molstar 4.2.0 → 4.3.0

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/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/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/ntc-tube/behavior.js

@@ -41,10 +41,10 @@ export const NtCTubePreset = StructureRepresentationPresetProvider({
     }
 });
 export function NtCTubeSegmentLabel(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/geo-export/usdz-exporter.js

@@ -24,20 +24,20 @@ export class UsdzExporter extends MeshExporter {
         const materialKey = this.materialMap.size;
         this.materialMap.set(hash, materialKey);
         const [r, g, b] = Color.toRgbNormalized(color).map(v => Math.round(v * 1000) / 1000);
-        this.materials.push(`
-def Material "material${materialKey}"
-{
-    token outputs:surface.connect = </material${materialKey}/shader.outputs:surface>
-    def Shader "shader"
-    {
-        uniform token info:id = "UsdPreviewSurface"
-        color3f inputs:diffuseColor = (${r},${g},${b})
-        float inputs:opacity = ${alpha}
-        float inputs:metallic = ${metalness}
-        float inputs:roughness = ${roughness}
-        token outputs:surface
-    }
-}
+        this.materials.push(`
+def Material "material${materialKey}"
+{
+    token outputs:surface.connect = </material${materialKey}/shader.outputs:surface>
+    def Shader "shader"
+    {
+        uniform token info:id = "UsdPreviewSurface"
+        color3f inputs:diffuseColor = (${r},${g},${b})
+        float inputs:opacity = ${alpha}
+        float inputs:metallic = ${metalness}
+        float inputs:roughness = ${roughness}
+        token outputs:surface
+    }
+}
 `);
         return materialKey;
     }
@@ -144,41 +144,41 @@ def Material "material${materialKey}"
             else {
                 const geomSubsets = [];
                 faceIndicesByMaterial.forEach((faceIndices, materialKey) => {
-                    geomSubsets.push(`
-    def GeomSubset "g${materialKey}"
-    {
-        uniform token elementType = "face"
-        uniform token familyName = "materialBind"
-        int[] indices = [${faceIndices.join(',')}]
-        rel material:binding = </material${materialKey}>
-    }
+                    geomSubsets.push(`
+    def GeomSubset "g${materialKey}"
+    {
+        uniform token elementType = "face"
+        uniform token familyName = "materialBind"
+        int[] indices = [${faceIndices.join(',')}]
+        rel material:binding = </material${materialKey}>
+    }
 `);
                 });
                 materialBinding = geomSubsets.join('');
             }
-            this.meshes.push(`
-def Mesh "mesh${this.meshes.length}"
-{
-    int[] faceVertexCounts = [${new Array(drawCount / 3).fill(3).join(',')}]
-    int[] faceVertexIndices = [${StringBuilder.getString(indexBuilder)}]
-    point3f[] points = [${StringBuilder.getString(vertexBuilder)}]
-    normal3f[] primvars:normals = [${StringBuilder.getString(normalBuilder)}] (
-        interpolation = "vertex"
-    )
-    uniform token subdivisionScheme = "none"
-    ${materialBinding}
-}
+            this.meshes.push(`
+def Mesh "mesh${this.meshes.length}"
+{
+    int[] faceVertexCounts = [${new Array(drawCount / 3).fill(3).join(',')}]
+    int[] faceVertexIndices = [${StringBuilder.getString(indexBuilder)}]
+    point3f[] points = [${StringBuilder.getString(vertexBuilder)}]
+    normal3f[] primvars:normals = [${StringBuilder.getString(normalBuilder)}] (
+        interpolation = "vertex"
+    )
+    uniform token subdivisionScheme = "none"
+    ${materialBinding}
+}
 `);
         }
     }
     async getData(ctx) {
-        const header = `#usda 1.0
-(
-    customLayerData = {
-        string creator = "Mol* ${PLUGIN_VERSION}"
-    }
-    metersPerUnit = 1
-)
+        const header = `#usda 1.0
+(
+    customLayerData = {
+        string creator = "Mol* ${PLUGIN_VERSION}"
+    }
+    metersPerUnit = 1
+)
 `;
         const usda = [header, ...this.materials, ...this.meshes].join('');
         const usdaData = new Uint8Array(usda.length);

package/lib/extensions/meshes/mesh-extension.d.ts

@@ -44,6 +44,7 @@ declare const MeshlistStateObject_base: {
         type: PluginStateObject.TypeInfo;
         /** Data type for `MeshlistStateObject` - list of meshes */
         label: string;
+        /** Data type for `MeshlistStateObject` - list of meshes */
         description?: string | undefined;
         data: MeshlistData;
     };

