include occupancy & B_iso_or_equiv in model conformation

CHANGELOG.md

@@ -19,6 +19,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fix overpaint/transparency/substance smoothing not updated when geometry changes
 - Fix camera project/unproject when using offset viewport
 - Add `Frustum3D` and `Plane3D` math primitives
+- Include `occupancy` and `B_iso_or_equiv` when creating `Conformation` from `Model`
 
 ## [v3.32.0] - 2023-03-20
 

src/mol-model/structure/coordinates/coordinates.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -99,7 +99,7 @@ namespace Coordinates {
     /**
      * Only use ordering if it's not identity.
      */
-    export function getAtomicConformation(frame: Frame, atomId: Column<number>, ordering?: ArrayLike<number>): AtomicConformation {
+    export function getAtomicConformation(frame: Frame, fields: { atomId: Column<number>, occupancy?: Column<number>, B_iso_or_equiv?: Column<number> }, ordering?: ArrayLike<number>): AtomicConformation {
         let { x, y, z } = frame;
 
         if (frame.xyzOrdering.frozen) {
@@ -143,9 +143,9 @@ namespace Coordinates {
 
         return {
             id: UUID.create22(),
-            atomId,
-            occupancy: Column.ofConst(1, frame.elementCount, Column.Schema.int),
-            B_iso_or_equiv: Column.ofConst(0, frame.elementCount, Column.Schema.float),
+            atomId: fields.atomId,
+            occupancy: fields.occupancy ?? Column.ofConst(1, frame.elementCount, Column.Schema.int),
+            B_iso_or_equiv: fields.B_iso_or_equiv ?? Column.ofConst(0, frame.elementCount, Column.Schema.float),
             xyzDefined: true,
             x,
             y,

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2023 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>
@@ -112,7 +112,11 @@ export namespace Model {
                 ...model,
                 id: UUID.create22(),
                 modelNum: i,
-                atomicConformation: Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray),
+                atomicConformation: Coordinates.getAtomicConformation(f, {
+                    atomId: model.atomicConformation.atomId,
+                    occupancy: model.atomicConformation.occupancy,
+                    B_iso_or_equiv: model.atomicConformation.B_iso_or_equiv
+                }, srcIndexArray),
                 // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates?
                 // coarseConformation: coarse.conformation,
                 customProperties: new CustomProperties(),