From 31eb9ae4bb38eb560f95ef021a0a01fcc240d7ea Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 2 May 2018 17:02:03 +0200
Subject: [PATCH] Updated coarse unit model
---
src/apps/structure-info/model.ts | 3 +-
.../model/properties/coarse-grained.ts | 2 +-
src/mol-model/structure/query/properties.ts | 23 +++----
.../structure/structure/structure.ts | 7 +--
src/mol-model/structure/structure/unit.ts | 63 ++++++++++++-------
5 files changed, 54 insertions(+), 44 deletions(-)
diff --git a/src/apps/structure-info/model.ts b/src/apps/structure-info/model.ts
index 8ab4ad1db..b284d0422 100644
--- a/src/apps/structure-info/model.ts
+++ b/src/apps/structure-info/model.ts
@@ -15,7 +15,6 @@ import { Model, Structure, Element, ElementSet, Unit, ElementGroup, Queries } fr
import { OrderedSet } from 'mol-data/int';
import { Table } from 'mol-data/db';
import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
-import CoarseGrained from 'mol-model/structure/model/properties/coarse-grained';
import { openCif, downloadCif } from './helpers';
@@ -97,7 +96,7 @@ export function printUnits(structure: Structure) {
if (Unit.isAtomic(l.unit)) {
console.log(`Atomic unit ${unitId}: ${size} elements`);
} else if (Unit.isCoarse(l.unit)) {
- console.log(`Coarse unit ${unitId} (${l.unit.elementType === CoarseGrained.ElementType.Sphere ? 'spheres' : 'gaussians'}): ${size} elements.`);
+ console.log(`Coarse unit ${unitId} (${Unit.isCoarseSpheres(l.unit) ? 'spheres' : 'gaussians'}): ${size} elements.`);
const props = Queries.props.coarse_grained;
const seq = l.unit.model.sequence;
diff --git a/src/mol-model/structure/model/properties/coarse-grained.ts b/src/mol-model/structure/model/properties/coarse-grained.ts
index 392f06a2c..ac5ba1084 100644
--- a/src/mol-model/structure/model/properties/coarse-grained.ts
+++ b/src/mol-model/structure/model/properties/coarse-grained.ts
@@ -45,7 +45,7 @@ namespace CoarseGrained {
entityKey: ArrayLike<number>
}
- export type SiteBases = Common & { [P in keyof SiteBase]: Column<SiteBase[P]> }
+ export type SitesBase = Common & { [P in keyof SiteBase]: Column<SiteBase[P]> }
export type Spheres = Common & { [P in keyof Sphere]: Column<Sphere[P]> }
export type Gaussians = Common & { matrix_space: Tensor.Space } & { [P in keyof Gaussian]: Column<Gaussian[P]> }
}
diff --git a/src/mol-model/structure/query/properties.ts b/src/mol-model/structure/query/properties.ts
index 8a766f9b5..f358b3deb 100644
--- a/src/mol-model/structure/query/properties.ts
+++ b/src/mol-model/structure/query/properties.ts
@@ -5,7 +5,6 @@
*/
import { Element, Unit } from '../structure'
-import CoarseGrained from '../model/properties/coarse-grained';
const constant = {
true: Element.property(l => true),
@@ -61,26 +60,22 @@ const chain = {
}
const coarse_grained = {
- modelKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.siteBases.modelKey[l.element]),
- entityKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.siteBases.entityKey[l.element]),
+ modelKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.modelKey[l.element]),
+ entityKey: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.entityKey[l.element]),
x: atom.x,
y: atom.y,
z: atom.z,
- asym_id: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.siteBases.asym_id.value(l.element)),
- seq_id_begin: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.siteBases.seq_id_begin.value(l.element)),
- seq_id_end: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.siteBases.seq_id_end.value(l.element)),
+ asym_id: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.asym_id.value(l.element)),
+ seq_id_begin: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.seq_id_begin.value(l.element)),
+ seq_id_end: Element.property(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.sites.seq_id_end.value(l.element)),
- sphere_radius: Element.property(l => !Unit.isCoarse(l.unit) || l.unit.elementType !== CoarseGrained.ElementType.Sphere
- ? notCoarse('spheres') : l.unit.spheres.radius.value(l.element)),
- sphere_rmsf: Element.property(l => !Unit.isCoarse(l.unit) || l.unit.elementType !== CoarseGrained.ElementType.Sphere
