Merge branch 'master' of https://github.com/molstar/molstar into forkdev

CHANGELOG.md

@@ -4,6 +4,17 @@ All notable changes to this project will be documented in this file, following t
 Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
 
 
+## [Unreleased]
+
+- Add Charmm saccharide names
+- Treat missing occupancy column as occupany of 1
+- Fix line shader not accounting for aspect ratio
+- [Breaking] Fix point repr & shader
+    - Was unusable with ``wboit``
+    - Replaced ``pointFilledCircle`` & ``pointEdgeBleach`` params by ``pointStyle`` (square, circle, fuzzy)
+    - Set ``pointSizeAttenuation`` to false by default
+    - Set ``sizeTheme`` to ``uniform`` by default
+
 ## [v2.3.0] - 2021-09-06
 
 - Take include/exclude flags into account when displaying aromatic bonds

src/apps/viewer/index.html

@@ -52,12 +52,16 @@
             var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
+            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
             var viewer = new molstar.Viewer('app', {
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
                 collapseLeftPanel: collapseLeftPanel,
                 pdbProvider: pdbProvider || 'pdbe',
                 emdbProvider: emdbProvider || 'pdbe',
+                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
+                    ? 'https://maps.rcsb.org'
+                    : 'https://www.ebi.ac.uk/pdbe/densities'
             });
 
             var snapshotId = getParam('snapshot-id', '[^&]+').trim();

src/mol-geo/geometry/points/points.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -117,12 +117,19 @@ export namespace Points {
 
     //
 
+    export const StyleTypes = {
+        'square': 'Square',
+        'circle': 'Circle',
+        'fuzzy': 'Fuzzy',
+    };
+    export type StyleTypes = keyof typeof StyleTypes;
+    export const StyleTypeNames = Object.keys(StyleTypes) as StyleTypes[];
+
     export const Params = {
         ...BaseGeometry.Params,
         sizeFactor: PD.Numeric(1.5, { min: 0, max: 10, step: 0.1 }),
         pointSizeAttenuation: PD.Boolean(false),
-        pointFilledCircle: PD.Boolean(false),
-        pointEdgeBleach: PD.Numeric(0.2, { min: 0, max: 1, step: 0.05 }),
+        pointStyle: PD.Select('square', PD.objectToOptions(StyleTypes)),
     };
     export type Params = typeof Params
 
@@ -189,8 +196,7 @@ export namespace Points {
             ...BaseGeometry.createValues(props, counts),
             uSizeFactor: ValueCell.create(props.sizeFactor),
             dPointSizeAttenuation: ValueCell.create(props.pointSizeAttenuation),
-            dPointFilledCircle: ValueCell.create(props.pointFilledCircle),
-            uPointEdgeBleach: ValueCell.create(props.pointEdgeBleach),
+            dPointStyle: ValueCell.create(props.pointStyle),
         };
     }
 
@@ -204,8 +210,7 @@ export namespace Points {
         BaseGeometry.updateValues(values, props);
         ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor);
         ValueCell.updateIfChanged(values.dPointSizeAttenuation, props.pointSizeAttenuation);
-        ValueCell.updateIfChanged(values.dPointFilledCircle, props.pointFilledCircle);
-        ValueCell.updateIfChanged(values.uPointEdgeBleach, props.pointEdgeBleach);
+        ValueCell.updateIfChanged(values.dPointStyle, props.pointStyle);
     }
 
     function updateBoundingSphere(values: PointsValues, points: Points) {
@@ -229,10 +234,7 @@ export namespace Points {
 
     function updateRenderableState(state: RenderableState, props: PD.Values<Params>) {
         BaseGeometry.updateRenderableState(state, props);
-        state.opaque = state.opaque && (
-            !props.pointFilledCircle ||
-            (props.pointFilledCircle && props.pointEdgeBleach === 0)
-        );
+        state.opaque = state.opaque && props.pointStyle !== 'fuzzy';
         state.writeDepth = state.opaque;
     }
 }

src/mol-gl/_spec/renderer.spec.ts

@@ -85,8 +85,7 @@ function createPoints() {
 
         uSizeFactor: ValueCell.create(1),
         dPointSizeAttenuation: ValueCell.create(true),
-        dPointFilledCircle: ValueCell.create(false),
-        uPointEdgeBleach: ValueCell.create(0.5),
+        dPointStyle: ValueCell.create('square'),
     };
     const state: RenderableState = {
         disposed: false,

