diff --git a/CHANGELOG.md b/CHANGELOG.md
index bf25fdbbf75702333693826f711f73fe8d117339..2ee4e47af2c6575b785e6e0fd0d4729ceebc745b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Show histogram in direct volume control point settings
- Add `solidInterior` parameter to sphere/cylinder impostors
+- [Breaking] Tweak `ignoreHydrogens` non-polar handling (introduced in 3.27.0)
- Add `meshes` and `volumes-and-segmentations` extensions
- Fix missing support for info in `ParamDefinition.Converted`
- Add support for multi-visual volume representations
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index 2f5d6d410c7a7caadaee2844e4c6ae52404f61e9..57568a3ec3b663b7c574ac82d08de3093a69d32c 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -37,7 +37,7 @@ export namespace StructureRepresentationPresetProvider {
export const CommonParams = {
ignoreHydrogens: PD.Optional(PD.Boolean(false)),
- onlyPolarHydrogens: PD.Optional(PD.Boolean(false)),
+ ignoreHydrogensVariant: PD.Optional(PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const))),
ignoreLight: PD.Optional(PD.Boolean(false)),
quality: PD.Optional(PD.Select<VisualQuality>('auto', VisualQualityOptions)),
theme: PD.Optional(PD.Group({
@@ -69,15 +69,16 @@ export namespace StructureRepresentationPresetProvider {
export function reprBuilder(plugin: PluginContext, params: CommonParams, structure?: Structure) {
const update = plugin.state.data.build();
const builder = plugin.builders.structure.representation;
+ const h = plugin.managers.structure.component.state.options.hydrogens;
const typeParams = {
quality: plugin.managers.structure.component.state.options.visualQuality,
- ignoreHydrogens: plugin.managers.structure.component.state.options.hydrogens === 'hide-all',
- onlyPolarHydrogens: plugin.managers.structure.component.state.options.hydrogens === 'only-polar',
+ ignoreHydrogens: h !== 'all',
+ ignoreHydrogensVariant: (h === 'only-polar' ? 'non-polar' : 'all') as 'all' | 'non-polar',
ignoreLight: plugin.managers.structure.component.state.options.ignoreLight,
};
if (params.quality && params.quality !== 'auto') typeParams.quality = params.quality;
if (params.ignoreHydrogens !== void 0) typeParams.ignoreHydrogens = !!params.ignoreHydrogens;
- if (params.onlyPolarHydrogens !== void 0) typeParams.onlyPolarHydrogens = !!params.onlyPolarHydrogens;
+ if (params.ignoreHydrogensVariant !== void 0) typeParams.ignoreHydrogensVariant = params.ignoreHydrogensVariant;
if (params.ignoreLight !== void 0) typeParams.ignoreLight = !!params.ignoreLight;
const color: ColorTheme.BuiltIn | undefined = params.theme?.globalName ? params.theme?.globalName : void 0;
const ballAndStickColor: ColorTheme.BuiltInParams<'element-symbol'> = params.theme?.carbonColor !== undefined
diff --git a/src/mol-plugin-state/manager/structure/component.ts b/src/mol-plugin-state/manager/structure/component.ts
index d8c3f4d4873f0d9f0463067292bf1084e00620b7..5c72786cfd4c3e9fd3f4265100738d4a47889ed0 100644
--- a/src/mol-plugin-state/manager/structure/component.ts
+++ b/src/mol-plugin-state/manager/structure/component.ts
@@ -70,8 +70,8 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
return this.plugin.dataTransaction(async () => {
await update.commit();
await this.plugin.state.updateBehavior(StructureFocusRepresentation, p => {
- p.ignoreHydrogens = options.hydrogens === 'hide-all';
- p.onlyPolarHydrogens = options.hydrogens === 'only-polar';
+ p.ignoreHydrogens = options.hydrogens !== 'all';
+ p.ignoreHydrogensVariant = options.hydrogens === 'only-polar' ? 'non-polar' : 'all';
p.ignoreLight = options.ignoreLight;
p.material = options.materialStyle;
p.clip = options.clipObjects;
@@ -82,16 +82,16 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
private updateReprParams(update: StateBuilder.Root, component: StructureComponentRef) {
const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
- const ignoreHydrogens = hydrogens === 'hide-all';
- const onlyPolarHydrogens = hydrogens === 'only-polar';
+ const ignoreHydrogens = hydrogens !== 'all';
+ const ignoreHydrogensVariant = hydrogens === 'only-polar' ? 'non-polar' : 'all';
for (const r of component.representations) {
if (r.cell.transform.transformer !== StructureRepresentation3D) continue;
