molstar 3.4.0 → 3.6.1

package/lib/mol-math/geometry/gaussian-density/cpu.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -127,7 +127,7 @@ export function GaussianDensityCPU(ctx, position, box, radius, props) {
                     transform = Mat4.identity();
                     Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
                     Mat4.setTranslation(transform, expandedBox.min);
-                    return [2 /*return*/, { field: field, idField: idField, transform: transform, radiusFactor: 1, resolution: resolution }];
+                    return [2 /*return*/, { field: field, idField: idField, transform: transform, radiusFactor: 1, resolution: resolution, maxRadius: maxRadius }];
             }
         });
     });

package/lib/mol-math/geometry/gaussian-density/gpu.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>

package/lib/mol-math/geometry/gaussian-density/gpu.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
@@ -56,11 +56,11 @@ export function GaussianDensityGPU(position, box, radius, props, webgl) {
     // it's faster than texture3d
     // console.time('GaussianDensityTexture2d')
     var tmpTexture = getTexture('tmp', webgl, 'image-uint8', 'rgba', 'ubyte', 'linear');
-    var _a = calcGaussianDensityTexture2d(webgl, position, box, radius, false, props, tmpTexture), scale = _a.scale, bbox = _a.bbox, texture = _a.texture, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
+    var _a = calcGaussianDensityTexture2d(webgl, position, box, radius, false, props, tmpTexture), scale = _a.scale, bbox = _a.bbox, texture = _a.texture, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
     // webgl.waitForGpuCommandsCompleteSync()
     // console.timeEnd('GaussianDensityTexture2d')
     var _b = fieldFromTexture2d(webgl, texture, gridDim, gridTexDim), field = _b.field, idField = _b.idField;
-    return { field: field, idField: idField, transform: getTransform(scale, bbox), radiusFactor: radiusFactor, resolution: resolution };
+    return { field: field, idField: idField, transform: getTransform(scale, bbox), radiusFactor: radiusFactor, resolution: resolution, maxRadius: maxRadius };
 }
 export function GaussianDensityTexture(webgl, position, box, radius, props, oldTexture) {
     return webgl.isWebGL2 ?
@@ -74,8 +74,8 @@ export function GaussianDensityTexture3d(webgl, position, box, radius, props, ol
     return finalizeGaussianDensityTexture(calcGaussianDensityTexture3d(webgl, position, box, radius, props, oldTexture));
 }
 function finalizeGaussianDensityTexture(_a) {
-    var texture = _a.texture, scale = _a.scale, bbox = _a.bbox, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, gridTexScale = _a.gridTexScale, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
-    return { transform: getTransform(scale, bbox), texture: texture, bbox: bbox, gridDim: gridDim, gridTexDim: gridTexDim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution };
+    var texture = _a.texture, scale = _a.scale, bbox = _a.bbox, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, gridTexScale = _a.gridTexScale, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
+    return { transform: getTransform(scale, bbox), texture: texture, bbox: bbox, gridDim: gridDim, gridTexDim: gridTexDim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution, maxRadius: maxRadius };
 }
 function getTransform(scale, bbox) {
     var transform = Mat4.identity();
@@ -151,7 +151,7 @@ function calcGaussianDensityTexture2d(webgl, position, box, radius, powerOfTwo,
         render(texture, false);
     }
     // printTexture(webgl, minDistTex, 0.75);
-    return { texture: texture, scale: scale, bbox: expandedBox, gridDim: dim, gridTexDim: gridTexDim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution };
+    return { texture: texture, scale: scale, bbox: expandedBox, gridDim: dim, gridTexDim: gridTexDim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution, maxRadius: maxRadius };
 }
 function calcGaussianDensityTexture3d(webgl, position, box, radius, props, texture) {
     // console.log('3d');
@@ -195,7 +195,7 @@ function calcGaussianDensityTexture3d(webgl, position, box, radius, props, textu
     render(minDistTex, true);
     setupGroupIdRendering(webgl, renderable);
     render(texture, false);
-    return { texture: texture, scale: scale, bbox: expandedBox, gridDim: dim, gridTexDim: dim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution };
+    return { texture: texture, scale: scale, bbox: expandedBox, gridDim: dim, gridTexDim: dim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution, maxRadius: maxRadius };
 }
 //
 function prepareGaussianDensityData(position, box, radius, props) {

