Issue #2: biomatrix implementation is in progress

src/extensions/tmdet/behavior.ts

@@ -133,8 +133,9 @@ export async function loadWithUNITMPMembraneRepresentation(plugin: PluginUIConte
     requestAnimationFrame(() => plugin.canvas3d?.requestCameraReset());
 }
 
+type PDBTMChainLabel = string;
 type PDBTMChain = {
-    chain_label: string,
+    chain_label: PDBTMChainLabel,
     additional_chain_annotations: {
         type: string,
         num_tm: number
@@ -162,9 +163,25 @@ type PDBTMDescriptor = {
             normal: PDBTMVec3,
             transformation_matrix: PDBTMTransformationMatrix,
             radius: number
+        },
+        biomatrix: {
+            chain_deletes: string[],
+            matrix_list: {
+                matrix_id: string,
+                apply_to_chain_list: {
+                    chain_id: PDBTMChainLabel,
+                    new_chain_id: PDBTMChainLabel
+                }[],
+                transformation_matrix: PDBTMTransformationMatrix
+            }[]
         }
     }
 };
+type TrajectoryType = StateObjectSelector<
+    PluginStateObject.Molecule.Trajectory,
+    StateTransformer<StateObject<any, StateObject.Type<any>>,
+    StateObject<any, StateObject.Type<any>>, any>
+>;
 
 function createMembraneOrientation(pdbtmDescriptor: PDBTMDescriptor): MembraneOrientation {
     const normal = pdbtmDescriptor.additional_entry_annotations.membrane.normal;
@@ -219,7 +236,7 @@ async function createStructureRepresentation(plugin: PluginUIContext, pdbtmDescr
             regionsBySite[siteIndex].auth_ids.push(Number(residueItem.pdb_res_label));
         }
 
-        console.log(`REGIONS-${chain.chain_label}`, regionsBySite);
+        //console.log(`REGIONS-${chain.chain_label}`, regionsBySite);
         regionsBySite.map((region: PDBTMRegion) => {
             const regionUpdates = plugin.build();
             createRegionRepresentation(plugin, chain.chain_label, region, regionUpdates.to(structure));
@@ -271,6 +288,18 @@ async function loadStructure(ctx: PluginUIContext, params: any, pdbtmDescriptor:
         isBinary: false
     }); // , { state: { isGhost: true } });
     const trajectory = await builders.structure.parseTrajectory(data, 'mmcif');
+
+    // TODO: DEBUG logs
+    console.log('ATOMIC CONFORMATION', trajectory.data!.representative.atomicConformation);
+    console.log('ATOMIC RANGES', trajectory.data!.representative.atomicRanges);
+    console.log('ATOMIC HIER', trajectory.data!.representative.atomicHierarchy);
+    console.log('ATOMIC ENTITIES', trajectory.data!.representative.entities);
+
+
+    //       ctx.managers.structure.hierarchy.getStructuresWithSelection();
+
+
+
     await applyTransformations(pdbtmDescriptor, trajectory);
 
     // create membrane representation
@@ -278,30 +307,36 @@ async function loadStructure(ctx: PluginUIContext, params: any, pdbtmDescriptor:
         trajectory, 'default', { representationPreset: 'preset-membrane-orientation' as any });
 }
 
-async function applyTransformations(pdbtmDescriptor: PDBTMDescriptor, trajectory: any) {
+async function applyTransformations(pdbtmDescriptor: PDBTMDescriptor, trajectory: TrajectoryType) {
+    console.log('BIOMX', pdbtmDescriptor.additional_entry_annotations.biomatrix);
     if (trajectory.data != null) {
-        let new_x = [];
-        let new_y = [];
-        let new_z = [];
-        let atomicConformationX = trajectory.data.representative.atomicConformation.x;
-        let atomicConformationY = trajectory.data.representative.atomicConformation.y;
-        let atomicConformationZ = trajectory.data.representative.atomicConformation.z;
+        let atomicConformation = trajectory.data.representative.atomicConformation;
         let tmatrix = pdbtmDescriptor.additional_entry_annotations.membrane.transformation_matrix;
+        let newConformation = {
+            atomId: [] as number[],
+            x: [] as number[],
+            y: [] as number[],
+            z: [] as number[],
+            B_iso_or_equiv: [] as number[],
+            occupancy: [] as number[]
+        };
 
-        for (let i = 0; i < atomicConformationX.length; i++) {
+        for (let i = 0; i < atomicConformation.x.length; i++) {
             let coords = {
-                x: atomicConformationX[i],
-                y: atomicConformationY[i],
-                z: atomicConformationZ[i]
+                x: atomicConformation.x[i],
+                y: atomicConformation.y[i],
+                z: atomicConformation.z[i]
             };
             coords = applyTransformationMatrix(coords, tmatrix);
-            new_x.push(coords.x);
-            new_y.push(coords.y);
-            new_z.push(coords.z);
+            newConformation.x.push(coords.x);
+            newConformation.y.push(coords.y);
+            newConformation.z.push(coords.z);
+
+            // copy old values
         }
-        trajectory.data.representative.atomicConformation.x = new_x;
-        trajectory.data.representative.atomicConformation.y = new_y;
-        trajectory.data.representative.atomicConformation.z = new_z;
+        atomicConformation.x = newConformation.x;
+        atomicConformation.y = newConformation.y;
+        atomicConformation.z = newConformation.z;
     }
 }
 
@@ -318,7 +353,7 @@ function vectorMultiply(v1: PDBTMVec3, v2: PDBTMVec3): number {
 }
 
 function getAtomGroupExpression(chainId: string, auth_array: number[]): Expression {
-    console.log('auth_array:', auth_array);
+    // TODO console.log('auth_array:', auth_array);
     const query: Expression =
         MS.struct.generator.atomGroups({
             'residue-test': MS.core.set.has([MS.set( ...auth_array ), MS.ammp('auth_seq_id')]),