Fix producePdb atom num for >100k atoms

Author: RubenChM

src/routes/projects/structure/produce-pdb/index.js

@@ -57,7 +57,8 @@ const producePdb = (topologyData, frameCoordinates, atomIndices) => {
         const tempFactor = '0.00';
         // Add 1 to de count and set the PDB index according to the count
         count += 1;
-        const pdbCount = count.toString().padStart(5, ' ');
+        // Wrap the displayed serial to 1 after 99999 to keep its five-column field fixed.
+        const pdbCount = ((count - 1) % 99999 + 1).toString().padStart(5, ' ');
         // Add the new line to the PDB content
         pdbContent += `ATOM  ${pdbCount} ${pdbAtomName} ${pdbResidueName}${pdbChainName}${pdbResidueNumber}` +
             `${pdbResidueIcode}   ${xCoord}${yCoord}${zCoord}  ${occupancy}  ${tempFactor}          ${pdbAtomElements}\n`;
@@ -66,4 +67,4 @@ const producePdb = (topologyData, frameCoordinates, atomIndices) => {
     return pdbContent;
 };
 
-module.exports = producePdb;
+module.exports = producePdb;

src/routes/projects/structure/produce-pdb/index.test.js

@@ -0,0 +1,33 @@
+const producePdb = require('.');
+
+test('atom serial rollover preserves fixed columns and coordinate indexing', () => {
+  const nAtoms = 200001;
+  const topology = {
+    atom_names: Array(nAtoms).fill('CA'),
+    atom_elements: Array(nAtoms).fill('C'),
+    atom_residue_indices: Array(nAtoms).fill(0),
+    residue_names: ['ALA'],
+    residue_numbers: [1],
+    residue_chain_indices: [0],
+    chain_names: ['A'],
+  };
+  const coordinates = Array(nAtoms).fill([1.25, -2.5, 3.75]);
+  coordinates[99999] = [4.5, 5.25, -6.75];
+  const lines = producePdb(topology, coordinates).trimEnd().split('\n').slice(1);
+
+  expect(lines).toHaveLength(nAtoms);
+  for (const [index, serial] of [[0, '    1'], [99998, '99999'],
+    [99999, '    1'], [100000, '    2'], [199997, '99999'],
+    [199998, '    1'], [199999, '    2'], [200000, '    3']]) {
+    const line = lines[index];
+    expect(line).toHaveLength(78);
+    expect(line.slice(6, 11)).toBe(serial);
+    expect(line.slice(12, 16)).toBe(' CA ');
+    expect(line.slice(17, 20)).toBe('ALA');
+    expect(line[21]).toBe('A');
+    expect(line.slice(22, 26)).toBe('   1');
+    expect([line.slice(30, 38), line.slice(38, 46), line.slice(46, 54)].map(Number))
+      .toEqual(coordinates[index]);
+    expect(line.slice(76, 78)).toBe(' C');
+  }
+});