diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0e022d7ac4ace871e72769c72f3fc3c297ad04d3..ef6b0bd6c30ca87c543fbc09f248f3361ff42be3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ Note that since we don't clearly distinguish between a public and private interf
- Fix `QualityAssessment` assignment bug for structures with different auth vs label sequence numbering
- Refresh `ApplyActionControl`'s param definition when toggling expanded state
- Fix `struct_conn` bond assignment for ions
+- Ability to show only polar hydrogens
## [v3.26.0] - 2022-12-04
diff --git a/src/extensions/cellpack/model.ts b/src/extensions/cellpack/model.ts
index 91ea9c33315343732112fe22b80829545b5edc90..6293d8a729b7eea644f1cda9ca58f684e9c9ff34 100644
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -585,7 +585,7 @@ export const LoadCellPackModel = StateAction.build({
... ctx.managers.structure.component.state.options,
visualQuality: 'custom',
ignoreLight: true,
- showHydrogens: false,
+ hydrogens: 'hide-all',
});
ctx.canvas3d?.setProps({
multiSample: { mode: 'off' },
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index 25f2d1f907f1772b52a9da01ff27d0d91df9bfad..2f5d6d410c7a7caadaee2844e4c6ae52404f61e9 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -37,6 +37,7 @@ export namespace StructureRepresentationPresetProvider {
export const CommonParams = {
ignoreHydrogens: PD.Optional(PD.Boolean(false)),
+ onlyPolarHydrogens: PD.Optional(PD.Boolean(false)),
ignoreLight: PD.Optional(PD.Boolean(false)),
quality: PD.Optional(PD.Select<VisualQuality>('auto', VisualQualityOptions)),
theme: PD.Optional(PD.Group({
@@ -70,11 +71,13 @@ export namespace StructureRepresentationPresetProvider {
const builder = plugin.builders.structure.representation;
const typeParams = {
quality: plugin.managers.structure.component.state.options.visualQuality,
- ignoreHydrogens: !plugin.managers.structure.component.state.options.showHydrogens,
+ ignoreHydrogens: plugin.managers.structure.component.state.options.hydrogens === 'hide-all',
+ onlyPolarHydrogens: plugin.managers.structure.component.state.options.hydrogens === 'only-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.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 229ece724ee5a43a85473309cbba47870268bfb3..d8c3f4d4873f0d9f0463067292bf1084e00620b7 100644
--- a/src/mol-plugin-state/manager/structure/component.ts
+++ b/src/mol-plugin-state/manager/structure/component.ts
@@ -70,7 +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.showHydrogens;
+ p.ignoreHydrogens = options.hydrogens === 'hide-all';
+ p.onlyPolarHydrogens = options.hydrogens === 'only-polar';
p.ignoreLight = options.ignoreLight;
p.material = options.materialStyle;
p.clip = options.clipObjects;
@@ -80,15 +81,17 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
}
private updateReprParams(update: StateBuilder.Root, component: StructureComponentRef) {
- const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
- const ignoreHydrogens = !showHydrogens;
+ const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
+ const ignoreHydrogens = hydrogens === 'hide-all';
+ const onlyPolarHydrogens = hydrogens === 'only-polar';
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.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.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)) {
update.to(r.cell).update(old => {
old.type.params.ignoreHydrogens = ignoreHydrogens;
+ old.type.params.onlyPolarHydrogens = onlyPolarHydrogens;
old.type.params.quality = quality;
old.type.params.ignoreLight = ignoreLight;
old.type.params.material = material;
@@ -311,9 +314,10 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
addRepresentation(components: ReadonlyArray<StructureComponentRef>, type: string) {
if (components.length === 0) return;
- const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
- const ignoreHydrogens = !showHydrogens;
- const typeParams = { ignoreHydrogens, quality, ignoreLight, material, clip };
+ 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 };
return this.plugin.dataTransaction(async () => {
for (const component of components) {
@@ -348,9 +352,10 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
const xs = structures || this.currentStructures;
if (xs.length === 0) return;
- const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
- const ignoreHydrogens = !showHydrogens;
- const typeParams = { ignoreHydrogens, quality, ignoreLight, material, clip };
+ 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 componentKey = UUID.create22();
for (const s of xs) {
@@ -458,9 +463,13 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
namespace StructureComponentManager {
export const OptionsParams = {
- showHydrogens: PD.Boolean(true, { description: 'Toggle display of hydrogen atoms in representations' }),
+ hydrogens: PD.Select(
+ 'all',
+ [['all', 'Show All'], ['hide-all', 'Hide All'], ['only-polar', 'Only Polar']] as const,
+ { description: 'Determine display of hydrogen atoms in representations' }
+ ),
