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@@ -6,13 +6,18 @@
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*/
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import { ParamDefinition as PD } from '../../mol-util/param-definition';
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-import { Structure } from '../../mol-model/structure';
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+import { Structure, StructureProperties } from '../../mol-model/structure';
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import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
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-import { ANVILParams, ANVILProps, computeANVIL } from './ANVIL';
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-import { MembraneOrientation } from '../../mol-model/structure/model/properties/membrane-orientation';
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+import { ANVILParams, ANVILProps, computeANVIL, isInMembranePlane } from './ANVIL';
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import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
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import { CustomProperty } from '../../mol-model-props/common/custom-property';
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import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area';
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+import { Vec3 } from '../../mol-math/linear-algebra';
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+import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
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+import { CustomPropSymbol } from '../../mol-script/language/symbol';
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+import Type from '../../mol-script/language/type';
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+import { StructureSelectionQuery, StructureSelectionCategory } from '../../mol-plugin-state/helpers/structure-selection-query';
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+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
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export const MembraneOrientationParams = {
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...ANVILParams
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@@ -20,10 +25,59 @@ export const MembraneOrientationParams = {
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export type MembraneOrientationParams = typeof MembraneOrientationParams
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export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
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+interface MembraneOrientation {
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+ // point in membrane boundary
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+ readonly p1: Vec3,
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+ // point in opposite side of membrane boundary
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+ readonly p2: Vec3,
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+ // normal vector of membrane layer
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+ readonly normal: Vec3,
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+ // the radius of the membrane layer
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+ readonly radius: number,
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+ readonly centroid: Vec3
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+}
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+
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+namespace MembraneOrientation {
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+ const pos = Vec3();
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+ export const symbols = {
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+ isTransmembrane: QuerySymbolRuntime.Dynamic(CustomPropSymbol('membrane-orientation', 'is-transmembrane', Type.Bool),
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+ ctx => {
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+ const structure = ctx.currentStructure;
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+ const { x, y, z } = StructureProperties.atom;
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+ if (!structure.isAtomic) return false;
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+ const membraneOrientation = MembraneOrientationProvider.get(structure).value;
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+ if (!membraneOrientation) return false;
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+ Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
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+ const { normal, p1, p2 } = membraneOrientation!;
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+ return isInMembranePlane(pos, normal, p1, p2);
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+ })
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+ };
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+
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+ export const isTransmembrane = StructureSelectionQuery('Residues embedded in membrane', MS.struct.modifier.union([
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+ MS.struct.modifier.wholeResidues([
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+ MS.struct.modifier.union([
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+ MS.struct.generator.atomGroups({
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+ 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
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+ 'atom-test': symbols.isTransmembrane.symbol(),
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+ })
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+ ])
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+ ])
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+ ]), {
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+ description: 'Select residues that are embedded between the membrane layers.',
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+ category: StructureSelectionCategory.Residue,
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+ ensureCustomProperties: (ctx, structure) => {
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+ return MembraneOrientationProvider.attach(ctx, structure);
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+ }
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+ });
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+}
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+
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+export { MembraneOrientation };
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+
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export const MembraneOrientationProvider: CustomStructureProperty.Provider<MembraneOrientationParams, MembraneOrientation> = CustomStructureProperty.createProvider({
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label: 'Membrane Orientation',
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descriptor: CustomPropertyDescriptor({
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name: 'molstar_computed_membrane_orientation',
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+ symbols: MembraneOrientation.symbols
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// TODO `cifExport`
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}),
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type: 'root',
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JonStargaryen