molstar 4.0.1 → 4.2.0

package/lib/extensions/alpha-orbitals/gpu/shader.frag.js

@@ -3,141 +3,141 @@
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
-export const UTILS = `
-float L1(vec3 p, float a0, float a1, float a2) {
-    return a0 * p.z + a1 * p.x + a2 * p.y;
-}
-
-float L2(vec3 p, float a0, float a1, float a2, float a3, float a4) {
-    float x = p.x, y = p.y, z = p.z;
-    float xx = x * x, yy = y * y, zz = z * z;
-    return (
-        a0 * (-0.5 * xx - 0.5 * yy + zz) +
-        a1 * (1.7320508075688772 * x * z) +
-        a2 * (1.7320508075688772 * y * z) +
-        a3 * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
-        a4 * (1.7320508075688772 * x * y)
-    );
-}
-
-float L3(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6) {
-    float x = p.x, y = p.y, z = p.z;
-    float xx = x * x, yy = y * y, zz = z * z;
-    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
-    return (
-        a0 * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
-        a1 * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
-        a2 * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
-        a3 * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
-        a4 * (3.872983346207417 * x * y * z) +
-        a5 * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
-        a6 * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
-    );
-}
-
-float L4(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6, float a7, float a8) {
-    float x = p.x, y = p.y, z = p.z;
-    float xx = x * x, yy = y * y, zz = z * z;
-    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
-    float xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
-    return (
-        a0 * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
-        a1 * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
-        a2 * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
-        a3 * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
-        a4 * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
-        a5 * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
-        a6 * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
-        a7 * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
-        a8 * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
-    );
-}
-
-float alpha(float offset, float f) {
-    #ifdef WEBGL1
-        // in webgl1, the value is in the alpha channel!
-        return texture2D(tAlpha, vec2(offset * f, 0.5)).a;
-    #else
-        return texture2D(tAlpha, vec2(offset * f, 0.5)).x;
-    #endif
-}
-
-float Y(int L, vec3 X, float aO, float fA) {
-    if (L == 0) {
-        return alpha(aO, fA);
-    } else if (L == 1) {
-        return L1(X,
-            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA)
-        );
-    } else if (L == 2) {
-        return L2(X,
-            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA)
-        );
-    } else if (L == 3) {
-        return L3(X,
-            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
-            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA)
-        );
-    } else if (L == 4) {
-        return L4(X,
-            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
-            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA), alpha(aO + 7.0, fA), alpha(aO + 8.0, fA)
-        );
-    }
-    // TODO: do we need L > 4?
-    return 0.0;
-}
-
-#ifndef WEBGL1
-    float R(float R2, int start, int end, float fCoeff) {
-        float gauss = 0.0;
-        for (int i = start; i < end; i++) {
-            vec2 c = texture2D(tCoeff, vec2(float(i) * fCoeff, 0.5)).xy;
-            gauss += c.x * exp(-c.y * R2);
-        }
-        return gauss;
-    }
-#else
-    float R(float R2, int start, int end, float fCoeff) {
-        float gauss = 0.0;
-        int o = start;
-        for (int i = 0; i < uMaxCoeffs; i++) {
-            if (o >= end) break;
-
-            vec2 c = texture2D(tCoeff, vec2(float(o) * fCoeff, 0.5)).xy;
-            gauss += c.x * exp(-c.y * R2);
-            o++;
-        }
-        return gauss;
-    }
-#endif
+export const UTILS = `
+float L1(vec3 p, float a0, float a1, float a2) {
+    return a0 * p.z + a1 * p.x + a2 * p.y;
+}
+
+float L2(vec3 p, float a0, float a1, float a2, float a3, float a4) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    return (
+        a0 * (-0.5 * xx - 0.5 * yy + zz) +
+        a1 * (1.7320508075688772 * x * z) +
+        a2 * (1.7320508075688772 * y * z) +
+        a3 * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
+        a4 * (1.7320508075688772 * x * y)
+    );
+}
+