const params = r.cell.transform.params as StateTransformer.Params<StructureRepresentation3D>;
- if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || !!params.type.params.onlyPolarHydrogens !== onlyPolarHydrogens || params.type.params.quality !== quality || params.type.params.ignoreLight !== ignoreLight || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
+ if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.ignoreHydrogensVariant !== ignoreHydrogensVariant || params.type.params.quality !== quality || params.type.params.ignoreLight !== ignoreLight || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
update.to(r.cell).update(old => {
old.type.params.ignoreHydrogens = ignoreHydrogens;
- old.type.params.onlyPolarHydrogens = onlyPolarHydrogens;
+ old.type.params.ignoreHydrogensVariant = ignoreHydrogensVariant;
old.type.params.quality = quality;
old.type.params.ignoreLight = ignoreLight;
old.type.params.material = material;
@@ -315,9 +315,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
if (components.length === 0) return;
const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
- const ignoreHydrogens = hydrogens === 'hide-all';
- const onlyPolarHydrogens = hydrogens === 'only-polar';
- const typeParams = { ignoreHydrogens, onlyPolarHydrogens, quality, ignoreLight, material, clip };
+ const ignoreHydrogens = hydrogens !== 'all';
+ const ignoreHydrogensVariant = hydrogens === 'only-polar' ? 'non-polar' : 'all';
+ const typeParams = { ignoreHydrogens, ignoreHydrogensVariant, quality, ignoreLight, material, clip };
return this.plugin.dataTransaction(async () => {
for (const component of components) {
@@ -353,9 +353,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
if (xs.length === 0) return;
const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
- const ignoreHydrogens = hydrogens === 'hide-all';
- const onlyPolarHydrogens = hydrogens === 'only-polar';
- const typeParams = { ignoreHydrogens, onlyPolarHydrogens, quality, ignoreLight, material, clip };
+ const ignoreHydrogens = hydrogens !== 'all';
+ const ignoreHydrogensVariant = hydrogens === 'only-polar' ? 'non-polar' : 'all';
+ const typeParams = { ignoreHydrogens, ignoreHydrogensVariant, quality, ignoreLight, material, clip };
const componentKey = UUID.create22();
for (const s of xs) {
diff --git a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
index e548d8e8b0117d630ce2bdb6b85d4440e73618e0..344b5b1bbf0b30f65b1e99c2fe3ca860b5c4bf7d 100644
--- a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
+++ b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
@@ -52,7 +52,7 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
components: PD.MultiSelect(FocusComponents, PD.arrayToOptions(FocusComponents)),
excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
ignoreLight: PD.Boolean(false),
material: Material.getParam(),
clip: PD.Group(Clip.Params),
@@ -81,7 +81,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
...reprParams,
type: {
name: reprParams.type.name,
- params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, onlyPolarHydrogens: this.params.onlyPolarHydrogens, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip }
+ params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, ignoreHydrogensVariant: this.params.ignoreHydrogensVariant, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip }
}
};
}
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
index 0d9476ce3d49cffac7f03538de7c9e25939c18ca..de91c4d9b737618af0d715be2f60409767d184a6 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
@@ -222,7 +222,7 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.linkCap !== currentProps.linkCap ||
newProps.aromaticScale !== currentProps.aromaticScale ||
newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
@@ -265,7 +265,7 @@ export function InterUnitBondCylinderMeshVisual(materialId: number): ComplexVisu
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.linkCap !== currentProps.linkCap ||
newProps.aromaticScale !== currentProps.aromaticScale ||
newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-line.ts b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
index ab6c1436b2bf8e72ea202baf37d17af9fbb73de9..7840e0abbc81bde59f54ea3a134f4382676e7b55 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