src/mol-gl/renderable/points.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -7,9 +7,10 @@
 import { Renderable, RenderableState, createRenderable } from '../renderable';
 import { WebGLContext } from '../webgl/context';
 import { createGraphicsRenderItem } from '../webgl/render-item';
-import { GlobalUniformSchema, BaseSchema, AttributeSpec, UniformSpec, DefineSpec, Values, InternalSchema, SizeSchema, InternalValues, GlobalTextureSchema } from './schema';
+import { GlobalUniformSchema, BaseSchema, AttributeSpec, DefineSpec, Values, InternalSchema, SizeSchema, InternalValues, GlobalTextureSchema } from './schema';
 import { PointsShaderCode } from '../shader-code';
 import { ValueCell } from '../../mol-util';
+import { Points } from '../../mol-geo/geometry/points/points';
 
 export const PointsSchema = {
     ...BaseSchema,
@@ -17,8 +18,7 @@ export const PointsSchema = {
     aGroup: AttributeSpec('float32', 1, 0),
     aPosition: AttributeSpec('float32', 3, 0),
     dPointSizeAttenuation: DefineSpec('boolean'),
-    dPointFilledCircle: DefineSpec('boolean'),
-    uPointEdgeBleach: UniformSpec('f'),
+    dPointStyle: DefineSpec('string', Points.StyleTypeNames),
 };
 export type PointsSchema = typeof PointsSchema
 export type PointsValues = Values<PointsSchema>

src/mol-gl/renderable/schema.ts

@@ -121,7 +121,6 @@ export const GlobalUniformSchema = {
 
     uIsOrtho: UniformSpec('f'),
     uPixelRatio: UniformSpec('f'),
-    uViewportHeight: UniformSpec('f'),
     uViewport: UniformSpec('v4'),
     uViewOffset: UniformSpec('v2'),
     uDrawingBufferSize: UniformSpec('v2'),

src/mol-gl/renderer.ts

@@ -233,7 +233,6 @@ namespace Renderer {
             uViewOffset: ValueCell.create(viewOffset),
 
             uPixelRatio: ValueCell.create(ctx.pixelRatio),
-            uViewportHeight: ValueCell.create(viewport.height),
             uViewport: ValueCell.create(Viewport.toVec4(Vec4(), viewport)),
             uDrawingBufferSize: ValueCell.create(drawingBufferSize),
 
@@ -571,7 +570,7 @@ namespace Renderer {
                 // TODO: simplify, handle in renderable.state???
                 // uAlpha is updated in "render" so we need to recompute it here
                 const alpha = clamp(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
-                if (alpha === 1 && r.values.transparencyAverage.ref.value !== 1 && r.values.dRenderMode?.ref.value !== 'volume' && !r.values.dPointFilledCircle?.ref.value && !r.values.dXrayShaded?.ref.value) {
+                if (alpha === 1 && r.values.transparencyAverage.ref.value !== 1 && r.values.dRenderMode?.ref.value !== 'volume' && r.values.dPointStyle?.ref.value !== 'fuzzy' && !r.values.dXrayShaded?.ref.value) {
                     renderObject(r, 'colorWboit');
                 }
             }
@@ -587,7 +586,7 @@ namespace Renderer {
                 // TODO: simplify, handle in renderable.state???
                 // uAlpha is updated in "render" so we need to recompute it here
                 const alpha = clamp(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
-                if (alpha < 1 || r.values.transparencyAverage.ref.value > 0 || r.values.dRenderMode?.ref.value === 'volume' || r.values.dPointFilledCircle?.ref.value || !!r.values.uBackgroundColor || r.values.dXrayShaded?.ref.value) {
+                if (alpha < 1 || r.values.transparencyAverage.ref.value > 0 || r.values.dRenderMode?.ref.value === 'volume' || r.values.dPointStyle?.ref.value === 'fuzzy' || !!r.values.uBackgroundColor || r.values.dXrayShaded?.ref.value) {
                     renderObject(r, 'colorWboit');
                 }
             }
@@ -700,7 +699,6 @@ namespace Renderer {
                 gl.scissor(x, y, width, height);
                 if (x !== viewport.x || y !== viewport.y || width !== viewport.width || height !== viewport.height) {
                     Viewport.set(viewport, x, y, width, height);
-                    ValueCell.update(globalUniforms.uViewportHeight, height);
                     ValueCell.update(globalUniforms.uViewport, Vec4.set(globalUniforms.uViewport.ref.value, x, y, width, height));
                 }
             },