visualQuality: PD.Select('auto', VisualQualityOptions, { description: 'Control the visual/rendering quality of representations' }),
- ignoreLight: PD.Boolean(false, { description: 'Ignore light for stylized rendering of representtions' }),
+ ignoreLight: PD.Boolean(false, { description: 'Ignore light for stylized rendering of representations' }),
materialStyle: Material.getParam(),
clipObjects: PD.Group(Clip.Params),
interactions: PD.Group(InteractionsProvider.defaultParams, { label: 'Non-covalent Interactions' }),
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 a53dab23f2b1f6e707186d64713d8e744d01941f..e548d8e8b0117d630ce2bdb6b85d4440e73618e0 100644
--- a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
+++ b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
@@ -52,6 +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),
ignoreLight: PD.Boolean(false),
material: Material.getParam(),
clip: PD.Group(Clip.Params),
@@ -80,7 +81,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
...reprParams,
type: {
name: reprParams.type.name,
- params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip }
+ params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, onlyPolarHydrogens: this.params.onlyPolarHydrogens, 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 d097587e911fdc6910d6b8bb8e574433a79cce2c..0d9476ce3d49cffac7f03538de7c9e25939c18ca 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
@@ -222,6 +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.linkCap !== currentProps.linkCap ||
newProps.aromaticScale !== currentProps.aromaticScale ||
newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
@@ -264,6 +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.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 f7cda2e4aac21e0ff604a2ac7ed311a98b85175c..ab6c1436b2bf8e72ea202baf37d17af9fbb73de9 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
@@ -138,6 +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 ||
!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 ec837f48eebd89e02b9fbcf1af3095eb6785560e..5e2e95dadf39197bfeb4ec4078b4712e43187573 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -239,6 +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.linkCap !== currentProps.linkCap ||
newProps.aromaticScale !== currentProps.aromaticScale ||
newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
@@ -286,6 +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.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 68d1ca4f957cdaa27a37a280f6c41cc7823f9eeb..640d93cda7384a7e2ba470aacfb29c2a113b4141 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
@@ -164,6 +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 ||
!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 557a970feedadcd0090fc661e273dc0d7647df62..d69d80ba3a583ffa01dd3c7106ca245b4ce91f5c 100644
--- a/src/mol-repr/structure/visual/element-cross.ts
+++ b/src/mol-repr/structure/visual/element-cross.ts
@@ -27,6 +27,7 @@ export const ElementCrossParams = {
...UnitsLinesParams,
lineSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
+ onlyPolarHydrogens: PD.Boolean(false),
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 }),
@@ -85,6 +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.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 05dd4740d4e5b9f921511604fa02363f3b0c7454..a50e5fc9cdd5e39f01bccd79b29e7b84dccac7c2 100644
--- a/src/mol-repr/structure/visual/element-point.ts
+++ b/src/mol-repr/structure/visual/element-point.ts
@@ -23,6 +23,7 @@ export const ElementPointParams = {
...UnitsPointsParams,
pointSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
+ onlyPolarHydrogens: PD.Boolean(false),
traceOnly: PD.Boolean(false),
};
export type ElementPointParams = typeof ElementPointParams
@@ -89,6 +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.traceOnly !== currentProps.traceOnly
);
}
diff --git a/src/mol-repr/structure/visual/element-sphere.ts b/src/mol-repr/structure/visual/element-sphere.ts
index e7fc70aa05915aa37240e705ef41c1f265c08e45..909934efd8b6e630921ca1e2126b12f7c27e60d4 100644
--- a/src/mol-repr/structure/visual/element-sphere.ts
+++ b/src/mol-repr/structure/visual/element-sphere.ts
@@ -20,6 +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),
traceOnly: PD.Boolean(false),
tryUseImpostor: PD.Boolean(true),
};
@@ -41,6 +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.traceOnly !== currentProps.traceOnly
);
},
@@ -62,6 +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.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 21deb9c37678c56fec7d16ba6d2996180a3d2323..e347f81433bc9acec7f99bc23a1fb2f9a0d7bd93 100644
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -43,6 +43,7 @@ export const GaussianDensityVolumeParams = {
...ComplexDirectVolumeParams,
...GaussianDensityParams,
ignoreHydrogens: PD.Boolean(false),
+ onlyPolarHydrogens: PD.Boolean(false),
includeParent: PD.Boolean(false, { isHidden: true }),
};
export type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams
@@ -59,6 +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.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
},