@@ -138,7 +138,7 @@ export function InterUnitBondLineVisual(materialId: number): ComplexVisual<Inter
newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
newProps.multipleBonds !== currentProps.multipleBonds
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
index 5e2e95dadf39197bfeb4ec4078b4712e43187573..3eaaf9b4de773d798fd10cab5acbf7ca0ea4b4ca 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -239,7 +239,7 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.linkCap !== currentProps.linkCap ||
newProps.aromaticScale !== currentProps.aromaticScale ||
newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
@@ -287,7 +287,7 @@ export function IntraUnitBondCylinderMeshVisual(materialId: number): UnitsVisual
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.linkCap !== currentProps.linkCap ||
newProps.aromaticScale !== currentProps.aromaticScale ||
newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-line.ts b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
index 640d93cda7384a7e2ba470aacfb29c2a113b4141..64bb78a1678c3483dda9857a7d306944ae4b2eb2 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
@@ -164,7 +164,7 @@ export function IntraUnitBondLineVisual(materialId: number): UnitsVisual<IntraUn
newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
newProps.aromaticBonds !== currentProps.aromaticBonds ||
diff --git a/src/mol-repr/structure/visual/element-cross.ts b/src/mol-repr/structure/visual/element-cross.ts
index d69d80ba3a583ffa01dd3c7106ca245b4ce91f5c..7955ab1c6c0ab31aada875d740365ccb8adc88b0 100644
--- a/src/mol-repr/structure/visual/element-cross.ts
+++ b/src/mol-repr/structure/visual/element-cross.ts
@@ -27,7 +27,7 @@ export const ElementCrossParams = {
...UnitsLinesParams,
lineSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
traceOnly: PD.Boolean(false),
crosses: PD.Select('lone', PD.arrayToOptions(['lone', 'all'] as const)),
crossSize: PD.Numeric(0.35, { min: 0, max: 2, step: 0.01 }),
@@ -86,7 +86,7 @@ export function ElementCrossVisual(materialId: number): UnitsVisual<ElementCross
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementCrossParams>, currentProps: PD.Values<ElementCrossParams>) => {
state.createGeometry = (
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.traceOnly !== currentProps.traceOnly ||
newProps.crosses !== currentProps.crosses ||
newProps.crossSize !== currentProps.crossSize
diff --git a/src/mol-repr/structure/visual/element-point.ts b/src/mol-repr/structure/visual/element-point.ts
index a50e5fc9cdd5e39f01bccd79b29e7b84dccac7c2..d6e24c3bc1c115a78d62c06f6639cfd62d2702e3 100644
--- a/src/mol-repr/structure/visual/element-point.ts
+++ b/src/mol-repr/structure/visual/element-point.ts
@@ -23,7 +23,7 @@ export const ElementPointParams = {
...UnitsPointsParams,
pointSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
traceOnly: PD.Boolean(false),
};
export type ElementPointParams = typeof ElementPointParams
@@ -90,7 +90,7 @@ export function ElementPointVisual(materialId: number): UnitsVisual<ElementPoint
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementPointParams>, currentProps: PD.Values<ElementPointParams>) => {
state.createGeometry = (
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.traceOnly !== currentProps.traceOnly
);
}
diff --git a/src/mol-repr/structure/visual/element-sphere.ts b/src/mol-repr/structure/visual/element-sphere.ts
index 909934efd8b6e630921ca1e2126b12f7c27e60d4..1e95bbdfdd59d1797cc48a60921ba62ffc167aec 100644
--- a/src/mol-repr/structure/visual/element-sphere.ts
+++ b/src/mol-repr/structure/visual/element-sphere.ts
@@ -20,7 +20,7 @@ export const ElementSphereParams = {
sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }),
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
traceOnly: PD.Boolean(false),
tryUseImpostor: PD.Boolean(true),
};
@@ -42,7 +42,7 @@ export function ElementSphereImpostorVisual(materialId: number): UnitsVisual<Ele
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementSphereParams>, currentProps: PD.Values<ElementSphereParams>) => {
state.createGeometry = (
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.traceOnly !== currentProps.traceOnly
