mmcif conformation parsing

src/mol-data/model/builders/mmcif.ts

@@ -13,6 +13,7 @@ import Interval from '../../../mol-base/collections/integer/interval'
 import Segmentation from '../../../mol-base/collections/integer/segmentation'
 import uuId from '../../../mol-base/utils/uuid'
 import * as Hierarchy from '../properties/hierarchy'
+import Conformation from '../properties/conformation'
 import findHierarchyKeys from '../utils/hierarchy-keys'
 
 function findModelBounds(data: mmCIF, startIndex: number) {
@@ -62,6 +63,16 @@ function createHierarchyData(data: mmCIF, bounds: Interval, offsets: { residues:
     return { atoms, residues, chains, entities: data.entity };
 }
 
+function getConformation(data: mmCIF, bounds: Interval): Conformation {
+    const start = Interval.start(bounds), end = Interval.end(bounds);
+    const { atom_site } = data;
+    return {
+        x: atom_site.Cartn_x.toArray({ array: Float32Array, start, end }),
+        y: atom_site.Cartn_y.toArray({ array: Float32Array, start, end }),
+        z: atom_site.Cartn_z.toArray({ array: Float32Array, start, end }),
+    }
+}
+
 function createModel(raw: RawData, data: mmCIF, bounds: Interval): Model {
     const hierarchyOffsets = findHierarchyOffsets(data, bounds);
 
@@ -77,7 +88,7 @@ function createModel(raw: RawData, data: mmCIF, bounds: Interval): Model {
         sourceData: raw,
         model_num: data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
         hierarchy: { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments },
-        conformation: 0 as any,
+        conformation: getConformation(data, bounds),
         version: { data: 0, conformation: 0 },
         atomCount: Interval.size(bounds)
     };

src/mol-data/model/properties/computed.ts

@@ -4,4 +4,20 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-// TODO: stuff like "residue type/flags", isRingAtom, rings, bonds??, wrap these in a computation?
+// TODO: stuff like "residue type/flags", isRingAtom, rings, bonds??, wrap these in a computation?
+// secondary structure is also a computed property
+
+// import { SecondaryStructureType } from '../constants'
+// import Segmentation from '../../../mol-base/collections/integer/segmentation'
+
+
+// interface SecondaryStructure {
+//     ofResidue: ArrayLike<SecondaryStructureType>,
+//     // atom segmentation??
+//     segments: Segmentation
+// }
+
+// interface Conformation {
+//     positions: Conformation,
+//     secondaryStructure: SecondaryStructure
+// }

src/mol-data/model/properties/conformation.ts

@@ -4,24 +4,10 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { SecondaryStructureType } from '../constants'
-import Segmentation from '../../../mol-base/collections/integer/segmentation'
-
-interface Positions {
+interface Conformation {
     x: ArrayLike<number>,
     y: ArrayLike<number>,
     z: ArrayLike<number>
 }
 
-interface SecondaryStructure {
-    ofResidue: ArrayLike<SecondaryStructureType>,
-    // atom segmentation??
-    segments: Segmentation
-}
-
-interface Conformation {
-    positions: Positions,
-    secondaryStructure: SecondaryStructure
-}
-
 export default Conformation

src/script.ts

@@ -126,6 +126,9 @@ async function runCIF(input: string | Uint8Array) {
     console.log(models[0].hierarchy.chains.auth_asym_id.value(0));
     console.log(models[0].hierarchy.chains.auth_asym_id.value(1));
     console.log(models[0].hierarchy.chains.label_asym_id.value(1));
+    console.log(models[0].conformation.x[0]);
+    console.log(models[0].conformation.y[0]);
+    console.log(models[0].conformation.z[0]);
 
     // const schema = await _dic()
     // if (schema) {