package/lib/mol-math/geometry/gaussian-density.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -16,11 +16,11 @@ export declare const DefaultGaussianDensityProps: {
 export declare type GaussianDensityProps = typeof DefaultGaussianDensityProps;
 export declare type GaussianDensityData = {
     radiusFactor: number;
-    resolution: number;
 } & DensityData;
 export declare type GaussianDensityTextureData = {
     radiusFactor: number;
     resolution: number;
+    maxRadius: number;
 } & DensityTextureData;
 export declare function computeGaussianDensity(position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps): Task<GaussianDensityData>;
 export declare function computeGaussianDensityTexture(position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<GaussianDensityTextureData>;

package/lib/mol-math/geometry/gaussian-density.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-math/geometry/molecular-surface.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Fred Ludlow <fred.ludlow@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -29,4 +29,5 @@ export declare function calcMolecularSurface(ctx: RuntimeContext, position: Requ
     idField: Tensor;
     transform: Mat4;
     resolution: number;
+    maxRadius: number;
 }>;

package/lib/mol-math/geometry/molecular-surface.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Fred Ludlow <fred.ludlow@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -345,7 +345,7 @@ export function calcMolecularSurface(ctx, position, boundary, maxRadius, box, pr
                     Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
                     Mat4.setTranslation(transform, expandedBox.min);
                     // console.log({ field, idField, transform, updateChunk })
-                    return [2 /*return*/, { field: field, idField: idField, transform: transform, resolution: resolution }];
+                    return [2 /*return*/, { field: field, idField: idField, transform: transform, resolution: resolution, maxRadius: maxRadius }];
             }
         });
     });

package/lib/mol-math/geometry/primitives/box3d.js

@@ -27,8 +27,9 @@ function Box3D() {
     Box3D.clone = clone;
     /** Get box from sphere, uses extrema if available */
     function fromSphere3D(out, sphere) {
-        if (Sphere3D.hasExtrema(sphere))
+        if (Sphere3D.hasExtrema(sphere) && sphere.extrema.length >= 14) { // 14 extrema with coarse boundary helper
             return fromVec3Array(out, sphere.extrema);
+        }
         var r = Vec3.create(sphere.radius, sphere.radius, sphere.radius);
         Vec3.sub(out.min, sphere.center, r);
         Vec3.add(out.max, sphere.center, r);

package/lib/mol-math/geometry/primitives/sphere3d.js

@@ -202,15 +202,21 @@ function Sphere3D() {
             var axes_1 = PrincipalAxes.calculateMomentsAxes(positions);
             Axes3D.scale(axes_1, Axes3D.normalize(axes_1, axes_1), delta);
             setExtrema(out, sphere.extrema.map(function (e) {
-                Vec3.sub(tmpDir, e, sphere.center);
-                var out = Vec3.clone(e);
+                Vec3.normalize(tmpDir, Vec3.sub(tmpDir, e, sphere.center));
+                var o = Vec3.clone(e);
                 var sA = Vec3.dot(tmpDir, axes_1.dirA) < 0 ? -1 : 1;
-                Vec3.scaleAndAdd(out, out, axes_1.dirA, sA);
+                Vec3.scaleAndAdd(o, o, axes_1.dirA, sA);
                 var sB = Vec3.dot(tmpDir, axes_1.dirB) < 0 ? -1 : 1;
-                Vec3.scaleAndAdd(out, out, axes_1.dirB, sB);
+                Vec3.scaleAndAdd(o, o, axes_1.dirB, sB);
                 var sC = Vec3.dot(tmpDir, axes_1.dirC) < 0 ? -1 : 1;
-                Vec3.scaleAndAdd(out, out, axes_1.dirC, sC);
-                return out;
+                Vec3.scaleAndAdd(o, o, axes_1.dirC, sC);
+                if (Vec3.distance(out.center, o) > out.radius) {
+                    if (sphere.extrema.length >= 14) { // 14 extrema with coarse boundary helper
+                        Vec3.normalize(tmpDir, Vec3.sub(tmpDir, o, sphere.center));
+                    }
+                    Vec3.scaleAndAdd(o, out.center, tmpDir, out.radius);
+                }
+                return o;
             }));
         }
         return out;