);
},
@@ -64,7 +64,7 @@ export function ElementSphereMeshVisual(materialId: number): UnitsVisual<Element
newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.detail !== currentProps.detail ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
- newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
+ newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
newProps.traceOnly !== currentProps.traceOnly
);
},
diff --git a/src/mol-repr/structure/visual/gaussian-density-volume.ts b/src/mol-repr/structure/visual/gaussian-density-volume.ts
index e347f81433bc9acec7f99bc23a1fb2f9a0d7bd93..b4c9ccaaf71b90c0e5150107cdf54a8ff49e69b2 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -43,7 +43,7 @@ export const GaussianDensityVolumeParams = {
...ComplexDirectVolumeParams,
...GaussianDensityParams,
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
includeParent: PD.Boolean(false, { isHidden: true }),
};
export type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams
@@ -60,7 +60,7 @@ export function GaussianDensityVolumeVisual(materialId: number): ComplexVisual<G
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
},
@@ -101,7 +101,7 @@ export const UnitsGaussianDensityVolumeParams = {
...UnitsDirectVolumeParams,
...GaussianDensityParams,
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
includeParent: PD.Boolean(false, { isHidden: true }),
};
export type UnitsGaussianDensityVolumeParams = typeof UnitsGaussianDensityVolumeParams
@@ -118,7 +118,7 @@ export function UnitsGaussianDensityVolumeVisual(materialId: number): UnitsVisua
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
},
diff --git a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
index 06e2116850896ac4603e87c509e2731448396bd2..76249617a9f321174499d93cbe8213396d151f93 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -34,7 +34,7 @@ const SharedParams = {
...GaussianDensityParams,
...ColorSmoothingParams,
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
tryUseGpu: PD.Boolean(true),
includeParent: PD.Boolean(false, { isHidden: true }),
};
@@ -128,7 +128,7 @@ export function GaussianSurfaceMeshVisual(materialId: number): UnitsVisual<Gauss
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
@@ -195,7 +195,7 @@ export function StructureGaussianSurfaceMeshVisual(materialId: number): ComplexV
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
state.updateColor = true;
@@ -267,7 +267,7 @@ export function GaussianSurfaceTextureMeshVisual(materialId: number): UnitsVisua
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
@@ -343,7 +343,7 @@ export function StructureGaussianSurfaceTextureMeshVisual(materialId: number): C
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
diff --git a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
index 59eb1bc9cd1f924d947c3a88a868597a3ee361fe..8512cc36279ab7327299ee57f6f986cdd4ba16af 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -41,7 +41,7 @@ export const GaussianWireframeParams = {
sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
lineSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
includeParent: PD.Boolean(false, { isHidden: true }),
};
export type GaussianWireframeParams = typeof GaussianWireframeParams
@@ -58,7 +58,7 @@ export function GaussianWireframeVisual(materialId: number): UnitsVisual<Gaussia
if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
}
diff --git a/src/mol-repr/structure/visual/molecular-surface-mesh.ts b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
index 5e0608039b102033f7f1754abd0a4c4dd1c77590..bd53471ce766d53103ce93fa8335ecedbae3fdd8 100644
--- a/src/mol-repr/structure/visual/molecular-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
@@ -83,7 +83,7 @@ export function MolecularSurfaceMeshVisual(materialId: number): UnitsVisual<Mole
if (newProps.probeRadius !== currentProps.probeRadius) state.createGeometry = true;
if (newProps.probePositions !== currentProps.probePositions) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
@@ -152,7 +152,7 @@ export function StructureMolecularSurfaceMeshVisual(materialId: number): Complex
if (newProps.probeRadius !== currentProps.probeRadius) state.createGeometry = true;
if (newProps.probePositions !== currentProps.probePositions) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
