Issue #2: coloring is in progress

src/apps/viewer/index.html

@@ -55,7 +55,7 @@
             });
 
             // Set PDB Id here
-            var pdbId = '1a0s';
+            var pdbId = '1afo';
             function loadPdb() {
                 molstar.loadWithUNITMPMembraneRepresentation(viewer.plugin, {
                     structureUrl: `https://cs.litemol.org/${pdbId}/full`,

src/extensions/tmdet/behavior.ts

@@ -193,34 +193,38 @@ async function createStructureRepresentation(plugin: PluginUIContext, pdbtmDescr
 
     await buildStructureRepresentation(plugin, components);
 
-    // // TODO: colors of not curated sites
-    // const siteColors = [
-    //     [255,100,100], // Side1
-    //     [100,100,255], // Side2
-    //     [255,255,0],   // TM alpha
-    //     [255,255,0],   // TM beta
-    //     [255,127,0],   // TM re-entrant loop
-    //     [0,255,  0],   // Interfacial Helix
-    //     [196,196,196], // Unknow localization
-    //     [0,255,  0],   // Membrane Inside
-    // ];
-    // const siteDefinitions = pdbtmDescriptor.sites.map(
-    //     (siteDefinition: any) => siteDefinition.label
-    // );
-    // pdbtmDescriptor.chains.forEach((chain: any) => {
-
-    //     for (let residueItem of chain.residues) {
-    //         const siteIndex = residueItem.site_data[0].site_id_ref - 1;
-    //         const residue: PDBTMRegion = {
-    //             "auth_ids": [ Number(residueItem.pdb_res_label) ],
-    //             "color": siteColors[siteIndex],
-    //             "site": siteDefinitions[siteIndex]
-    //         };
-    //         const regionUpdates = plugin.build();
-    //         createRegionRepresentation(plugin, chain.chain_label, residue, regionUpdates.to(structure));
-    //         regionUpdates.commit();
-    //     }
-    // });
+    // TODO: colors of not curated sites
+    const siteColors = [
+        [255,100,100], // Side1
+        [100,100,255], // Side2
+        [255,255,0],   // TM alpha
+        [255,255,0],   // TM beta
+        [255,127,0],   // TM re-entrant loop
+        [0,255,  0],   // Interfacial Helix
+        [196,196,196], // Unknow localization
+        [0,255,  0],   // Membrane Inside
+    ];
+    const siteDefinitions = pdbtmDescriptor.sites.map(
+        (siteDefinition: any) => siteDefinition.label
+    );
+
+    pdbtmDescriptor.chains.forEach((chain: any) => {
+
+        let regionsBySite: PDBTMRegion[] = siteColors.map((color):PDBTMRegion => {
+            return { site: "valami", auth_ids: [], color: color };
+        });
+
+        for (let residueItem of chain.residues) {
+            const siteIndex = residueItem.site_data[0].site_id_ref - 1;
+            regionsBySite[siteIndex].auth_ids.push(Number(residueItem.pdb_res_label));
+        }
+
+        console.log(`REGIONS-${chain.chain_label}`, regionsBySite);
+        const regionUpdates = plugin.build();
+        createRegionRepresentation(plugin, chain.chain_label, regionsBySite[0], regionUpdates.to(structure));
+        regionUpdates.commit();
+
+    });
 }
 
 async function createStructureComponents(plugin: PluginUIContext, structure: StateObjectCell<PMS, StateTransform<StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>>) {
@@ -236,7 +240,6 @@ function createRegionRepresentation(plugin: PluginUIContext, chain: string, resi
     const color: Color = Color.fromArray(residue.color, 0);
     const query: Expression = getAtomGroupExpression(chain, residue.auth_ids);
 
-
     // based on https://github.com/molstar/molstar/issues/209
     update
         .apply(StateTransforms.Model.StructureSelectionFromExpression, { label: regionLabel, expression: query })
@@ -266,7 +269,14 @@ async function loadStructure(ctx: PluginUIContext, params: any, pdbtmDescriptor:
         isBinary: false
     }); // , { state: { isGhost: true } });
     const trajectory = await builders.structure.parseTrajectory(data, 'mmcif');
+    await applyTransformations(pdbtmDescriptor, trajectory);
 
+    // create membrane representation
+    await builders.structure.hierarchy.applyPreset(
+        trajectory, 'default', { representationPreset: 'preset-membrane-orientation' as any });
+}
+
+async function applyTransformations(pdbtmDescriptor: PDBTMDescriptor, trajectory: any) {
     if (trajectory.data != null) {
         let new_x = [];
         let new_y = [];
@@ -291,10 +301,6 @@ async function loadStructure(ctx: PluginUIContext, params: any, pdbtmDescriptor:
         trajectory.data.representative.atomicConformation.y = new_y;
         trajectory.data.representative.atomicConformation.z = new_z;
     }
-
-    // create membrane representation
-    await builders.structure.hierarchy.applyPreset(
-        trajectory, 'default', { representationPreset: 'preset-membrane-orientation' as any });
 }
 
 function applyTransformationMatrix(coords: PDBTMVec3, tmatrix: PDBTMTransformationMatrix): PDBTMVec3 {
@@ -310,6 +316,7 @@ function vectorMultiply(v1: PDBTMVec3, v2: PDBTMVec3): number {
 }
 
 function getAtomGroupExpression(chainId: string, auth_array: number[]): Expression {
+    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')]),