src/mol-gl/shader/lines.vert.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  *
@@ -18,7 +18,7 @@ precision highp int;
 #include common_clip
 
 uniform float uPixelRatio;
-uniform float uViewportHeight;
+uniform vec4 uViewport;
 
 attribute mat4 aTransform;
 attribute float aInstance;
@@ -39,6 +39,8 @@ void trimSegment(const in vec4 start, inout vec4 end) {
 }
 
 void main(){
+    float aspect = uViewport.z / uViewport.w;
+
     #include assign_group
     #include assign_color_varying
     #include assign_marker_varying
@@ -83,15 +85,15 @@ void main(){
     vec2 dir = ndcEnd - ndcStart;
 
     // account for clip-space aspect ratio
-    dir.x *= uPixelRatio;
+    dir.x *= aspect;
     dir = normalize(dir);
 
     // perpendicular to dir
     vec2 offset = vec2(dir.y, - dir.x);
 
     // undo aspect ratio adjustment
-    dir.x /= uPixelRatio;
-    offset.x /= uPixelRatio;
+    dir.x /= aspect;
+    offset.x /= aspect;
 
     // sign flip
     if (aMapping.x < 0.0) offset *= -1.0;
@@ -99,7 +101,7 @@ void main(){
     // calculate linewidth
     float linewidth;
     #ifdef dLineSizeAttenuation
-        linewidth = size * uPixelRatio * ((uViewportHeight / 2.0) / -start.z) * 5.0;
+        linewidth = size * uPixelRatio * ((uViewport.w / 2.0) / -start.z) * 5.0;
     #else
         linewidth = size * uPixelRatio;
     #endif
@@ -108,7 +110,7 @@ void main(){
     offset *= linewidth;
 
     // adjust for clip-space to screen-space conversion
-    offset /= uViewportHeight;
+    offset /= uViewport.w;
 
     // select end
     vec4 clip = (aMapping.y < 0.5) ? clipStart : clipEnd;

src/mol-gl/shader/points.frag.ts

@@ -13,10 +13,6 @@ precision highp int;
 #include color_frag_params
 #include common_clip
 
-#ifdef dPointFilledCircle
-    uniform float uPointEdgeBleach;
-#endif
-
 const vec2 center = vec2(0.5);
 const float radius = 0.5;
 
@@ -27,6 +23,15 @@ void main(){
     bool interior = false;
     #include assign_material_color
 
+    #if defined(dPointStyle_circle)
+        float dist = distance(gl_PointCoord, center);
+        if (dist > radius) discard;
+    #elif defined(dPointStyle_fuzzy)
+        float dist = distance(gl_PointCoord, center);
+        float fuzzyAlpha = 1.0 - smoothstep(0.0, radius, dist);
+        if (fuzzyAlpha < 0.0001) discard;
+    #endif
+
     #if defined(dRenderVariant_pick)
         #include check_picking_alpha
         gl_FragColor = material;
@@ -37,11 +42,8 @@ void main(){
     #elif defined(dRenderVariant_color)
         gl_FragColor = material;
 
-        #ifdef dPointFilledCircle
-            float dist = distance(gl_PointCoord, center);
-            float alpha = 1.0 - smoothstep(radius - uPointEdgeBleach, radius, dist);
-            if (alpha < 0.0001) discard;
-            gl_FragColor.a *= alpha;
+        #if defined(dPointStyle_fuzzy)
+            gl_FragColor.a *= fuzzyAlpha;
         #endif
 
         #include apply_marker_color

src/mol-gl/shader/points.vert.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -16,7 +16,7 @@ precision highp int;
 #include common_clip
 
 uniform float uPixelRatio;
-uniform float uViewportHeight;
+uniform vec4 uViewport;
 
 attribute vec3 aPosition;
 attribute mat4 aTransform;
@@ -32,7 +32,7 @@ void main(){
     #include assign_size
 