@@ -99,6 +101,7 @@ export const UnitsGaussianDensityVolumeParams = {
...UnitsDirectVolumeParams,
...GaussianDensityParams,
ignoreHydrogens: PD.Boolean(false),
+ onlyPolarHydrogens: PD.Boolean(false),
includeParent: PD.Boolean(false, { isHidden: true }),
};
export type UnitsGaussianDensityVolumeParams = typeof UnitsGaussianDensityVolumeParams
@@ -115,6 +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.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 b8223d3a42185024d59922bd4976c790e9be0321..06e2116850896ac4603e87c509e2731448396bd2 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -34,6 +34,7 @@ const SharedParams = {
...GaussianDensityParams,
...ColorSmoothingParams,
ignoreHydrogens: PD.Boolean(false),
+ onlyPolarHydrogens: PD.Boolean(false),
tryUseGpu: PD.Boolean(true),
includeParent: PD.Boolean(false, { isHidden: true }),
};
@@ -127,6 +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.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
@@ -193,6 +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.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
state.updateColor = true;
@@ -264,6 +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.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
@@ -339,6 +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.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 aa5cddb98437596aeb3d70dab436cf1448524d81..59eb1bc9cd1f924d947c3a88a868597a3ee361fe 100644
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -41,6 +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),
includeParent: PD.Boolean(false, { isHidden: true }),
};
export type GaussianWireframeParams = typeof GaussianWireframeParams
@@ -57,6 +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.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 d30c6d4ee499bb239587182177d6916da47f471f..5e0608039b102033f7f1754abd0a4c4dd1c77590 100644
--- a/src/mol-repr/structure/visual/molecular-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
@@ -83,6 +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.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
@@ -151,6 +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.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 f3a2c07788a8676a98933609e2ae2b0057840d7c..45b93917a3c66a3aeca9a00e968e0d50c06aa97d 100644
--- a/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
@@ -57,6 +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.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 61086d2585c30e9da0ba80ce8ec7338581bdac45..4fc89d01935a742bceaebb76e6c962ff18681ce2 100644
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -2,6 +2,7 @@
* Copyright (c) 2018-2022 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>
*/
import { BondType } from '../../../../mol-model/structure/model/types';
@@ -14,11 +15,13 @@ 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';
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),
aromaticBonds: PD.Boolean(true, { description: 'Display aromatic bonds with dashes' }),
multipleBonds: PD.Select('symmetric', PD.arrayToOptions(['off', 'symmetric', 'offset'] as const)),
};
@@ -51,7 +54,7 @@ export function makeIntraBondIgnoreTest(structure: Structure, unit: Unit.Atomic,
const { a, b, edgeProps } = bonds;
const { flags: _flags } = edgeProps;
- const { ignoreHydrogens, includeTypes, excludeTypes } = props;
+ const { ignoreHydrogens, onlyPolarHydrogens, includeTypes, excludeTypes } = props;
const include = BondType.fromNames(includeTypes);
const exclude = BondType.fromNames(excludeTypes);
@@ -61,14 +64,31 @@ 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 && !ignoreHydrogens && !child) return;
+ if (allBondTypes && !onlyPolarHydrogens && !ignoreHydrogens && !child) return;
return (edgeIndex: number) => {
- return (
- (!!childUnit && !SortedArray.has(childUnit.elements, elements[a[edgeIndex]])) ||
- (ignoreHydrogens && (isH(atomicNumber, elements[a[edgeIndex]]) || isH(atomicNumber, elements[b[edgeIndex]]))) ||
- (!allBondTypes && ignoreBondType(include, exclude, _flags[edgeIndex]))
- );
+ const aI = a[edgeIndex];
+ const bI = b[edgeIndex];
+
+ if ((!!childUnit && !SortedArray.has(childUnit.elements, elements[aI]))) {
+ return true;
+ }
+
+ if (!allBondTypes && ignoreBondType(include, exclude, _flags[edgeIndex])) {
+ 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;
+ }
+
+ return false;
};
}
@@ -76,7 +96,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
const bonds = structure.interUnitBonds;
const { edges } = bonds;
- const { ignoreHydrogens, includeTypes, excludeTypes } = props;
+ const { ignoreHydrogens, onlyPolarHydrogens, includeTypes, excludeTypes } = props;
const include = BondType.fromNames(includeTypes);
const exclude = BondType.fromNames(excludeTypes);
@@ -84,7 +104,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
const { child } = structure;
- if (allBondTypes && !ignoreHydrogens && !child) return;
+ if (allBondTypes && !onlyPolarHydrogens && !ignoreHydrogens && !child) return;
return (edgeIndex: number) => {
if (child) {
@@ -104,6 +124,18 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