+float L3(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    return (
+        a0 * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
+        a1 * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
+        a2 * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
+        a3 * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
+        a4 * (3.872983346207417 * x * y * z) +
+        a5 * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
+        a6 * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
+    );
+}
+
+float L4(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6, float a7, float a8) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    float xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
+    return (
+        a0 * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
+        a1 * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
+        a2 * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
+        a3 * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
+        a4 * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
+        a5 * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
+        a6 * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
+        a7 * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
+        a8 * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
+    );
+}
+
+float alpha(float offset, float f) {
+    #ifdef WEBGL1
+        // in webgl1, the value is in the alpha channel!
+        return texture2D(tAlpha, vec2(offset * f, 0.5)).a;
+    #else
+        return texture2D(tAlpha, vec2(offset * f, 0.5)).x;
+    #endif
+}
+
+float Y(int L, vec3 X, float aO, float fA) {
+    if (L == 0) {
+        return alpha(aO, fA);
+    } else if (L == 1) {
+        return L1(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA)
+        );
+    } else if (L == 2) {
+        return L2(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA)
+        );
+    } else if (L == 3) {
+        return L3(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
+            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA)
+        );
+    } else if (L == 4) {
+        return L4(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
+            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA), alpha(aO + 7.0, fA), alpha(aO + 8.0, fA)
+        );
+    }
+    // TODO: do we need L > 4?
+    return 0.0;
+}
+
+#ifndef WEBGL1
+    float R(float R2, int start, int end, float fCoeff) {
+        float gauss = 0.0;
+        for (int i = start; i < end; i++) {
+            vec2 c = texture2D(tCoeff, vec2(float(i) * fCoeff, 0.5)).xy;
+            gauss += c.x * exp(-c.y * R2);
+        }
+        return gauss;
+    }
+#else
+    float R(float R2, int start, int end, float fCoeff) {
+        float gauss = 0.0;
+        int o = start;
+        for (int i = 0; i < uMaxCoeffs; i++) {
+            if (o >= end) break;
+
+            vec2 c = texture2D(tCoeff, vec2(float(o) * fCoeff, 0.5)).xy;
+            gauss += c.x * exp(-c.y * R2);
+            o++;
+        }
+        return gauss;
+    }
+#endif
 `;
-export const MAIN = `
-    float fCenter = 1.0 / float(uNCenters - 1);
-    float fCoeff = 1.0 / float(uNCoeff - 1);
-    float fA = 1.0 / float(uNAlpha - 1);
-
-    float v = 0.0;
-
-    for (int i = 0; i < uNCenters; i++) {
-        vec2 cCoord = vec2(float(i) * fCenter, 0.5);
-
-        vec4 center = texture2D(tCenters, cCoord);
-        vec3 X = xyz - center.xyz;
-        float R2 = dot(X, X);
-
-        // center.w is squared cutoff radius
-        if (R2 > center.w) {
-            continue;
-        }
-
-        vec4 info = texture2D(tInfo, cCoord);
-
-        int L = int(info.x);
-        float aO = info.y;
-        int coeffStart = int(info.z);
-        int coeffEnd = int(info.w);
-
-        v += R(R2, coeffStart, coeffEnd, fCoeff) * Y(L, X, aO, fA);
-    }
+export const MAIN = `
+    float fCenter = 1.0 / float(uNCenters - 1);
+    float fCoeff = 1.0 / float(uNCoeff - 1);
+    float fA = 1.0 / float(uNAlpha - 1);
+
+    float v = 0.0;
+
+    for (int i = 0; i < uNCenters; i++) {
+        vec2 cCoord = vec2(float(i) * fCenter, 0.5);
+
+        vec4 center = texture2D(tCenters, cCoord);
+        vec3 X = xyz - center.xyz;
+        float R2 = dot(X, X);
+
+        // center.w is squared cutoff radius
+        if (R2 > center.w) {
+            continue;
+        }
+
+        vec4 info = texture2D(tInfo, cCoord);
+
+        int L = int(info.x);
+        float aO = info.y;
+        int coeffStart = int(info.z);
+        int coeffEnd = int(info.w);
+
+        v += R(R2, coeffStart, coeffEnd, fCoeff) * Y(L, X, aO, fA);
+    }
 `;