     #ifdef dPointSizeAttenuation
-        gl_PointSize = size * uPixelRatio * ((uViewportHeight / 2.0) / -mvPosition.z) * 5.0;
+        gl_PointSize = size * uPixelRatio * ((uViewport.w / 2.0) / -mvPosition.z) * 5.0;
     #else
         gl_PointSize = size * uPixelRatio;
     #endif

src/mol-gl/shader/text.vert.ts

@@ -31,7 +31,7 @@ uniform float uOffsetZ;
 
 // uniform bool ortho;
 uniform float uPixelRatio;
-uniform float uViewportHeight;
+uniform vec4 uViewport;
 
 varying vec2 vTexCoord;
 
@@ -60,9 +60,9 @@ void main(void){
     // TODO
     // #ifdef FIXED_SIZE
     //     if (ortho) {
-    //         scale /= pixelRatio * ((uViewportHeight / 2.0) / -uCameraPosition.z) * 0.1;
+    //         scale /= pixelRatio * ((uViewport.w / 2.0) / -uCameraPosition.z) * 0.1;
     //     } else {
-    //         scale /= pixelRatio * ((uViewportHeight / 2.0) / -mvPosition.z) * 0.1;
+    //         scale /= pixelRatio * ((uViewport.w / 2.0) / -mvPosition.z) * 0.1;
     //     }
     // #endif
 

src/mol-io/reader/common/text/column/token.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Column, ColumnHelpers } from '../../../../../mol-data/db';
@@ -50,4 +51,12 @@ export function areValuesEqualProvider(tokens: Tokens) {
         }
         return true;
     };
+}
+
+export function areTokensEmpty(tokens: Tokens) {
+    const { count, indices } = tokens;
+    for (let i = 0; i < count; ++i) {
+        if (indices[2 * i] !== indices[2 * i + 1]) return false;
+    }
+    return true;
 }

src/mol-model-formats/structure/basic/atomic.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -100,7 +100,7 @@ function getConformation(atom_site: AtomSite): AtomicConformation {
     return {
         id: UUID.create22(),
         atomId: atom_site.id,
-        occupancy: atom_site.occupancy,
+        occupancy: atom_site.occupancy.isDefined ? atom_site.occupancy : Column.ofConst(1, atom_site._rowCount, Column.Schema.float),
         B_iso_or_equiv: atom_site.B_iso_or_equiv,
         xyzDefined: atom_site.Cartn_x.isDefined && atom_site.Cartn_y.isDefined && atom_site.Cartn_z.isDefined,
         x: atom_site.Cartn_x.toArray({ array: Float32Array }),

src/mol-model-formats/structure/pdb/atom-site.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,6 +10,7 @@ import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { TokenBuilder, Tokenizer } from '../../../mol-io/reader/common/text/tokenizer';
 import { guessElementSymbolTokens } from '../util';
 import { Column } from '../../../mol-data/db';
+import { areTokensEmpty } from '../../../mol-io/reader/common/text/column/token';
 
 type AtomSiteTemplate = typeof getAtomSiteTemplate extends (...args: any) => infer T ? T : never
 export function getAtomSiteTemplate(data: string, count: number) {
@@ -63,7 +64,7 @@ export function getAtomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema
         label_seq_id: CifField.ofUndefined(sites.index, Column.Schema.int),
         label_entity_id: CifField.ofStrings(sites.label_entity_id),
 
-        occupancy: CifField.ofTokens(sites.occupancy),
+        occupancy: areTokensEmpty(sites.occupancy) ? CifField.ofUndefined(sites.index, Column.Schema.float) : CifField.ofTokens(sites.occupancy),
         type_symbol: CifField.ofTokens(sites.type_symbol),
 
         pdbx_PDB_ins_code: CifField.ofTokens(sites.pdbx_PDB_ins_code),

src/mol-model/structure/structure/carbohydrates/constants.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -309,14 +309,48 @@ const UnknownSaccharideNames = [
     'PUF', 'GDA', '9WJ', // via updated CCD
 ];
 
