ModelServer SDF/MOL2 ligand export: fix atom indices for atoms not present in the CCD (#1007)

* ModelServer: fix atom indices upon additional hydrogen atoms

* cl

* ignore all non-CCD atoms

CHANGELOG.md

@@ -6,7 +6,8 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
-- Fix measurement label `offsetZ` default: not needed when `scaleByRadius` is enbaled
+- Fix measurement label `offsetZ` default: not needed when `scaleByRadius` is enabled
+- ModelServer SDF/MOL2 ligand export: fix atom indices when additional atoms are present
 
 ## [v3.43.1] - 2023-12-04
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
@@ -88,14 +88,14 @@ export abstract class LigandEncoder implements Encoder<string> {
         return StringBuilder.getString(this.builder);
     }
 
-    protected getAtoms<Ctx>(instance: Category.Instance<Ctx>, source: any): Map<string, Atom> {
+    protected getAtoms<Ctx>(instance: Category.Instance<Ctx>, source: any, ccdAtoms: ComponentAtom.Entry['map']): Map<string, Atom> {
         const sortedFields = this.getSortedFields(instance, ['Cartn_x', 'Cartn_y', 'Cartn_z']);
         const label_atom_id = this.getField(instance, 'label_atom_id');
         const type_symbol = this.getField(instance, 'type_symbol');
-        return this._getAtoms(source, sortedFields, label_atom_id, type_symbol);
+        return this._getAtoms(source, sortedFields, label_atom_id, type_symbol, ccdAtoms);
     }
 
-    private _getAtoms(source: any, fields: Field<any, any>[], label_atom_id: Field<any, any>, type_symbol: Field<any, any>): Map<string, Atom> {
+    private _getAtoms(source: any, fields: Field<any, any>[], label_atom_id: Field<any, any>, type_symbol: Field<any, any>, ccdAtoms: ComponentAtom.Entry['map']): Map<string, Atom> {
         const atoms = new Map<string, Atom>();
         let index = 0;
 
@@ -111,6 +111,8 @@ export abstract class LigandEncoder implements Encoder<string> {
                 const key = it.move();
 
                 const lai = label_atom_id.value(key, data, index) as string;
+                // ignore all atoms not registered in the CCD
+                if (!ccdAtoms.has(lai)) continue;
                 // ignore all alternate locations after the first
                 if (atoms.has(lai)) continue;
 

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

@@ -34,7 +34,7 @@ export class MolEncoder extends LigandEncoder {
         let chiral = false;
 
         // traverse once to determine all actually present atoms
-        const atoms = this.getAtoms(instance, source);
+        const atoms = this.getAtoms(instance, source, atomMap.map);
         atoms.forEach((atom1, label_atom_id1) => {
             const { index: i1, type_symbol: type_symbol1 } = atom1;
             const atomMapData1 = atomMap.map.get(label_atom_id1);

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

@@ -36,7 +36,7 @@ export class Mol2Encoder extends LigandEncoder {
         let atomCount = 0;
         let bondCount = 0;
 
-        const atoms = this.getAtoms(instance, source);
+        const atoms = this.getAtoms(instance, source, atomMap.map);
         StringBuilder.writeSafe(a, '@<TRIPOS>ATOM\n');
         StringBuilder.writeSafe(b, '@<TRIPOS>BOND\n');
         atoms.forEach((atom1, label_atom_id1) => {

src/servers/model/version.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-export const VERSION = '0.9.10';
+export const VERSION = '0.9.11';