diff --git a/src/mol-repr/structure/visual/molecular-surface-wireframe.ts b/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
index 45b93917a3c66a3aeca9a00e968e0d50c06aa97d..fcb097227d0f9dcc6db2e347f63d83ce232680fe 100644
--- a/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
@@ -57,7 +57,7 @@ export function MolecularSurfaceWireframeVisual(materialId: number): UnitsVisual
if (newProps.probeRadius !== currentProps.probeRadius) state.createGeometry = true;
if (newProps.probePositions !== currentProps.probePositions) state.createGeometry = true;
if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
- if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
+ if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
}
}, materialId);
diff --git a/src/mol-repr/structure/visual/util/bond.ts b/src/mol-repr/structure/visual/util/bond.ts
index 4fc89d01935a742bceaebb76e6c962ff18681ce2..723d17e8bcf2a13efd9a2cb400207e7a2505d28a 100644
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -14,14 +14,13 @@ import { ObjectKeys } from '../../../../mol-util/type-helpers';
import { PickingId } from '../../../../mol-geo/geometry/picking';
import { EmptyLoci, Loci } from '../../../../mol-model/loci';
import { Interval, OrderedSet, SortedArray } from '../../../../mol-data/int';
-import { isH, isHydrogen, StructureGroup } from './common';
-import { hasPolarNeighbour } from '../../../../mol-model-props/computed/chemistry/functional-group';
+import { isHydrogen, StructureGroup } from './common';
export const BondParams = {
includeTypes: PD.MultiSelect(ObjectKeys(BondType.Names), PD.objectToOptions(BondType.Names)),
excludeTypes: PD.MultiSelect([] as BondType.Names[], PD.objectToOptions(BondType.Names)),
ignoreHydrogens: PD.Boolean(false),
- onlyPolarHydrogens: PD.Boolean(false),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
aromaticBonds: PD.Boolean(true, { description: 'Display aromatic bonds with dashes' }),
multipleBonds: PD.Select('symmetric', PD.arrayToOptions(['off', 'symmetric', 'offset'] as const)),
};
@@ -49,12 +48,11 @@ export function ignoreBondType(include: BondType.Flag, exclude: BondType.Flag, f
export function makeIntraBondIgnoreTest(structure: Structure, unit: Unit.Atomic, props: BondProps): undefined | ((edgeIndex: number) => boolean) {
const elements = unit.elements;
- const { atomicNumber } = unit.model.atomicHierarchy.derived.atom;
const bonds = unit.bonds;
const { a, b, edgeProps } = bonds;
const { flags: _flags } = edgeProps;
- const { ignoreHydrogens, onlyPolarHydrogens, includeTypes, excludeTypes } = props;
+ const { ignoreHydrogens, ignoreHydrogensVariant, includeTypes, excludeTypes } = props;
const include = BondType.fromNames(includeTypes);
const exclude = BondType.fromNames(excludeTypes);
@@ -64,7 +62,7 @@ export function makeIntraBondIgnoreTest(structure: Structure, unit: Unit.Atomic,
const childUnit = child?.unitMap.get(unit.id);
if (child && !childUnit) throw new Error('expected childUnit to exist if child exists');
- if (allBondTypes && !onlyPolarHydrogens && !ignoreHydrogens && !child) return;
+ if (allBondTypes && !ignoreHydrogens && !child) return;
return (edgeIndex: number) => {
const aI = a[edgeIndex];
@@ -78,15 +76,9 @@ export function makeIntraBondIgnoreTest(structure: Structure, unit: Unit.Atomic,
return true;
}
- if (!ignoreHydrogens && !onlyPolarHydrogens) return false;
- if (isH(atomicNumber, elements[aI])) {
- if (ignoreHydrogens) return true;
- if (onlyPolarHydrogens && !hasPolarNeighbour(structure, unit, aI)) return true;
- }
- if (isH(atomicNumber, elements[bI])) {
- if (ignoreHydrogens) return true;
- if (onlyPolarHydrogens && !hasPolarNeighbour(structure, unit, bI)) return true;
- }
+ if (!ignoreHydrogens) return false;
+
+ if (isHydrogen(structure, unit, elements[aI], ignoreHydrogensVariant) || isHydrogen(structure, unit, elements[bI], ignoreHydrogensVariant)) return true;
return false;
};
@@ -96,7 +88,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
const bonds = structure.interUnitBonds;
const { edges } = bonds;
- const { ignoreHydrogens, onlyPolarHydrogens, includeTypes, excludeTypes } = props;
+ const { ignoreHydrogens, ignoreHydrogensVariant, includeTypes, excludeTypes } = props;
