handle missing atoms (ignore hydrogen, fail for heavy)

src/mol-io/writer/ligand-encoder.ts

@@ -137,6 +137,10 @@ export abstract class LigandEncoder implements Encoder<string> {
         if (this.hydrogens) {
             return false;
         }
+        return this.isHydrogen(type_symbol);
+    }
+
+    protected isHydrogen(type_symbol: string & { '@type': 'element-symbol' }) {
         return isHydrogen(getElementIdx(type_symbol));
     }
 

src/mol-io/writer/mol/encoder.ts

@@ -35,8 +35,18 @@ export class MolEncoder extends LigandEncoder {
         // traverse once to determine all actually present atoms
         const atoms = this.getAtoms(instance, source);
         atoms.forEach((atom1, label_atom_id1) => {
-            const { index: i1 } = atom1;
-            const { charge, stereo_config } = atomMap.map.get(label_atom_id1)!;
+            const { index: i1, type_symbol: type_symbol1 } = atom1;
+            const atomMapData1 = atomMap.map.get(label_atom_id1);
+
+            if (!atomMapData1) {
+                if (this.isHydrogen(type_symbol1)) {
+                    return;
+                } else {
+                    throw Error(`Unknown atom ${label_atom_id1} for component ${name}`);
+                }
+            }
+
+            const { charge, stereo_config } = atomMapData1;
             StringBuilder.writePadLeft(ctab, atom1.Cartn_x.toFixed(4), 10);
             StringBuilder.writePadLeft(ctab, atom1.Cartn_y.toFixed(4), 10);
             StringBuilder.writePadLeft(ctab, atom1.Cartn_z.toFixed(4), 10);

src/mol-io/writer/mol2/encoder.ts

@@ -29,14 +29,27 @@ export class Mol2Encoder extends LigandEncoder {
         const name = this.getName(instance, source);
         StringBuilder.writeSafe(this.builder, `# Name: ${name}\n# Created by ${this.encoder}\n\n`);
 
+        const atomMap = this.componentAtomData.entries.get(name)!;
         const bondMap = this.componentBondData.entries.get(name)!;
+        // happens for the unknown ligands (UNL)
+        if (!atomMap) throw Error(`The Chemical Component Dictionary doesn't hold any atom data for ${name}`);
         let bondCount = 0;
 
         const atoms = this.getAtoms(instance, source);
         StringBuilder.writeSafe(a, '@<TRIPOS>ATOM\n');
         StringBuilder.writeSafe(b, '@<TRIPOS>BOND\n');
         atoms.forEach((atom1, label_atom_id1) => {
-            const { index: i1 } = atom1;
+            const { index: i1, type_symbol: type_symbol1 } = atom1;
+            const atomMapData1 = atomMap.map.get(label_atom_id1);
+
+            if (!atomMapData1) {
+                if (this.isHydrogen(type_symbol1)) {
+                    return;
+                } else {
+                    throw Error(`Unknown atom ${label_atom_id1} for component ${name}`);
+                }
+            }
+
             if (bondMap?.map) {
                 bondMap.map.get(label_atom_id1)!.forEach((bond, label_atom_id2) => {
                     const atom2 = atoms.get(label_atom_id2);
@@ -52,7 +65,7 @@ export class Mol2Encoder extends LigandEncoder {
                 });
             }
 
-            const sybyl = bondMap?.map ? this.mapToSybyl(label_atom_id1, atom1.type_symbol, bondMap) : atom1.type_symbol;
+            const sybyl = bondMap?.map ? this.mapToSybyl(label_atom_id1, type_symbol1, bondMap) : type_symbol1;
             StringBuilder.writeSafe(a, `${i1 + 1} ${label_atom_id1} ${atom1.Cartn_x.toFixed(3)} ${atom1.Cartn_y.toFixed(3)} ${atom1.Cartn_z.toFixed(3)} ${sybyl} 1 ${name} 0.000\n`);
         });
 

src/servers/model/server/query.ts

@@ -237,10 +237,8 @@ async function resolveJobEntry(entry: JobEntry, structure: StructureWrapper, enc
         encoder.writeCategory(_model_server_params, entry);
 
         if (entry.queryDefinition.niceName === 'Ligand') {
-            if (encoder instanceof MolEncoder) {
-                encoder.setComponentAtomData(ComponentAtom.Provider.get(structure.models[0])!);
-            }
             if (encoder instanceof MolEncoder || encoder instanceof Mol2Encoder) {
+                encoder.setComponentAtomData(ComponentAtom.Provider.get(structure.models[0])!);
                 encoder.setComponentBondData(ComponentBond.Provider.get(structure.models[0])!);
             }
         }