package/lib/extensions/alpha-orbitals/transforms.d.ts

@@ -17,7 +17,7 @@ declare const BasisAndOrbitals_base: {
         label: string;
         description?: string | undefined;
     } | undefined): {
-        id: import("../../mol-util/uuid").UUID;
+        id: import("../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
         description?: string | undefined;
@@ -28,7 +28,7 @@ declare const BasisAndOrbitals_base: {
         };
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>> | undefined): obj is import("../../mol-state/object").StateObject<{
+    is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<{
         basis: Basis;
         order: SphericalBasisOrder;
         orbitals: AlphaOrbital[];

package/lib/extensions/anvil/behavior.d.ts

@@ -36,8 +36,9 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
         variant: any;
         objects: any;
     }>;
+    emissive: number;
     instanceGranularity: boolean;
-    lod: import("../../mol-math/linear-algebra/3d/vec3").Vec3;
+    lod: import("../../mol-math/linear-algebra").Vec3;
     cellSize: number;
     batchSize: number;
     sectorOpacity: number;
@@ -68,19 +69,19 @@ export declare const MembraneOrientationPreset: StructureRepresentationPresetPro
     representations?: undefined;
 } | {
     components: {
-        polymer: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
     } | {
-        all: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        all: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>> | undefined;
         branched: undefined;
     } | undefined;
     representations: {
-        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     } | {
-        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
-        polymer: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
+        polymer: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     } | {
-        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
-        all: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+        membraneOrientation: import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
+        all: import("../../mol-state").StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;
-export declare function tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<MembraneOrientation3D>, initialState?: Partial<StateTransform.State>): Promise<import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>;
+export declare function tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<MembraneOrientation3D>, initialState?: Partial<StateTransform.State>): Promise<import("../../mol-state").StateObjectSelector<PluginStateObject.Shape.Representation3D, StateTransformer<import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>>, any>>>;

package/lib/extensions/anvil/representation.d.ts

@@ -38,6 +38,7 @@ declare const BilayerPlanesParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -69,6 +70,7 @@ declare const BilayerRimsParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -101,6 +103,7 @@ export declare const MembraneOrientationParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -142,6 +145,7 @@ export declare function getMembraneOrientationParams(ctx: ThemeRegistryContext,
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -183,6 +187,7 @@ export declare const MembraneOrientationRepresentationProvider: StructureReprese
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/extensions/assembly-symmetry/behavior.d.ts

@@ -42,8 +42,9 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
         variant: any;
         objects: any;
     }>;
+    emissive: number;
     instanceGranularity: boolean;
-    lod: import("../../mol-math/linear-algebra/3d/vec3").Vec3;
+    lod: import("../../mol-math/linear-algebra").Vec3;
     cellSize: number;
     batchSize: number;
     axesColor: PD.NamedParams<PD.Normalize<{

package/lib/extensions/assembly-symmetry/prop.js

@@ -14,30 +14,30 @@ import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { compile } from '../../mol-script/runtime/query/compiler';
 import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 import { Asset } from '../../mol-util/assets';
-const rcsb_symmetry_gql = /* GraphQL */ `
-query AssemblySymmetry($assembly_id: String!, $entry_id: String!) {
-    assembly(assembly_id: $assembly_id, entry_id: $entry_id) {
-        rcsb_struct_symmetry {
-            clusters {
-                avg_rmsd
-                members {
-                    asym_id
-                    pdbx_struct_oper_list_ids
-                }
-            }
-            kind
-            oligomeric_state
-            rotation_axes {
-                order
-                start
-                end
-            }
-            stoichiometry
-            symbol
-            type
-        }
-    }
-}
+const rcsb_symmetry_gql = /* GraphQL */ `
+query AssemblySymmetry($assembly_id: String!, $entry_id: String!) {
+    assembly(assembly_id: $assembly_id, entry_id: $entry_id) {
+        rcsb_struct_symmetry {
+            clusters {
+                avg_rmsd
+                members {
+                    asym_id
+                    pdbx_struct_oper_list_ids
+                }
+            }
+            kind
+            oligomeric_state
+            rotation_axes {
+                order
+                start
+                end
+            }
+            stoichiometry
+            symbol
+            type
+        }
+    }
+}
 `;
 const BiologicalAssemblyNames = new Set([
     'author_and_software_defined_assembly',