const include = BondType.fromNames(includeTypes);
const exclude = BondType.fromNames(excludeTypes);
@@ -104,7 +96,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
const { child } = structure;
- if (allBondTypes && !onlyPolarHydrogens && !ignoreHydrogens && !child) return;
+ if (allBondTypes && !ignoreHydrogens && !child) return;
return (edgeIndex: number) => {
if (child) {
@@ -121,19 +113,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
const b = edges[edgeIndex];
const uA = structure.unitMap.get(b.unitA);
const uB = structure.unitMap.get(b.unitB);
- if (isHydrogen(uA, uA.elements[b.indexA]) || isHydrogen(uB, uB.elements[b.indexB])) return true;
- }
-
- if (onlyPolarHydrogens) {
- const b = edges[edgeIndex];
- const uA = structure.unitMap.get(b.unitA);
- if (isHydrogen(uA, uA.elements[b.indexA]) && !hasPolarNeighbour(structure, uA as Unit.Atomic, b.indexA)) {
- return true;
- }
- const uB = structure.unitMap.get(b.unitB);
- if (isHydrogen(uB, uB.elements[b.indexB]) && !hasPolarNeighbour(structure, uB as Unit.Atomic, b.indexB)) {
- return true;
- }
+ if (isHydrogen(structure, uA, uA.elements[b.indexA], ignoreHydrogensVariant) || isHydrogen(structure, uB, uB.elements[b.indexB], ignoreHydrogensVariant)) return true;
}
if (!allBondTypes) {
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index e2e9aa0156e51c1a612d79494d4afbfa46565d00..20dd1da691b7a677d4730c8b04fee82e9737293e 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -141,7 +141,7 @@ export function getConformation(unit: Unit) {
export const CommonSurfaceParams = {
ignoreHydrogens: PD.Boolean(false, { description: 'Whether or not to include hydrogen atoms in the surface calculation.' }),
- onlyPolarHydrogens: PD.Boolean(false, { description: 'Whether or not to include polar hydrogen atoms in the surface calculation.' }),
+ ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'] as const)),
traceOnly: PD.Boolean(false, { description: 'Whether or not to only use trace atoms in the surface calculation.' }),
includeParent: PD.Boolean(false, { description: 'Include elements of the parent structure in surface calculation to get a surface patch of the current structure.' }),
};
@@ -169,7 +169,7 @@ function filterUnitId(id: AssignableArrayLike<number>, elements: SortedArray, in
}
export function getUnitConformationAndRadius(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: CommonSurfaceProps) {
- const { ignoreHydrogens, onlyPolarHydrogens, traceOnly, includeParent } = props;
+ const { ignoreHydrogens, ignoreHydrogensVariant, traceOnly, includeParent } = props;
const rootUnit = includeParent ? structure.root.unitMap.get(unit.id) : unit;
const differentRoot = includeParent && rootUnit !== unit;
@@ -182,13 +182,12 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, s
let indices: SortedArray<ElementIndex>;
let id: AssignableArrayLike<number>;
- if (ignoreHydrogens || onlyPolarHydrogens || traceOnly || differentRoot) {
+ if (ignoreHydrogens || traceOnly || differentRoot) {
const _indices: number[] = [];
const _id: number[] = [];
for (let i = 0, il = elements.length; i < il; ++i) {
const eI = elements[i];
- if (ignoreHydrogens && isHydrogen(rootUnit, eI)) continue;
- if (onlyPolarHydrogens && isHydrogen(rootUnit, eI) && Unit.isAtomic(rootUnit) && !hasPolarNeighbour(structure, rootUnit, SortedArray.indexOf(rootUnit.elements, eI) as StructureElement.UnitIndex)) continue;
+ if (ignoreHydrogens && isHydrogen(structure, rootUnit, eI, ignoreHydrogensVariant)) continue;
if (traceOnly && !isTrace(rootUnit, eI)) continue;
if (differentRoot && squaredDistance(x[eI], y[eI], z[eI], center) > radiusSq) continue;
@@ -219,7 +218,7 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, s
}
export function getStructureConformationAndRadius(structure: Structure, sizeTheme: SizeTheme<any>, props: CommonSurfaceProps) {
- const { ignoreHydrogens, onlyPolarHydrogens, traceOnly, includeParent } = props;
+ const { ignoreHydrogens, ignoreHydrogensVariant, traceOnly, includeParent } = props;
const differentRoot = includeParent && !!structure.parent;
const l = StructureElement.Location.create(structure.root);
@@ -234,7 +233,7 @@ export function getStructureConformationAndRadius(structure: Structure, sizeThem
