make use of PDB TER record

src/mol-model-formats/structure/pdb/atom-site.ts

@@ -39,7 +39,7 @@ export function getAtomSiteTemplate(data: string, count: number) {
     };
 }
 
-export function getAtomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema['atom_site'] | 'partial_charge']?: CifField } {
+export function getAtomSite(sites: AtomSiteTemplate, hasTer: boolean): { [K in keyof mmCIF_Schema['atom_site'] | 'partial_charge']?: CifField } {
     const pdbx_PDB_model_num = CifField.ofStrings(sites.pdbx_PDB_model_num);
     const auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
     const auth_seq_id = CifField.ofTokens(sites.auth_seq_id);
@@ -89,7 +89,9 @@ export function getAtomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema
         }
 
         if (asymIdCounts.has(asymId)) {
-            if (asymIdChanged) {
+            // only change the chains name if there are TER records
+            // otherwise assume repeated chain name use is from interleaved chains
+            if (hasTer && asymIdChanged) {
                 const asymIdCount = asymIdCounts.get(asymId)! + 1;
                 asymIdCounts.set(asymId, asymIdCount);
                 currLabelAsymId = `${asymId}_${asymIdCount}`;

src/mol-model-formats/structure/pdb/to-cif.ts

@@ -51,6 +51,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
 
     let modelNum = 0, modelStr = '';
     let conectRange: [number, number] | undefined = undefined;
+    let hasTer = false;
 
     for (let i = 0, _i = lines.count; i < _i; i++) {
         let s = indices[2 * i], e = indices[2 * i + 1];
@@ -161,6 +162,10 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
                 }
                 // TODO: SCALE record => cif.atom_sites.fract_transf_matrix, cif.atom_sites.fract_transf_vector
                 break;
+            case 'T':
+                if (substringStartsWith(data, s, e, 'TER')) {
+                    hasTer = true;
+                }
         }
     }
 
@@ -178,7 +183,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
         atomSite.label_entity_id[i] = entityBuilder.getEntityId(compId, moleculeType, asymIds.value(i));
     }
 
-    const atom_site = getAtomSite(atomSite);
+    const atom_site = getAtomSite(atomSite, hasTer);
     if (!isPdbqt) delete atom_site.partial_charge;
 
     if (conectRange) {