package/lib/mol-model/structure/model/model.js

@@ -18,6 +18,7 @@ import { ModelSymmetry } from '../../../mol-model-formats/structure/property/sym
 import { Column } from '../../../mol-data/db';
 import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
 import { ArrayTrajectory } from '../trajectory';
+import { ModelSecondaryStructure } from '../../../mol-model-formats/structure/property/secondary-structure';
 { }
 export var Model;
 (function (Model) {
@@ -28,8 +29,12 @@ export var Model;
         var isIdentity = Column.isIdentity(srcIndex);
         var srcIndexArray = isIdentity ? void 0 : srcIndex.toArray({ array: Int32Array });
         var coarseGrained = isCoarseGrained(model);
+        var elementCount = model.atomicHierarchy.atoms._rowCount;
         for (var i = 0, il = frames.length; i < il; ++i) {
             var f = frames[i];
+            if (f.elementCount !== elementCount) {
+                throw new Error("Frame element count mismatch, got ".concat(f.elementCount, " but expected ").concat(elementCount, "."));
+            }
             var m = __assign(__assign({}, model), { id: UUID.create22(), modelNum: i, atomicConformation: Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray), 
                 // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates?
                 // coarseConformation: coarse.conformation,
@@ -215,7 +220,7 @@ export var Model;
             return false;
         var db = model.sourceData.data.db;
         for (var i = 0, il = db.database_2.database_id.rowCount; i < il; ++i) {
-            if (db.database_2.database_id.value(i) === 'PDB')
+            if (db.database_2.database_id.value(i) === 'pdb')
                 return true;
         }
         return false;
@@ -232,11 +237,14 @@ export var Model;
     }
     Model.hasPdbId = hasPdbId;
     function hasSecondaryStructure(model) {
-        if (!MmcifFormat.is(model.sourceData))
-            return false;
-        var db = model.sourceData.data.db;
-        return (db.struct_conf.id.isDefined ||
-            db.struct_sheet_range.id.isDefined);
+        if (MmcifFormat.is(model.sourceData)) {
+            var db = model.sourceData.data.db;
+            return (db.struct_conf.id.isDefined ||
+                db.struct_sheet_range.id.isDefined);
+        }
+        else {
+            return ModelSecondaryStructure.Provider.isApplicable(model);
+        }
     }
     Model.hasSecondaryStructure = hasSecondaryStructure;
     var tmpAngles90 = Vec3.create(1.5707963, 1.5707963, 1.5707963); // in radians

package/lib/mol-model/structure/model/properties/common.js

@@ -5,4 +5,4 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { Column } from '../../../../mol-data/db';
-export var EntitySubtype = Column.Schema.Aliased(Column.Schema.Str(''));
+export var EntitySubtype = Column.Schema.Aliased(Column.Schema.Str());