+/**
+ * From http://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/#CHARMM
+ */
+const CharmmSaccharideNames: { [k: string]: string[] } = {
+    Glc: ['AGLC', 'BGLC'],
+    GlcNAc: ['AGLCNA', 'BGLCNA', 'BGLCN0'],
+    GlcA: ['AGLCA', 'BGLCA', 'BGLCA0'],
+    Man: ['AMAN', 'BMAN'],
+    Rha: ['ARHM', 'BRHM'],
+    Ara: ['AARB', 'BARB'],
+    Gal: ['AGAL', 'BGAL'],
+    GalNAc: ['AGALNA', 'BGALNA'],
+    Gul: ['AGUL', 'BGUL'],
+    Alt: ['AALT', 'BALT'],
+    All: ['AALL', 'BALL'],
+    Tal: ['ATAL', 'BTAL'],
+    Ido: ['AIDO', 'BIDO'],
+    IdoA: ['AIDOA', 'BIDOA'],
+    Fuc: ['AFUC', 'BFUC'],
+    Lyx: ['ALYF', 'BLYF'],
+    Xyl: ['AXYL', 'BXYL', 'AXYF', 'BXYF'],
+    Rib: ['ARIB', 'BRIB'],
+    Fru: ['AFRU', 'BFRU'],
+    Neu5Ac: ['ANE5AC', 'BNE5AC'],
+};
+
 export const SaccharideCompIdMap = (function () {
     const map = new Map<string, SaccharideComponent>();
     for (let i = 0, il = Monosaccharides.length; i < il; ++i) {
         const saccharide = Monosaccharides[i];
-        const names = CommonSaccharideNames[saccharide.abbr];
-        if (names) {
-            for (let j = 0, jl = names.length; j < jl; ++j) {
-                map.set(names[j], saccharide);
+
+        const common = CommonSaccharideNames[saccharide.abbr];
+        if (common) {
+            for (let j = 0, jl = common.length; j < jl; ++j) {
+                map.set(common[j], saccharide);
+            }
+        }
+
+        const charmm = CharmmSaccharideNames[saccharide.abbr];
+        if (charmm) {
+            for (let j = 0, jl = charmm.length; j < jl; ++j) {
+                map.set(charmm[j], saccharide);
             }
         }
     }

src/mol-model/structure/structure/unit/bonds/intra-compute.ts

@@ -133,7 +133,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
 
                 const p = partnerA.atomIndex === aI ? partnerB : partnerA;
                 const _bI = SortedArray.indexOf(unit.elements, p.atomIndex) as StructureElement.UnitIndex;
-                if (_bI < 0) continue;
+                if (_bI < 0 || atoms[_bI] < aI) continue;
 
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;

src/mol-repr/representation.ts

@@ -226,7 +226,7 @@ namespace Representation {
         let version = 0;
         const updated = new Subject<number>();
         const currentState = stateBuilder.create();
-        const currentTheme = Theme.createEmpty();
+        let currentTheme = Theme.createEmpty();
 
         let currentParams: P;
         let currentProps: PD.Values<P>;
@@ -314,6 +314,7 @@ namespace Representation {
                 }
             },
             setTheme: (theme: Theme) => {
+                currentTheme = theme;
                 for (let i = 0, il = reprList.length; i < il; ++i) {
                     reprList[i].setTheme(theme);
                 }

src/mol-repr/structure/representation/point.ts

@@ -32,11 +32,11 @@ export function PointRepresentation(ctx: RepresentationContext, getParams: Repre
 export const PointRepresentationProvider = StructureRepresentationProvider({
     name: 'point',
     label: 'Point',
-    description: 'Displays elements (atoms, coarse spheres) as spheres.',
+    description: 'Displays elements (atoms, coarse spheres) as points.',
     factory: PointRepresentation,
     getParams: getPointParams,
     defaultValues: PD.getDefaultValues(PointParams),
     defaultColorTheme: { name: 'element-symbol' },
-    defaultSizeTheme: { name: 'physical' },
+    defaultSizeTheme: { name: 'uniform' },
     isApplicable: (structure: Structure) => structure.elementCount > 0
 });

src/mol-repr/structure/visual/element-point.ts

@@ -18,7 +18,7 @@ import { Sphere3D } from '../../../mol-math/geometry';
 
 export const ElementPointParams = {
     ...UnitsPointsParams,
-    pointSizeAttenuation: PD.Boolean(true),
+    pointSizeAttenuation: PD.Boolean(false),
     ignoreHydrogens: PD.Boolean(false),
     traceOnly: PD.Boolean(false),
 };