all entries from a local mirror.
 * Smoke test rather than thorough validation!
 */

const _ = require('browser-env')()
const fs = require('fs');
const path = require('path');

const { promisify } = require('util');

const NGL = require("./build/js/ngl.dev.js")

// Set pdbRoot appropriately to local mirror of PDB
const pdbRoot = "";
const cifRoot = pdbRoot + "/mmCIF/entries";

// Promisify the required functions
const readdir = promisify(fs.readdir);
const readFile = promisify(fs.readFile);


async function parseCifFiles() {
  try {
    // Read all subdirectories
    const subdirs = await readdir(cifRoot);
    
    for (const subdir of subdirs) {
      const subdirPath = path.join(cifRoot, subdir);
      
      // Ensure it's a directory
      if (!fs.lstatSync(subdirPath).isDirectory()) {
        continue;
      }
      // Read all CIF files in the subdirectory
      const files = await readdir(subdirPath);
      
      for (const file of files) {
        if (file.endsWith('.cif.gz')) {
          const filePath = path.join(subdirPath, file);
          
          await loadCif(filePath)
        }
      }
    }
  } catch (err) {
    console.error('Error reading directories:', err);
  }
}

async function loadCif(filePath) {
  try {
    const data = await readFile(filePath)
    const f = new File([data], filePath)
    await NGL.autoLoad(f)
    console.log(`Successfully parsed: ${filePath}`);
  } catch (err) {
    console.log(`Error parsing ${filePath}:`, err);
  }
}

parseCifFiles();