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 (!allBondTypes) {
if (ignoreBondType(include, exclude, edges[edgeIndex].props.flag)) return true;
}
diff --git a/src/mol-repr/structure/visual/util/common.ts b/src/mol-repr/structure/visual/util/common.ts
index 50d3f2659866cf41cfea42ed9147cb4a90dcc6b4..e2e9aa0156e51c1a612d79494d4afbfa46565d00 100644
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -2,6 +2,7 @@
* Copyright (c) 2018-2022 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>
*/
import { Unit, Structure, ElementIndex, StructureElement, ResidueIndex } from '../../../../mol-model/structure';
@@ -16,6 +17,7 @@ import { AssignableArrayLike } from '../../../../mol-util/type-helpers';
import { getBoundary } from '../../../../mol-math/geometry/boundary';
import { Box3D } from '../../../../mol-math/geometry';
import { SizeTheme } from '../../../../mol-theme/size';
+import { hasPolarNeighbour } from '../../../../mol-model-props/computed/chemistry/functional-group';
/** Return a Loci for the elements of a whole residue the elementIndex belongs to. */
export function getResidueLoci(structure: Structure, unit: Unit.Atomic, elementIndex: ElementIndex): Loci {
@@ -139,6 +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.' }),
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.' }),
};
@@ -166,7 +169,7 @@ function filterUnitId(id: AssignableArrayLike<number>, elements: SortedArray, in
}
export function getUnitConformationAndRadius(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: CommonSurfaceProps) {
- const { ignoreHydrogens, traceOnly, includeParent } = props;
+ const { ignoreHydrogens, onlyPolarHydrogens, traceOnly, includeParent } = props;
const rootUnit = includeParent ? structure.root.unitMap.get(unit.id) : unit;
const differentRoot = includeParent && rootUnit !== unit;
@@ -179,12 +182,13 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, s
let indices: SortedArray<ElementIndex>;
let id: AssignableArrayLike<number>;
- if (ignoreHydrogens || traceOnly || differentRoot) {
+ if (ignoreHydrogens || onlyPolarHydrogens || 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 (traceOnly && !isTrace(rootUnit, eI)) continue;
if (differentRoot && squaredDistance(x[eI], y[eI], z[eI], center) > radiusSq) continue;
@@ -215,7 +219,7 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, s
}
export function getStructureConformationAndRadius(structure: Structure, sizeTheme: SizeTheme<any>, props: CommonSurfaceProps) {
- const { ignoreHydrogens, traceOnly, includeParent } = props;
+ const { ignoreHydrogens, onlyPolarHydrogens, traceOnly, includeParent } = props;
const differentRoot = includeParent && !!structure.parent;
const l = StructureElement.Location.create(structure.root);
@@ -230,7 +234,7 @@ export function getStructureConformationAndRadius(structure: Structure, sizeThem
let id: AssignableArrayLike<number>;
let indices: OrderedSet<number>;
- if (ignoreHydrogens || traceOnly || differentRoot) {
+ if (ignoreHydrogens || onlyPolarHydrogens || traceOnly || differentRoot) {
const { getSerialIndex } = structure.serialMapping;
const units = differentRoot ? structure.root.units : structure.units;
@@ -249,6 +253,7 @@ export function getStructureConformationAndRadius(structure: Structure, sizeThem
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 (traceOnly && !isTrace(unit, eI)) continue;
const _x = x(eI), _y = y(eI), _z = z(eI);
diff --git a/src/mol-repr/structure/visual/util/element.ts b/src/mol-repr/structure/visual/util/element.ts
index 2c51b20c6eac4deaef9d914ec4761106f875a3a7..a55a776bec0fa596c5cadff9fdd2e30510fe93c8 100644
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -21,12 +21,14 @@ import { Spheres } from '../../../../mol-geo/geometry/spheres/spheres';
import { SpheresBuilder } from '../../../../mol-geo/geometry/spheres/spheres-builder';
import { isTrace, isH, StructureGroup } 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,
traceOnly: boolean,
}
@@ -36,7 +38,7 @@ export type ElementSphereMeshProps = {
} & ElementProps
export function makeElementIgnoreTest(structure: Structure, unit: Unit, props: ElementProps): undefined | ((i: ElementIndex) => boolean) {
- const { ignoreHydrogens, traceOnly } = props;
+ const { ignoreHydrogens, onlyPolarHydrogens, traceOnly } = props;
const { atomicNumber } = unit.model.atomicHierarchy.derived.atom;
const isCoarse = Unit.isCoarse(unit);
@@ -45,14 +47,26 @@ export function makeElementIgnoreTest(structure: Structure, unit: Unit, props: E
const childUnit = child?.unitMap.get(unit.id);
if (child && !childUnit) throw new Error('expected childUnit to exist if child exists');
- if (!child && !ignoreHydrogens && !traceOnly) return;
+ if (!child && !ignoreHydrogens && !traceOnly && !onlyPolarHydrogens) return;
return (element: ElementIndex) => {
- return (
- (!!childUnit && !SortedArray.has(childUnit.elements, element)) ||
- (!isCoarse && ignoreHydrogens && isH(atomicNumber, element)) ||
- (traceOnly && !isTrace(unit, element))
- );
+ 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;
};
}