Issue #2: inverted membrane transformation on membrane-orientation

src/extensions/tmdet/behavior.ts

@@ -25,9 +25,8 @@ import { Color } from '../../mol-util/color';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
 import { StateObjectSelector } from "../../mol-state/object";
-import { Vec3 } from '../../mol-math/linear-algebra';
-import { applyTransformations, getAtomGroupExpression } from './transformation';
-import { PDBTMDescriptor, PDBTMRegion, PDBTMTransformationMatrix, PMS } from './types';
+import { applyTransformations, createMembraneOrientation, getAtomGroupExpression } from './transformation';
+import { PDBTMDescriptor, PDBTMRegion, PMS } from './types';
 
 type StructureComponentType = StateObjectSelector<
         PMS,
@@ -131,37 +130,6 @@ export async function loadWithUNITMPMembraneRepresentation(plugin: PluginUIConte
     requestAnimationFrame(() => plugin.canvas3d?.requestCameraReset());
 }
 
-function vadd(a: Vec3, b: Vec3): Vec3 {
-    return Vec3.add(Vec3.zero(), a, b);
-}
-
-function vneg(u: Vec3): Vec3 {
-    return Vec3.negate(Vec3.zero(), u);
-}
-
-function createMembraneOrientation(pdbtmDescriptor: PDBTMDescriptor): MembraneOrientation {
-    const membrane = pdbtmDescriptor.additional_entry_annotations.membrane;
-    const mx: PDBTMTransformationMatrix = membrane.transformation_matrix;
-    const translation: Vec3 = Vec3.create(mx.rowx.t, mx.rowy.t, mx.rowz.t);
-    Vec3.negate(translation, translation);
-
-    const membraneNormal: Vec3 = Vec3.fromObj(membrane.normal);
-
-    const result: MembraneOrientation = {
-        planePoint1: vadd(membraneNormal, translation),
-        planePoint2: vadd(vneg(membraneNormal), translation),
-        centroid: translation,
-        normalVector: membraneNormal,
-
-        // (NOTE: the TMDET extension calculates and sets it during applying preset)
-        radius: membrane.radius
-    };
-    console.log("createMemOri\n", result);
-    Vec3.add(result.normalVector, result.normalVector, translation);
-    console.log("createMemOri2\n", result);
-    return result;
-}
-
 async function createStructureRepresentation(plugin: PluginUIContext, pdbtmDescriptor: any) {
     // get the first structure of the first model
     const structure: StateObjectRef<PMS> = plugin.managers.structure.hierarchy.current.models[0].structures[0].cell;

src/extensions/tmdet/transformation.ts

@@ -1,24 +1,16 @@
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { PluginUIContext } from '../../mol-plugin-ui/context';
-import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { Mat4, Vec3, Vec4 } from '../../mol-math/linear-algebra';
 import { PDBTMDescriptor, PDBTMTransformationMatrix, PMS } from './types';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
 import { StateObjectRef, StateBuilder } from '../../mol-state';
 import { Color } from '../../mol-util/color';
 import { Expression } from '../../mol-script/language/expression';
+import { MembraneOrientation } from './prop';
 
 export async function applyTransformations(ctx: PluginUIContext, pdbtmDescriptor: PDBTMDescriptor) {
     const annotations = pdbtmDescriptor.additional_entry_annotations;
-    const transformation = transformationForStateTransform(annotations.membrane.transformation_matrix);
-
-    // console.log("MEMBRANE TRNASFORMATION:\n\n", Mat4.makeTable(transformation));
-    // const structure: StateObjectRef<PMS> = ctx.managers.structure.hierarchy.current.models[0].structures[0].cell;
-    // const update: StateBuilder.To<any, any> = ctx.build().to(structure);
-    // update.apply(StateTransforms.Model.TransformStructureConformation, {
-    //     "transform": { name: "matrix", params: { data: transformation, transpose: false } }
-    // });
-    // update.commit();
 
     console.log('BIOMX', annotations.biomatrix);
     if (annotations.biomatrix == undefined) {
@@ -71,6 +63,45 @@ export async function applyTransformations(ctx: PluginUIContext, pdbtmDescriptor
     update.commit();
 }
 
+function vadd(a: Vec3, b: Vec3): Vec3 {
+    return Vec3.add(Vec3.zero(), a, b);
+}
+
+function vneg(u: Vec3): Vec3 {
+    return Vec3.negate(Vec3.zero(), u);
+}
+
+export function createMembraneOrientation(pdbtmDescriptor: PDBTMDescriptor): MembraneOrientation {
+    const annotations = pdbtmDescriptor.additional_entry_annotations;
+    const membrane = annotations.membrane;
+    const transformation: Mat4 = transformationForStateTransform(membrane.transformation_matrix);
+    const translation: Vec3 = Mat4.getTranslation(Vec3.zero(), transformation);
+
+    console.log("MEMBRANE TRNASFORMATION:\n\n", Mat4.makeTable(transformation));
+    Vec3.negate(translation, translation);
+    Mat4.setTranslation(transformation, translation);
+    console.log("MEMBRANE TRNASFORMATION: NEGATED trnltn:\n\n", Mat4.makeTable(transformation));
+
+    // transpose rotation of transformation (inverse rotation)
+    Mat4.transpose(transformation, Mat4.extractRotation(transformation, transformation));
+    console.log("MEMBRANE TRANSPOSED:\n\n", Mat4.makeTable(transformation));
+
+    // transform membrane normal
+    const membraneNormal: Vec3 = Vec3.fromObj(membrane.normal);
+    Vec3.transformMat4(membraneNormal, membraneNormal, transformation);
+
+    const result: MembraneOrientation = {
+        planePoint1: vadd(membraneNormal, translation),
+        planePoint2: vadd(vneg(membraneNormal), translation),
+        centroid: translation,
+        normalVector: membraneNormal,
+
+        // (NOTE: the TMDET extension calculates and sets it during applying preset)
+        radius: membrane.radius
+    };
+    return result;
+}
+
 export function transformationForStateTransform(tmatrix: PDBTMTransformationMatrix): Mat4 {
     // matrix expected in column-major order
     const mx: Mat4 = Mat4.fromArray(Mat4.zero(),