let id: AssignableArrayLike<number>;
let indices: OrderedSet<number>;
- if (ignoreHydrogens || onlyPolarHydrogens || traceOnly || differentRoot) {
+ if (ignoreHydrogens || traceOnly || differentRoot) {
const { getSerialIndex } = structure.serialMapping;
const units = differentRoot ? structure.root.units : structure.units;
@@ -252,8 +251,7 @@ export function getStructureConformationAndRadius(structure: Structure, sizeThem
l.unit = unit;
for (let j = 0, jl = elements.length; j < jl; ++j) {
const eI = elements[j];
- if (ignoreHydrogens && isHydrogen(unit, eI)) continue;
- if (onlyPolarHydrogens && isHydrogen(unit, eI) && Unit.isAtomic(unit) && !hasPolarNeighbour(structure, unit, SortedArray.indexOf(unit.elements, eI) as StructureElement.UnitIndex)) continue;
+ if (ignoreHydrogens && isHydrogen(structure, unit, eI, ignoreHydrogensVariant)) continue;
if (traceOnly && !isTrace(unit, eI)) continue;
const _x = x(eI), _y = y(eI), _z = z(eI);
@@ -316,9 +314,12 @@ export function getStructureConformationAndRadius(structure: Structure, sizeThem
}
const _H = AtomicNumbers['H'];
-export function isHydrogen(unit: Unit, element: ElementIndex) {
+export function isHydrogen(structure: Structure, unit: Unit, element: ElementIndex, variant: 'all' | 'non-polar') {
if (Unit.isCoarse(unit)) return false;
- return unit.model.atomicHierarchy.derived.atom.atomicNumber[element] === _H;
+ return (
+ unit.model.atomicHierarchy.derived.atom.atomicNumber[element] === _H &&
+ (variant === 'all' || !hasPolarNeighbour(structure, unit, SortedArray.indexOf(unit.elements, element) as StructureElement.UnitIndex))
+ );
}
export function isH(atomicNumber: ArrayLike<number>, element: ElementIndex) {
return atomicNumber[element] === _H;
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index a55a776bec0fa596c5cadff9fdd2e30510fe93c8..d19d99f2cb774aa9821946739d354109c81826a6 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -19,16 +19,15 @@ import { VisualContext } from '../../../../mol-repr/visual';
import { Theme } from '../../../../mol-theme/theme';
import { Spheres } from '../../../../mol-geo/geometry/spheres/spheres';
import { SpheresBuilder } from '../../../../mol-geo/geometry/spheres/spheres-builder';
-import { isTrace, isH, StructureGroup } from './common';
+import { isTrace, StructureGroup, isHydrogen } from './common';
import { Sphere3D } from '../../../../mol-math/geometry';
-import { hasPolarNeighbour } from '../../../../mol-model-props/computed/chemistry/functional-group';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const v3add = Vec3.add;
type ElementProps = {
ignoreHydrogens: boolean,
- onlyPolarHydrogens: boolean,
+ ignoreHydrogensVariant: 'all' | 'non-polar',
traceOnly: boolean,
}
@@ -38,35 +37,22 @@ export type ElementSphereMeshProps = {
} & ElementProps
export function makeElementIgnoreTest(structure: Structure, unit: Unit, props: ElementProps): undefined | ((i: ElementIndex) => boolean) {
- const { ignoreHydrogens, onlyPolarHydrogens, traceOnly } = props;
+ const { ignoreHydrogens, ignoreHydrogensVariant, traceOnly } = props;
- const { atomicNumber } = unit.model.atomicHierarchy.derived.atom;
const isCoarse = Unit.isCoarse(unit);
const { child } = structure;
const childUnit = child?.unitMap.get(unit.id);
if (child && !childUnit) throw new Error('expected childUnit to exist if child exists');
- if (!child && !ignoreHydrogens && !traceOnly && !onlyPolarHydrogens) return;
+ if (!child && !ignoreHydrogens && !traceOnly) return;
return (element: ElementIndex) => {
- if (!!childUnit && !SortedArray.has(childUnit.elements, element)) {
- return true;
- }
-
- if (traceOnly && !isTrace(unit, element)) {
- return true;
- }
-
- if (isCoarse) return false;
-
- if (!isH(atomicNumber, element)) return false;
- if (ignoreHydrogens) return true;
- if (onlyPolarHydrogens) {
- return !hasPolarNeighbour(structure, unit, SortedArray.indexOf(unit.elements, element) as StructureElement.UnitIndex);
- }
-
- return false;
+ return (
+ (!!childUnit && !SortedArray.has(childUnit.elements, element)) ||
+ (!isCoarse && ignoreHydrogens && isHydrogen(structure, unit, element, ignoreHydrogensVariant)) ||
+ (traceOnly && !isTrace(unit, element))
+ );
};
}