package/lib/extensions/assembly-symmetry/representation.d.ts

@@ -36,6 +36,7 @@ export declare const AssemblySymmetryParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;

package/lib/extensions/backgrounds/index.d.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
-export declare const Backgrounds: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;
+export declare const Backgrounds: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {}>;

package/lib/extensions/backgrounds/index.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -76,6 +76,7 @@ export const Backgrounds = PluginBehavior.create({
                                 saturation: 0,
                                 opacity: 1,
                                 blur: 0.3,
+                                rotation: { x: 0, y: 0, z: 0 },
                             }
                         }
                     }, 'Purple Nebula Skybox'],

package/lib/extensions/dnatco/behavior.d.ts

@@ -5,7 +5,7 @@
  * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
  */
 import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
-export declare const DnatcoNtCs: import("../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+export declare const DnatcoNtCs: import("../../mol-state").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
     autoAttach: boolean;
     showToolTip: boolean;
 }>;

package/lib/extensions/dnatco/confal-pyramids/behavior.d.ts

@@ -24,23 +24,23 @@ export declare const ConfalPyramidsPreset: StructureRepresentationPresetProvider
     representations?: undefined;
 } | {
     components: {
-        pyramids: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        pyramids: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
     } | {
-        pyramids: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        pyramids: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
     } | {
-        pyramids: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        pyramids: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
         branched: undefined;
     };
     representations: {
-        pyramidsRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        pyramidsRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
     } | {
-        pyramidsRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        pyramidsRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
     } | {
-        pyramidsRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
-        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+        pyramidsRepr: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>> | undefined;
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state").StateTransformer<import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>>, any>>;
     };
 }>;
 export declare function confalPyramidLabel(step: DnatcoTypes.Step): string;

package/lib/extensions/dnatco/confal-pyramids/behavior.js

@@ -41,10 +41,10 @@ export const ConfalPyramidsPreset = StructureRepresentationPresetProvider({
     }
 });
 export function confalPyramidLabel(step) {
-    return `
-        <b>${step.auth_asym_id_1}</b> |
-        <b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}
-           ${step.label_comp_id_2} ${step.auth_seq_id_2}${step.PDB_ins_code_2}${step.label_alt_id_2.length > 0 ? ` (alt ${step.label_alt_id_2})` : ''} </b><br />
-        <i>NtC:</i> ${step.NtC} | <i>Confal score:</i> ${step.confal_score} | <i>RMSD:</i> ${step.rmsd.toFixed(2)}
+    return `
+        <b>${step.auth_asym_id_1}</b> |
+        <b>${step.label_comp_id_1} ${step.auth_seq_id_1}${step.PDB_ins_code_1}${step.label_alt_id_1.length > 0 ? ` (alt ${step.label_alt_id_1})` : ''}
+           ${step.label_comp_id_2} ${step.auth_seq_id_2}${step.PDB_ins_code_2}${step.label_alt_id_2.length > 0 ? ` (alt ${step.label_alt_id_2})` : ''} </b><br />
+        <i>NtC:</i> ${step.NtC} | <i>Confal score:</i> ${step.confal_score} | <i>RMSD:</i> ${step.rmsd.toFixed(2)}
     `;
 }

package/lib/extensions/dnatco/confal-pyramids/representation.d.ts

@@ -37,6 +37,7 @@ export declare const ConfalPyramidsParams: {
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -71,6 +72,7 @@ export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, struc
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;
@@ -106,6 +108,7 @@ export declare const ConfalPyramidsRepresentationProvider: StructureRepresentati
             scale: any;
         }>[];
     }>>;
+    emissive: PD.Numeric;
     instanceGranularity: PD.BooleanParam;
     lod: PD.Vec3;
     cellSize: PD.Numeric;