package/lib/mol-model/structure/model/types.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -62,32 +62,33 @@ export declare const PolymerTypeAtomRoleId: {
 };
 export declare const ProteinBackboneAtoms: Set<string>;
 export declare const NucleicBackboneAtoms: Set<string>;
+declare type ChemCompType = mmCIF_chemComp_schema['type']['T'];
 /** Chemical component type names for D-linked protein */
-export declare const DProteinComponentTypeNames: Set<string>;
+export declare const DProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for L-linked protein */
-export declare const LProteinComponentTypeNames: Set<string>;
+export declare const LProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for gamma protein, overlaps with D/L-linked */
-export declare const GammaProteinComponentTypeNames: Set<string>;
+export declare const GammaProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for beta protein, overlaps with D/L-linked */
-export declare const BetaProteinComponentTypeNames: Set<string>;
+export declare const BetaProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for protein termini, overlaps with D/L-linked */
-export declare const ProteinTerminusComponentTypeNames: Set<string>;
+export declare const ProteinTerminusComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for peptide-like protein */
-export declare const OtherProteinComponentTypeNames: Set<string>;
+export declare const OtherProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for protein */
-export declare const ProteinComponentTypeNames: Set<string>;
+export declare const ProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for DNA */
-export declare const DNAComponentTypeNames: Set<string>;
+export declare const DNAComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for RNA */
-export declare const RNAComponentTypeNames: Set<string>;
+export declare const RNAComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for saccharide */
 export declare const SaccharideComponentTypeNames: Set<string>;
 /** Chemical component type names for other */
-export declare const OtherComponentTypeNames: Set<string>;
+export declare const OtherComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for ion (extension to mmcif) */
-export declare const IonComponentTypeNames: Set<string>;
+export declare const IonComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for lipid (extension to mmcif) */
-export declare const LipidComponentTypeNames: Set<string>;
+export declare const LipidComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Common names for water molecules */
 export declare const WaterNames: Set<string>;
 export declare const AminoAcidNamesL: Set<string>;
@@ -103,12 +104,12 @@ export declare const isPurineBase: (compId: string) => boolean;
 export declare const isPyrimidineBase: (compId: string) => boolean;
 export declare const PolymerNames: Set<string>;
 /** get the molecule type from component type and id */
-export declare function getMoleculeType(compType: string, compId: string): MoleculeType;
-export declare function getPolymerType(compType: string, molType: MoleculeType): PolymerType;
-export declare function getComponentType(compId: string): mmCIF_chemComp_schema['type']['T'];
+export declare function getMoleculeType(compType: ChemCompType, compId: string): MoleculeType;
+export declare function getPolymerType(compType: ChemCompType, molType: MoleculeType): PolymerType;
+export declare function getComponentType(compId: string): ChemCompType;
 export declare function getDefaultChemicalComponent(compId: string): ChemicalComponent;
 export declare function getEntityType(compId: string): mmCIF_Schema['entity']['type']['T'];
-export declare function getEntitySubtype(compId: string, compType: string): EntitySubtype;
+export declare function getEntitySubtype(compId: string, compType: ChemCompType): EntitySubtype;
 export declare function isPolymer(moleculeType: MoleculeType): boolean;
 export declare function isNucleic(moleculeType: MoleculeType): boolean;
 export declare function isProtein(moleculeType: MoleculeType): boolean;
@@ -259,3 +260,4 @@ export declare const ResidueHydrophobicity: {
     HIP: number[];
 };
 export declare const DefaultResidueHydrophobicity: number[];
+export {};

