molstar 4.2.0 → 4.3.0

package/lib/commonjs/examples/alpha-orbitals/example-data.js

@@ -1,166 +1,166 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.DemoOrbitals = exports.DemoMoleculeSDF = void 0;
-exports.DemoMoleculeSDF = `60823
-  -OEChem-10232017443D
-
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-    3.3901   -2.4373    3.0602 O   0  0  0  0  0  0  0  0  0  0  0  0
-    5.8234   -0.9362   -0.1694 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -4.0484   -0.0236    1.5867 O   0  0  0  0  0  0  0  0  0  0  0  0
-    5.9513   -3.8220   -3.4785 O   0  0  0  0  0  0  0  0  0  0  0  0
-    5.7344   -1.5960   -3.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
-    0.3212    0.0758    1.5166 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.4511   -1.1575   -0.3628 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.8535   -0.6250    1.5997 C   0  0  0  0  0  0  0  0  0  0  0  0
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-M  END
+exports.DemoMoleculeSDF = `60823
+  -OEChem-10232017443D
+
+ 76 79  0     1  0  0  0  0  0999 V2000
+    4.2325    4.8495   -0.2414 F   0  0  0  0  0  0  0  0  0  0  0  0
+    3.3901   -2.4373    3.0602 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.8234   -0.9362   -0.1694 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.0484   -0.0236    1.5867 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.9513   -3.8220   -3.4785 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.7344   -1.5960   -3.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3212    0.0758    1.5166 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.4511   -1.1575   -0.3628 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.8535   -0.6250    1.5997 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.5803   -0.3344    2.1283 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1278    1.2100    0.7719 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.9533   -1.9004    2.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4473   -1.2165    1.2192 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8115    0.0728    0.8978 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1907    1.2338    0.3742 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7416   -1.7120    1.8781 C   0  0  2  0  0  0  0  0  0  0  0  0
+    4.5791   -2.6487    0.9881 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.1949    2.1553    0.5088 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -8.0344   -3.3656   -1.8250 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1 33  1  0  0  0  0
+  2 16  1  0  0  0  0
+  2 61  1  0  0  0  0
+  3 22  1  0  0  0  0
+  3 67  1  0  0  0  0
+  4 23  2  0  0  0  0
+  5 35  1  0  0  0  0
+  5 73  1  0  0  0  0
+  6 35  2  0  0  0  0
+  7  9  1  0  0  0  0
+  7 10  1  0  0  0  0
+  7 11  1  0  0  0  0
+  8 23  1  0  0  0  0
+  8 34  1  0  0  0  0
+  8 64  1  0  0  0  0
+  9 12  1  0  0  0  0
+  9 14  2  0  0  0  0
+ 10 13  1  0  0  0  0
+ 10 42  1  0  0  0  0
+ 10 43  1  0  0  0  0
+ 11 15  2  0  0  0  0
+ 11 18  1  0  0  0  0
+ 12 19  1  0  0  0  0
+ 12 20  1  0  0  0  0
+ 12 44  1  0  0  0  0
+ 13 16  1  0  0  0  0
+ 13 45  1  0  0  0  0
+ 13 46  1  0  0  0  0
+ 14 15  1  0  0  0  0
+ 14 23  1  0  0  0  0
+ 15 21  1  0  0  0  0
+ 16 17  1  0  0  0  0
+ 16 47  1  0  0  0  0
+ 17 22  1  0  0  0  0
+ 17 48  1  0  0  0  0
+ 17 49  1  0  0  0  0
+ 18 25  2  0  0  0  0
+ 18 26  1  0  0  0  0
+ 19 50  1  0  0  0  0
+ 19 51  1  0  0  0  0
+ 19 52  1  0  0  0  0
+ 20 53  1  0  0  0  0
+ 20 54  1  0  0  0  0
+ 20 55  1  0  0  0  0
+ 21 27  2  0  0  0  0
+ 21 28  1  0  0  0  0
+ 22 24  1  0  0  0  0
+ 22 56  1  0  0  0  0
+ 24 35  1  0  0  0  0
+ 24 57  1  0  0  0  0
+ 24 58  1  0  0  0  0
+ 25 29  1  0  0  0  0
+ 25 59  1  0  0  0  0
+ 26 30  2  0  0  0  0
+ 26 60  1  0  0  0  0
+ 27 31  1  0  0  0  0
+ 27 62  1  0  0  0  0
+ 28 32  2  0  0  0  0
+ 28 63  1  0  0  0  0
+ 29 33  2  0  0  0  0
+ 29 65  1  0  0  0  0
+ 30 33  1  0  0  0  0
+ 30 66  1  0  0  0  0
+ 31 36  2  0  0  0  0
+ 31 68  1  0  0  0  0
+ 32 36  1  0  0  0  0
+ 32 69  1  0  0  0  0
+ 34 37  2  0  0  0  0
+ 34 38  1  0  0  0  0
+ 36 70  1  0  0  0  0
+ 37 39  1  0  0  0  0
+ 37 71  1  0  0  0  0
+ 38 40  2  0  0  0  0
+ 38 72  1  0  0  0  0
+ 39 41  2  0  0  0  0
+ 39 74  1  0  0  0  0
+ 40 41  1  0  0  0  0
+ 40 75  1  0  0  0  0
+ 41 76  1  0  0  0  0
+M  END
 `;
 exports.DemoOrbitals = {
     order: 'cca-reverse',

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

@@ -6,141 +6,141 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MAIN = exports.UTILS = void 0;
-exports.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
+exports.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
 `;
-exports.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);
-    }
+exports.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/commonjs/extensions/assembly-symmetry/prop.js

@@ -17,30 +17,30 @@ const builder_1 = require("../../mol-script/language/builder");
 const compiler_1 = require("../../mol-script/runtime/query/compiler");
 const custom_property_1 = require("../../mol-model/custom-property");
 const assets_1 = require("../../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',