handle missing occupancy column

- treat as occ 1

CHANGELOG.md

@@ -7,6 +7,7 @@ Note that since we don't clearly distinguish between a public and private interf
 ## [Unreleased]
 
 - Add Charmm saccharide names
+- Treat missing occupancy column as occupany of 1
 
 ## [v2.3.0] - 2021-09-06
 

src/mol-io/reader/common/text/column/token.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Column, ColumnHelpers } from '../../../../../mol-data/db';
@@ -50,4 +51,12 @@ export function areValuesEqualProvider(tokens: Tokens) {
         }
         return true;
     };
+}
+
+export function areTokensEmpty(tokens: Tokens) {
+    const { count, indices } = tokens;
+    for (let i = 0; i < count; ++i) {
+        if (indices[2 * i] !== indices[2 * i + 1]) return false;
+    }
+    return true;
 }

src/mol-model-formats/structure/basic/atomic.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -100,7 +100,7 @@ function getConformation(atom_site: AtomSite): AtomicConformation {
     return {
         id: UUID.create22(),
         atomId: atom_site.id,
-        occupancy: atom_site.occupancy,
+        occupancy: atom_site.occupancy.isDefined ? atom_site.occupancy : Column.ofConst(1, atom_site._rowCount, Column.Schema.float),
         B_iso_or_equiv: atom_site.B_iso_or_equiv,
         xyzDefined: atom_site.Cartn_x.isDefined && atom_site.Cartn_y.isDefined && atom_site.Cartn_z.isDefined,
         x: atom_site.Cartn_x.toArray({ array: Float32Array }),

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,6 +10,7 @@ import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { TokenBuilder, Tokenizer } from '../../../mol-io/reader/common/text/tokenizer';
 import { guessElementSymbolTokens } from '../util';
 import { Column } from '../../../mol-data/db';
+import { areTokensEmpty } from '../../../mol-io/reader/common/text/column/token';
 
 type AtomSiteTemplate = typeof getAtomSiteTemplate extends (...args: any) => infer T ? T : never
 export function getAtomSiteTemplate(data: string, count: number) {
@@ -63,7 +64,7 @@ export function getAtomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema
         label_seq_id: CifField.ofUndefined(sites.index, Column.Schema.int),
         label_entity_id: CifField.ofStrings(sites.label_entity_id),
 
-        occupancy: CifField.ofTokens(sites.occupancy),
+        occupancy: areTokensEmpty(sites.occupancy) ? CifField.ofUndefined(sites.index, Column.Schema.float) : CifField.ofTokens(sites.occupancy),
         type_symbol: CifField.ofTokens(sites.type_symbol),
 
         pdbx_PDB_ins_code: CifField.ofTokens(sites.pdbx_PDB_ins_code),