package/lib/mol-model/structure/model/types.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -117,63 +117,65 @@ export var NucleicBackboneAtoms = new Set([
 ]);
 /** Chemical component type names for D-linked protein */
 export var DProteinComponentTypeNames = new Set([
-    'D-PEPTIDE LINKING', 'D-PEPTIDE NH3 AMINO TERMINUS',
-    'D-PEPTIDE COOH CARBOXY TERMINUS', 'D-GAMMA-PEPTIDE, C-DELTA LINKING',
-    'D-BETA-PEPTIDE, C-GAMMA LINKING'
+    'd-peptide linking', 'd-peptide nh3 amino terminus',
+    'd-peptide cooh carboxy terminus', 'd-gamma-peptide, c-delta linking',
+    'd-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for L-linked protein */
 export var LProteinComponentTypeNames = new Set([
-    'L-PEPTIDE LINKING', 'L-PEPTIDE NH3 AMINO TERMINUS',
-    'L-PEPTIDE COOH CARBOXY TERMINUS', 'L-GAMMA-PEPTIDE, C-DELTA LINKING',
-    'L-BETA-PEPTIDE, C-GAMMA LINKING'
+    'l-peptide linking', 'l-peptide nh3 amino terminus',
+    'l-peptide cooh carboxy terminus', 'l-gamma-peptide, c-delta linking',
+    'l-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for gamma protein, overlaps with D/L-linked */
 export var GammaProteinComponentTypeNames = new Set([
-    'D-GAMMA-PEPTIDE, C-DELTA LINKING', 'L-GAMMA-PEPTIDE, C-DELTA LINKING'
+    'd-gamma-peptide, c-delta linking', 'l-gamma-peptide, c-delta linking'
 ]);
 /** Chemical component type names for beta protein, overlaps with D/L-linked */
 export var BetaProteinComponentTypeNames = new Set([
-    'D-BETA-PEPTIDE, C-GAMMA LINKING', 'L-BETA-PEPTIDE, C-GAMMA LINKING'
+    'd-beta-peptide, c-gamma linking', 'l-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for protein termini, overlaps with D/L-linked */
 export var ProteinTerminusComponentTypeNames = new Set([
-    'D-PEPTIDE NH3 AMINO TERMINUS', 'D-PEPTIDE COOH CARBOXY TERMINUS',
-    'L-PEPTIDE NH3 AMINO TERMINUS', 'L-PEPTIDE COOH CARBOXY TERMINUS'
+    'd-peptide nh3 amino terminus', 'd-peptide cooh carboxy terminus',
+    'l-peptide nh3 amino terminus', 'l-peptide cooh carboxy terminus'
 ]);
 /** Chemical component type names for peptide-like protein */
 export var OtherProteinComponentTypeNames = new Set([
-    'PEPTIDE LINKING', 'PEPTIDE-LIKE',
+    'peptide linking', 'peptide-like',
 ]);
 /** Chemical component type names for protein */
 export var ProteinComponentTypeNames = SetUtils.unionMany(DProteinComponentTypeNames, LProteinComponentTypeNames, OtherProteinComponentTypeNames);
 /** Chemical component type names for DNA */
 export var DNAComponentTypeNames = new Set([
-    'DNA LINKING', 'L-DNA LINKING', 'DNA OH 5 PRIME TERMINUS', 'DNA OH 3 PRIME TERMINUS',
+    'dna linking', 'l-dna linking', 'dna oh 5 prime terminus', 'dna oh 3 prime terminus',
 ]);
 /** Chemical component type names for RNA */
 export var RNAComponentTypeNames = new Set([
-    'RNA LINKING', 'L-RNA LINKING', 'RNA OH 5 PRIME TERMINUS', 'RNA OH 3 PRIME TERMINUS',
+    'rna linking', 'l-rna linking', 'rna oh 5 prime terminus', 'rna oh 3 prime terminus',
 ]);
 /** Chemical component type names for saccharide */
-export var SaccharideComponentTypeNames = new Set([
-    'D-SACCHARIDE, BETA LINKING', 'L-SACCHARIDE, BETA LINKING',
-    'D-SACCHARIDE, ALPHA LINKING', 'L-SACCHARIDE, ALPHA LINKING',