package/lib/extensions/mp4-export/encoder.js

@@ -47,7 +47,7 @@ export async function encodeMp4Animation(plugin, ctx, params) {
         await plugin.managers.animation.play(params.animation.definition, params.animation.params);
         stoppedAnimation = false;
         for (let i = 0; i <= N; i++) {
-            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true });
+            await loop.tick(i * dt, { isSynchronous: true, animation: { currentFrame: i, frameCount: N }, manualDraw: true, updateControls: true });
             const image = params.pass.getImageData(width, height, normalizedViewport);
             encoder.addFrameRgba(image.data);
             if (ctx.shouldUpdate) {

package/lib/extensions/mvs/components/annotation-label/representation.d.ts

@@ -77,7 +77,6 @@ export declare const MVSAnnotationLabelParams: {
     ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    /** Parameter values for representation type "MVS Annotation Label" */
     annotationId: PD.Text<string>;
     fieldName: PD.Text<string>;
 };
@@ -155,7 +154,6 @@ export declare const MVSAnnotationLabelRepresentationProvider: StructureRepresen
     ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    /** Parameter values for representation type "MVS Annotation Label" */
     annotationId: PD.Text<string>;
     fieldName: PD.Text<string>;
 }, "mvs-annotation-label">;

package/lib/extensions/mvs/components/custom-label/representation.d.ts

@@ -15,7 +15,7 @@ export declare const CustomLabelParams: {
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
         isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
+        isOptional?: boolean | undefined; /** A thingy that is needed to register representation type "Custom Label", allowing user-defined labels at at user-defined positions */
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../../../mol-util/legend").Legend | undefined;
@@ -101,7 +101,7 @@ export declare const CustomLabelRepresentationProvider: StructureRepresentationP
         defaultValue: import("../../../../mol-util/color").Color;
         type: "color";
         isExpanded?: boolean | undefined;
-        isOptional?: boolean | undefined;
+        isOptional?: boolean | undefined; /** A thingy that is needed to register representation type "Custom Label", allowing user-defined labels at at user-defined positions */
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../../../mol-util/legend").Legend | undefined;

package/lib/extensions/mvs/tree/mvs/mvs-builder.d.ts

@@ -85,7 +85,6 @@ declare class _Base<TKind extends MVSKind> {
                 }[]>;
             };
             component_from_uri: {
-                /** Add a 'representation' node and return builder pointing to it. 'representation' node instructs to create a visual representation of a component. */
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
                 uri: import("../generic/params-schema").RequiredField<string>;
                 format: import("../generic/params-schema").RequiredField<"json" | "cif" | "bcif">;
@@ -97,6 +96,7 @@ declare class _Base<TKind extends MVSKind> {
             };
             component_from_source: {
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -152,6 +152,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             color_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -171,6 +172,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             label_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -190,6 +192,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             tooltip_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -266,7 +269,6 @@ declare class _Base<TKind extends MVSKind> {
                 }[]>;
             };
             component_from_uri: {
-                /** Add a 'representation' node and return builder pointing to it. 'representation' node instructs to create a visual representation of a component. */
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
                 uri: import("../generic/params-schema").RequiredField<string>;
                 format: import("../generic/params-schema").RequiredField<"json" | "cif" | "bcif">;
@@ -278,6 +280,7 @@ declare class _Base<TKind extends MVSKind> {
             };
             component_from_source: {
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -333,6 +336,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             color_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -352,6 +356,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             label_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -371,6 +376,7 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             tooltip_from_source: {
+                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;

package/lib/extensions/sb-ncbr/index.d.ts

@@ -1,3 +1,11 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dominik Tichý <tichydominik451@gmail.com>
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
 export { SbNcbrPartialCharges } from './partial-charges/behavior';
 export { SbNcbrPartialChargesPreset } from './partial-charges/preset';
 export { SbNcbrPartialChargesPropertyProvider } from './partial-charges/property';
+export { SbNcbrTunnels } from './tunnels/behavior';
+export { TunnelsFromRawData, SelectTunnel, TunnelFromRawData, TunnelShapeProvider } from './tunnels/representation';

package/lib/extensions/sb-ncbr/index.js

@@ -1,3 +1,11 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Dominik Tichý <tichydominik451@gmail.com>
+ * @author Dušan Veľký <dvelky@mail.muni.cz>
+ */
 export { SbNcbrPartialCharges } from './partial-charges/behavior';
 export { SbNcbrPartialChargesPreset } from './partial-charges/preset';
 export { SbNcbrPartialChargesPropertyProvider } from './partial-charges/property';
+export { SbNcbrTunnels } from './tunnels/behavior';
+export { TunnelsFromRawData, SelectTunnel, TunnelFromRawData, TunnelShapeProvider } from './tunnels/representation';