Issue #2: bugfix of chain exclusion

src/extensions/tmdet/symmetry.ts

@@ -9,27 +9,29 @@ import { PDBTMDescriptor } from './types';
 
 export function registerTmDetSymmetry(pdbtmDescriptor: PDBTMDescriptor) {
     ModelSymmetry.Provider.formatRegistry.remove('mmCIF');
-    const chains = constructChainListFromOperations(pdbtmDescriptor);
+    const excludedChains = constructChainListFromOperations(pdbtmDescriptor);
     ModelSymmetry.Provider.formatRegistry.add('mmCIF',  function(model: Model) {
-        return tmDetSymmetryFromMmCif(model, chains);
+        return tmDetSymmetryFromMmCif(model, excludedChains);
     });
 }
 
 function constructChainListFromOperations(pdbtmDescriptor: PDBTMDescriptor): string[] {
-    console.log("PDBTMDesc", pdbtmDescriptor);
     const excludedChains: string[] = [];
     // add chain deletes
-    pdbtmDescriptor.additional_entry_annotations.biomatrix.chain_deletes.forEach(
-        chainId => excludedChains.push(chainId)
-    );
+    const biomatrix = pdbtmDescriptor.additional_entry_annotations.biomatrix;
+    if (biomatrix != undefined && biomatrix.chain_deletes != undefined) {
+        biomatrix.chain_deletes.forEach(
+            chainId => excludedChains.push(chainId)
+        );
+    }
     // exclude result of transformations
-    pdbtmDescriptor.additional_entry_annotations.biomatrix.matrix_list.forEach(
-        matrix => matrix.apply_to_chain_list.forEach(
-            applyItem => excludedChains.push(applyItem.new_chain_id)
-        )
-    );
-    console.log(excludedChains);
-    // todo all minus excluded
+    if (biomatrix != undefined && biomatrix.matrix_list != undefined) {
+        biomatrix.matrix_list.forEach(
+            matrix => matrix.apply_to_chain_list.forEach(
+                applyItem => excludedChains.push(applyItem.new_chain_id)
+            )
+        );
+    }
 
     return excludedChains;
 }
@@ -40,15 +42,13 @@ function tmDetSymmetryFromMmCif(model: Model, chainsForOperExpression: string[])
     let data = model.sourceData.data.db;
     let asymIdColumnData: string[][] = [];
     // update chains (asym) for each author_defined_assemly
-    for (let i = 0; i < data.pdbx_struct_assembly._rowCount; i++) {
-        if (data.pdbx_struct_assembly.details.value(i).startsWith('author_defined_assembly')) {
-            const currentAssemblyId: string = data.pdbx_struct_assembly_gen.assembly_id.value(i);
-            const result: string[][] = createAsymIdColumnData(
-                data.pdbx_struct_assembly_gen, currentAssemblyId, chainsForOperExpression
-            );
-            asymIdColumnData = asymIdColumnData.concat(result);
-        }
-    }
+    // NOTE: We assume that the first assembly is an author defined assembly.
+    const currentAssemblyId: string = data.pdbx_struct_assembly_gen.assembly_id.value(0);
+    const result: string[][] = createAsymIdColumnData(
+        data.pdbx_struct_assembly_gen, currentAssemblyId, chainsForOperExpression
+    );
+    asymIdColumnData = asymIdColumnData.concat(result);
+
     const asym_id_list_column = Column.ofStringListArray(asymIdColumnData);
     // create table with new column
     let updated_pdbx_struct_assembly_gen = Table.ofColumns(
@@ -56,8 +56,7 @@ function tmDetSymmetryFromMmCif(model: Model, chainsForOperExpression: string[])
         {
             assembly_id: data.pdbx_struct_assembly_gen.assembly_id,
             asym_id_list: asym_id_list_column,
-            oper_expression: data.pdbx_struct_assembly_gen.oper_expression,
-
+            oper_expression: data.pdbx_struct_assembly_gen.oper_expression
         }
     );