- ? notCoarse('spheres') : l.unit.spheres.rmsf.value(l.element)),
+ sphere_radius: Element.property(l => !Unit.isCoarseSpheres(l.unit) ? notCoarse('spheres') : l.unit.sites.radius.value(l.element)),
+ sphere_rmsf: Element.property(l => !Unit.isCoarseSpheres(l.unit) ? notCoarse('spheres') : l.unit.sites.rmsf.value(l.element)),
- gaussian_weight: Element.property(l => !Unit.isCoarse(l.unit) || l.unit.elementType !== CoarseGrained.ElementType.Gaussian
- ? notCoarse('gaussians') : l.unit.gaussians.weight.value(l.element)),
- gaussian_covariance_matrix: Element.property(l => !Unit.isCoarse(l.unit) || l.unit.elementType !== CoarseGrained.ElementType.Gaussian
- ? notCoarse('gaussians') : l.unit.gaussians.covariance_matrix.value(l.element)),
+ gaussian_weight: Element.property(l => !Unit.isCoarseGaussians(l.unit) ? notCoarse('gaussians') : l.unit.sites.weight.value(l.element)),
+ gaussian_covariance_matrix: Element.property(l => !Unit.isCoarseGaussians(l.unit) ? notCoarse('gaussians') : l.unit.sites.covariance_matrix.value(l.element))
}
function eK(l: Element.Location) { return !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.hierarchy.entityKey.value(l.unit.chainIndex[l.element]); }
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 6572e03e1..99ac010ad 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -12,7 +12,6 @@ import Unit from './unit'
import ElementSet from './element/set'
import ElementGroup from './element/group'
import Element from './element'
-import CoarseGrained from '../model/properties/coarse-grained';
// A structure is a pair of "units" and an element set.
// Each unit contains the data and transformation of its corresponding elements.
@@ -36,7 +35,7 @@ namespace Structure {
for (let c = 0; c < chains.count; c++) {
const group = ElementGroup.createNew(OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
- const unit = Unit.createAtomic(model, SymmetryOperator.Default, group);
+ const unit = Unit.create(Unit.Kind.Atomic, model, SymmetryOperator.Default, group);
builder.add(unit, unit.fullGroup);
}
@@ -44,12 +43,12 @@ namespace Structure {
if (cs.isDefined) {
if (cs.spheres.count > 0) {
const group = ElementGroup.createNew(OrderedSet.ofBounds(0, cs.spheres.count));
- const unit = Unit.createCoarse(model, SymmetryOperator.Default, group, CoarseGrained.ElementType.Sphere);
+ const unit = Unit.create(Unit.Kind.CoarseSpheres, model, SymmetryOperator.Default, group);
builder.add(unit, unit.fullGroup);
}
if (cs.gaussians.count > 0) {
const group = ElementGroup.createNew(OrderedSet.ofBounds(0, cs.gaussians.count));
- const unit = Unit.createCoarse(model, SymmetryOperator.Default, group, CoarseGrained.ElementType.Gaussian);
+ const unit = Unit.create(Unit.Kind.CoarseGaussians, model, SymmetryOperator.Default, group);
builder.add(unit, unit.fullGroup);
}
}
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 596dd3580..0ef49b456 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -13,13 +13,15 @@ import CoarseGrained from '../model/properties/coarse-grained';
// A building block of a structure that corresponds to an atomic or a coarse grained representation
// 'conveniently grouped together'.
-type Unit = Unit.Atomic | Unit.Coarse
+type Unit = Unit.Atomic | Unit.CoarseSpheres | Unit.CoarseGaussians
namespace Unit {
- export const enum Kind { Atomic, Coarse }
+ export const enum Kind { Atomic, CoarseSpheres, CoarseGaussians }
export function isAtomic(u: Unit): u is Atomic { return u.kind === Kind.Atomic; }
- export function isCoarse(u: Unit): u is Coarse { return u.kind === Kind.Coarse; }
+ export function isCoarse(u: Unit): u is CoarseSpheres | CoarseGaussians { return u.kind === Kind.CoarseSpheres || u.kind === Kind.CoarseGaussians; }
+ export function isCoarseSpheres(u: Unit): u is CoarseSpheres { return u.kind === Kind.CoarseSpheres; }
+ export function isCoarseGaussians(u: Unit): u is CoarseGaussians { return u.kind === Kind.CoarseGaussians; }
export interface Base extends SymmetryOperator.ArrayMapping {
// Provides access to the underlying data.
