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@@ -8,41 +8,59 @@ import SymmetryOperator from 'mol-math/geometry/symmetry-operator'
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import AtomGroup from './atom/group'
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import { Model } from '../model'
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-// A bulding block of a structure that corresponds
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-// to a "natural group of atoms" (most often a "chain")
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-// together with a tranformation (rotation and translation)
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-// that is dynamically applied to the underlying atom set.
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-//
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-// An atom set can be referenced by multiple diffrent units which
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-// makes construction of assemblies and spacegroups very efficient.
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-interface Unit extends SymmetryOperator.ArrayMapping {
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- // Provides access to the underlying data.
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- readonly model: Model,
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-
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- // The "full" atom group corresponding to this unit.
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- // Every selection is a subset of this atoms group.
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- // Things like inter-unit bonds or spatial lookups
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- // can be be implemented efficiently as "views" of the
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- // full group.
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- readonly fullGroup: AtomGroup,
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-
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- // Reference some commonly accessed things for faster access.
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- readonly residueIndex: ArrayLike<number>,
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- readonly chainIndex: ArrayLike<number>,
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- readonly hierarchy: Model['hierarchy'],
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- readonly conformation: Model['conformation']
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-
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- // TODO: add velocity?
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- // AR: would fit into conformation, right?
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-}
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+// A building block of a structure that corresponds to an atomic or a coarse grained representation
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+// 'conveniently grouped together'.
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+type Unit = Unit.Atomic | Unit.Coarse
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namespace Unit {
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- export function create(model: Model, operator: SymmetryOperator, fullGroup: AtomGroup): Unit {
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+ export const enum Kind { Atomic, Coarse }
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+
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+ export function isAtomic(u: Unit): u is Atomic { return u.kind === Kind.Atomic; }
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+ export function isCoarse(u: Unit): u is Coarse { return u.kind === Kind.Coarse; }
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+
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+ export interface Base extends SymmetryOperator.ArrayMapping {
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+ // Provides access to the underlying data.
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+ readonly model: Model,
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+
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+ // The "full" atom group corresponding to this unit.
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+ // Every selection is a subset of this atoms group.
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+ // Things like inter-unit bonds or spatial lookups
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+ // can be be implemented efficiently as "views" of the
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+ // full group.
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+ readonly fullGroup: AtomGroup,
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+
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+ readonly hierarchy: Model['hierarchy'],
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+ }
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+
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+ // A bulding block of a structure that corresponds
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+ // to a "natural group of atoms" (most often a "chain")
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+ // together with a tranformation (rotation and translation)
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+ // that is dynamically applied to the underlying atom set.
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+ //
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+ // An atom set can be referenced by multiple diffrent units which
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+ // makes construction of assemblies and spacegroups very efficient.
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+ export interface Atomic extends Base {
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+ readonly kind: Unit.Kind.Atomic,
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+
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+ // Reference some commonly accessed things for faster access.
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+ readonly residueIndex: ArrayLike<number>,
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+ readonly chainIndex: ArrayLike<number>,
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+ readonly conformation: Model['conformation']
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+ }
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+
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+ // Coarse grained representations.
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+ // TODO: can we use the ArrayMapping here?
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+ export interface Coarse extends Base {
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+ readonly kind: Unit.Kind.Coarse
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+ }
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+
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+ export function createAtomic(model: Model, operator: SymmetryOperator, fullGroup: AtomGroup): Unit {
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const h = model.hierarchy;
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const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, model.conformation);
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return {
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model,
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+ kind: Kind.Atomic,
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operator,
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fullGroup,
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residueIndex: h.residueSegments.segmentMap,
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@@ -55,8 +73,15 @@ namespace Unit {
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};
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}
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- export function withOperator(unit: Unit, operator: SymmetryOperator) {
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- return create(unit.model, SymmetryOperator.compose(unit.operator, operator), unit.fullGroup);
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+ export function createCoarse(model: Model, operator: SymmetryOperator, fullGroup: AtomGroup): Unit {
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+ throw 'not implemented'
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+ }
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+
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+ export function withOperator(unit: Unit, operator: SymmetryOperator): Unit {
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+ switch (unit.kind) {
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+ case Kind.Atomic: return createAtomic(unit.model, SymmetryOperator.compose(unit.operator, operator), unit.fullGroup);
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+ case Kind.Coarse: return createCoarse(unit.model, SymmetryOperator.compose(unit.operator, operator), unit.fullGroup);
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+ }
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}
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}
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David Sehnal