-    'L-SACCHARIDE', 'D-SACCHARIDE', 'SACCHARIDE',
-    // the following four are marked to be deprecated in the mmCIF dictionary
-    'D-SACCHARIDE 1,4 AND 1,4 LINKING', 'L-SACCHARIDE 1,4 AND 1,4 LINKING',
-    'D-SACCHARIDE 1,4 AND 1,6 LINKING', 'L-SACCHARIDE 1,4 AND 1,6 LINKING',
-]);
+export var SaccharideComponentTypeNames = SetUtils.unionMany(new Set([
+    'd-saccharide, beta linking', 'l-saccharide, beta linking',
+    'd-saccharide, alpha linking', 'l-saccharide, alpha linking',
+    'l-saccharide', 'd-saccharide', 'saccharide',
+]), 
+// deprecated in the mmCIF dictionary, kept for backward compatibility
+new Set([
+    'd-saccharide 1,4 and 1,4 linking', 'l-saccharide 1,4 and 1,4 linking',
+    'd-saccharide 1,4 and 1,6 linking', 'l-saccharide 1,4 and 1,6 linking'
+]));
 /** Chemical component type names for other */
 export var OtherComponentTypeNames = new Set([
-    'NON-POLYMER', 'OTHER'
+    'non-polymer', 'other'
 ]);
 /** Chemical component type names for ion (extension to mmcif) */
 export var IonComponentTypeNames = new Set([
-    'ION'
+    'ion'
 ]);
 /** Chemical component type names for lipid (extension to mmcif) */
 export var LipidComponentTypeNames = new Set([
-    'LIPID'
+    'lipid'
 ]);
 /** Common names for water molecules */
 export var WaterNames = new Set([
@@ -230,7 +232,6 @@ export var isPyrimidineBase = function (compId) { return PyrimidineBaseNames.has
 export var PolymerNames = SetUtils.unionMany(AminoAcidNames, BaseNames);
 /** get the molecule type from component type and id */
 export function getMoleculeType(compType, compId) {
-    compType = compType.toUpperCase();
     compId = compId.toUpperCase();
     if (PeptideBaseNames.has(compId)) {
         return 8 /* PNA */;
@@ -258,7 +259,7 @@ export function getMoleculeType(compType, compId) {
     }
     else if (OtherComponentTypeNames.has(compType)) {
         if (SaccharideCompIdMap.has(compId)) {
-            // trust our saccharide table more than given 'non-polymer' or 'other' component type
+            // trust our saccharide table more than given 'NON-POLYMER' or 'OTHER' component type
             return 9 /* Saccharide */;
         }
         else if (AminoAcidNames.has(compId)) {
@@ -279,7 +280,6 @@ export function getMoleculeType(compType, compId) {
     }
 }
 export function getPolymerType(compType, molType) {
-    compType = compType.toUpperCase();
     if (molType === 5 /* Protein */) {
         if (GammaProteinComponentTypeNames.has(compType)) {
             return 2 /* GammaProtein */;
@@ -313,10 +313,10 @@ export function getComponentType(compId) {
         return 'peptide linking';
     }
     else if (RnaBaseNames.has(compId)) {
-        return 'RNA linking';
+        return 'rna linking';
     }
     else if (DnaBaseNames.has(compId)) {
-        return 'DNA linking';
+        return 'dna linking';
     }
     else if (SaccharideCompIdMap.has(compId)) {
         return 'saccharide';
@@ -355,7 +355,6 @@ export function getEntityType(compId) {
 }
 export function getEntitySubtype(compId, compType) {
     compId = compId.toUpperCase();
-    compType = compType.toUpperCase();
     if (LProteinComponentTypeNames.has(compType)) {
         return 'polypeptide(L)';
     }