@@ -41,7 +43,7 @@ namespace Unit {
// An atom set can be referenced by multiple diffrent units which
// makes construction of assemblies and spacegroups very efficient.
export interface Atomic extends Base {
- readonly kind: Unit.Kind.Atomic,
+ readonly kind: Kind.Atomic,
// Reference some commonly accessed things for faster access.
readonly residueIndex: ArrayLike<number>,
@@ -51,16 +53,23 @@ namespace Unit {
}
// Coarse grained representations.
- export interface Coarse extends Base {
- readonly kind: Unit.Kind.Coarse,
- readonly elementType: CoarseGrained.ElementType,
+ export interface CoarseBase<K extends Kind, S extends CoarseGrained.SitesBase> extends Base {
+ readonly kind: K,
+ readonly sites: S
+ }
+
+ export interface CoarseSpheres extends CoarseBase<Kind.CoarseSpheres, CoarseGrained.Spheres> { }
+ export interface CoarseGaussians extends CoarseBase<Kind.CoarseGaussians, CoarseGrained.Gaussians> { }
- readonly siteBases: CoarseGrained.SiteBases,
- readonly spheres: CoarseGrained.Spheres,
- readonly gaussians: CoarseGrained.Gaussians
+ export function create(kind: Kind, model: Model, operator: SymmetryOperator, fullGroup: ElementGroup): Unit {
+ switch (kind) {
+ case Kind.Atomic: return createAtomic(model, operator, fullGroup);
+ case Kind.CoarseSpheres: return createCoarseSpheres(model, operator, fullGroup);
+ case Kind.CoarseGaussians: return createCoarseGaussians(model, operator, fullGroup);
+ }
}
- export function createAtomic(model: Model, operator: SymmetryOperator, fullGroup: ElementGroup): Unit.Atomic {
+ function createAtomic(model: Model, operator: SymmetryOperator, fullGroup: ElementGroup): Unit.Atomic {
const h = model.hierarchy;
const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, model.atomSiteConformation);
@@ -79,19 +88,30 @@ namespace Unit {
};
}
- export function createCoarse(model: Model, operator: SymmetryOperator, fullGroup: ElementGroup, elementType: CoarseGrained.ElementType): Unit.Coarse {
- const siteBases = elementType === CoarseGrained.ElementType.Sphere ? model.coarseGrained.spheres : model.coarseGrained.gaussians;
- const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, siteBases);
+ function createCoarseSpheres(model: Model, operator: SymmetryOperator, fullGroup: ElementGroup): Unit.CoarseSpheres {
+ const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, model.coarseGrained.spheres);
return {
model,
- kind: Kind.Coarse,
- elementType,
+ kind: Kind.CoarseSpheres,
+ sites: model.coarseGrained.spheres,
+ operator,
+ fullGroup,
+ invariantPosition,
+ position,
+ x, y, z
+ };
+ }
+
+ function createCoarseGaussians(model: Model, operator: SymmetryOperator, fullGroup: ElementGroup): Unit.CoarseGaussians {
+ const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, model.coarseGrained.gaussians);
+
+ return {
+ model,
+ kind: Kind.CoarseGaussians,
+ sites: model.coarseGrained.gaussians,
operator,
fullGroup,
- siteBases,
- spheres: model.coarseGrained.spheres,
- gaussians: model.coarseGrained.gaussians,
invariantPosition,
position,
x, y, z
@@ -99,10 +119,7 @@ namespace Unit {
}
export function withOperator(unit: Unit, operator: SymmetryOperator): Unit {
- switch (unit.kind) {
- case Kind.Atomic: return createAtomic(unit.model, SymmetryOperator.compose(unit.operator, operator), unit.fullGroup);
- case Kind.Coarse: return createCoarse(unit.model, SymmetryOperator.compose(unit.operator, operator), unit.fullGroup, unit.elementType);
- }
+ return create(unit.kind, unit.model, SymmetryOperator.compose(unit.operator, operator), unit.fullGroup);
}
export function getLookup3d(unit: Unit, group: ElementGroup) {
--
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