fix wrong element assignment

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add ``CustomImportControls`` to left panel
 - Add Zenodo import extension (load structures, trajectories, volumes, and zip files)
 - Fix loading of some compressed files within sessions
+- Fix wrong element assignment for atoms with Charmm ion names
 
 ## [v3.3.1] - 2022-02-27
 

src/mol-model-formats/structure/cif-core.ts

@@ -100,7 +100,7 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
         const element_symbol = new Array<string>(atomCount);
         for (let i = 0; i < atomCount; ++i) {
             // TODO can take as is if type_symbol not given?
-            element_symbol[i] = guessElementSymbolString(label.value(i));
+            element_symbol[i] = guessElementSymbolString(label.value(i), '');
         }
         typeSymbol = Column.ofStringArray(element_symbol);
         formalCharge = Column.Undefined(atomCount, Column.Schema.int);

src/mol-model-formats/structure/gro.ts

@@ -27,6 +27,7 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
     const asymIds = new Array<string>(atoms.count);
     const seqIds = new Uint32Array(atoms.count);
     const ids = new Uint32Array(atoms.count);
+    const typeSymbol = new Array<string>(atoms.count);
 
     const entityBuilder = new EntityBuilder();
     const componentBuilder = new ComponentBuilder(atoms.residueNumber, atoms.atomName);
@@ -66,6 +67,8 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
         asymIds[i] = currentAsymId;
         seqIds[i] = currentSeqId;
         ids[i] = i;
+
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
     }
 
     const auth_asym_id = Column.ofStringArray(asymIds);
@@ -87,7 +90,7 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
         label_entity_id: Column.ofStringArray(entityIds),
 
         occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+        type_symbol: Column.ofStringArray(typeSymbol),
 
         pdbx_PDB_model_num: Column.ofConst(modelNum, atoms.count, Column.Schema.int),
     }, atoms.count);

src/mol-model-formats/structure/mol2.ts

@@ -41,7 +41,7 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
         for (let i = 0; i < atoms.count; ++i) {
             type_symbol[i] = hasAtomType
                 ? atoms.atom_type.value(i).split('.')[0].toUpperCase()
-                : guessElementSymbolString(atoms.atom_name.value(i));
+                : guessElementSymbolString(atoms.atom_name.value(i), atoms.subst_name.value(i));
         }
 
         const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {

src/mol-model-formats/structure/psf.ts

@@ -21,6 +21,7 @@ function getBasic(atoms: PsfFile['atoms']) {
     const asymIds = new Array<string>(atoms.count);
     const seqIds = new Uint32Array(atoms.count);
     const ids = new Uint32Array(atoms.count);
+    const typeSymbol = new Array<string>(atoms.count);
 
     const entityBuilder = new EntityBuilder();
     const componentBuilder = new ComponentBuilder(atoms.residueId, atoms.atomName);
@@ -68,6 +69,8 @@ function getBasic(atoms: PsfFile['atoms']) {
         asymIds[i] = currentAsymId;
         seqIds[i] = currentSeqId;
         ids[i] = i;
+
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
     }
 
     const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
@@ -84,7 +87,7 @@ function getBasic(atoms: PsfFile['atoms']) {
         label_entity_id: Column.ofStringArray(entityIds),
 
         occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+        type_symbol: Column.ofStringArray(typeSymbol),
 
         pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
     }, atoms.count);

src/mol-model-formats/structure/util.ts

@@ -47,30 +47,31 @@ export function guessElementSymbolTokens(tokens: Tokens, str: string, start: num
 }
 
 const reTrimSpacesAndNumbers = /^[\s\d]+|[\s\d]+$/g;
-export function guessElementSymbolString(str: string) {
+export function guessElementSymbolString(atomId: string, compId: string) {
     // trim spaces and numbers, convert to upper case
-    str = str.replace(reTrimSpacesAndNumbers, '').toUpperCase();
-    const l = str.length;
+    atomId = atomId.replace(reTrimSpacesAndNumbers, '').toUpperCase();
+    const l = atomId.length;
 
-    if (l === 0) return str; // empty
-    if (l === 1) return str; // one char
+    if (l === 0) return atomId; // empty
+    if (l === 1) return atomId; // one char
 
     if (l === 2) { // two chars
-        if (str === 'NA' || str === 'CL' || str === 'FE' || str === 'SI' ||
-            str === 'BR' || str === 'AS'
-        ) return str;
+        if (atomId === 'NA' || atomId === 'CL' || atomId === 'FE' || atomId === 'SI' ||
+            atomId === 'BR' || atomId === 'AS'
+        ) return atomId;
     }
 
-    if (l === 3) { // three chars
-        if (str === 'SOD') return 'NA';
-        if (str === 'POT') return 'K';
-        if (str === 'CES') return 'CS';
-        if (str === 'CAL') return 'CA';
-        if (str === 'CLA') return 'CL';
+    if (l === 3 && compId === atomId) { // three chars
+        if (atomId === 'SOD') return 'NA';
+        if (atomId === 'POT') return 'K';
+        if (atomId === 'CES') return 'CS';
+        if (atomId === 'CAL') return 'CA';
+        if (atomId === 'CLA') return 'CL';
     }
 
-    const c = str[0];
+    const c = atomId[0];
     if (c === 'C' || c === 'H' || c === 'N' || c === 'O' || c === 'P' || c === 'S') return c;
 
     return ''; // no reasonable guess, return empty string
-}
+}
+