package/lib/mol-model/structure/query/queries/generators.js

@@ -320,7 +320,7 @@ export function bondedAtomicPairs(bondTest) {
             atomicBond.a.unit = structure.unitMap.get(bond.unitA);
             atomicBond.a.element = atomicBond.a.unit.elements[bond.indexA];
             atomicBond.aIndex = bond.indexA;
-            atomicBond.b.unit = structure.unitMap.get(bond.unitA);
+            atomicBond.b.unit = structure.unitMap.get(bond.unitB);
             atomicBond.b.element = atomicBond.b.unit.elements[bond.indexB];
             atomicBond.bIndex = bond.indexB;
             atomicBond.order = bond.props.order;

package/lib/mol-model/structure/structure/properties.d.ts

@@ -41,7 +41,7 @@ declare const StructureProperties: {
         microheterogeneityCompIds: StructureElement.Property<string[]>;
         secondary_structure_type: StructureElement.Property<SecondaryStructureType>;
         secondary_structure_key: StructureElement.Property<number>;
-        chem_comp_type: StructureElement.Property<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        chem_comp_type: StructureElement.Property<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
     };
     chain: {
         key: StructureElement.Property<import("../model").ChainIndex>;

package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js

@@ -167,10 +167,8 @@ var DefaultInterBondComputationProps = __assign(__assign({}, DefaultBondComputat
 function findBonds(structure, props) {
     var builder = new InterUnitGraph.Builder();
     var hasIndexPairBonds = structure.models.some(function (m) { return IndexPairBonds.Provider.get(m); });
-    if (props.noCompute || (structure.isCoarseGrained && !hasIndexPairBonds)) {
-        // TODO add function that only adds bonds defined in structConn and avoids using
-        //      structure.lookup and unit.lookup (expensive for large structure and not
-        //      needed for archival files or files with an MD topology)
+    var hasExhaustiveStructConn = structure.models.some(function (m) { return StructConn.isExhaustive(m); });
+    if (props.noCompute || (structure.isCoarseGrained && !hasIndexPairBonds && !hasExhaustiveStructConn)) {
         return new InterUnitBonds(builder.getMap());
     }
     Structure.eachUnitPair(structure, function (unitA, unitB) {

package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js

@@ -221,9 +221,7 @@ function findBonds(unit, props) {
 }
 function computeIntraUnitBonds(unit, props) {
     var p = __assign(__assign({}, DefaultBondComputationProps), props);
-    if (p.noCompute || Model.isCoarseGrained(unit.model)) {
-        // TODO add function that only adds bonds defined in structConn of chemCompBond
-        //      and avoid using unit.lookup
+    if (p.noCompute || (Model.isCoarseGrained(unit.model) && !IndexPairBonds.Provider.get(unit.model) && !StructConn.isExhaustive(unit.model))) {
         return IntraUnitBonds.Empty;
     }
     if (!p.forceCompute && IndexPairBonds.Provider.get(unit.model)) {

package/lib/mol-model/structure/structure/unit/rings.js

@@ -127,6 +127,9 @@ var UnitRing;
             return false;
         if (ring.length < 5)
             return false;
+        // no planarity-based aromaticity if any aromatic flags are present
+        if (aromaticBondCount > 0)
+            return false;
         var ma = PrincipalAxes.calculateMomentsAxes(getPositions(unit, ring));
         return Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold;
     }

package/lib/mol-model-formats/shape/ply.d.ts

@@ -30,6 +30,7 @@ export declare const PlyShapeParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -71,6 +72,7 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/mol-model-formats/structure/basic/entities.js

@@ -96,7 +96,7 @@ export function getEntityData(data) {
                 var entityId = label_entity_id.value(i);
                 if (!entityIds.has(entityId)) {
                     var compId = label_comp_id.value(i);
-                    var compType = chemCompType.get(compId) || '';
+                    var compType = chemCompType.get(compId) || 'other';
                     subtypes[getEntityIndex(entityId)] = getEntitySubtype(compId, compType);
                     entityIds.add(entityId);
                 }

package/lib/mol-model-formats/structure/basic/schema.d.ts

@@ -88,7 +88,7 @@ export declare const BasicSchema: {
         type: import("../../../mol-data/db/column").Column.Schema.Aliased<"oligosaccharide">;
     };
     chem_comp: {
-        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
+        type: import("../../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
         formula: import("../../../mol-data/db/column").Column.Schema.Str;
         formula_weight: import("../../../mol-data/db/column").Column.Schema.Float;
         id: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -160,7 +160,7 @@ export declare const BasicSchema: {
     };
     pdbx_unobs_or_zero_occ_residues: {
         id: import("../../../mol-data/db/column").Column.Schema.Int;
-        polymer_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        polymer_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         occupancy_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"1" | "0">;
         PDB_model_num: import("../../../mol-data/db/column").Column.Schema.Int;
         auth_asym_id: import("../../../mol-data/db/column").Column.Schema.Str;