From 3babfb55c39f69eb57f4b1e1752d6e6ab6e916bc Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 26 Apr 2018 19:36:32 +0200
Subject: [PATCH] Renamed Conformation to AtomSiteConformation
---
src/mol-model/structure/model/formats/gro.ts | 8 ++++----
src/mol-model/structure/model/formats/mmcif.ts | 8 ++++----
src/mol-model/structure/model/model.ts | 4 ++--
.../{conformation.ts => atom-site-conformation.ts} | 0
.../structure/model/properties/coarse-grained.ts | 10 +++++++---
src/mol-model/structure/model/properties/hierarchy.ts | 7 +------
.../element/properties/bonds/group-compute.ts | 2 +-
src/mol-model/structure/structure/unit.ts | 8 ++++----
src/perf-tests/structure.ts | 6 +++---
9 files changed, 26 insertions(+), 27 deletions(-)
rename src/mol-model/structure/model/properties/{conformation.ts => atom-site-conformation.ts} (100%)
diff --git a/src/mol-model/structure/model/formats/gro.ts b/src/mol-model/structure/model/formats/gro.ts
index cad8c441a..cb868ff96 100644
--- a/src/mol-model/structure/model/formats/gro.ts
+++ b/src/mol-model/structure/model/formats/gro.ts
@@ -11,7 +11,7 @@ import { Atoms } from 'mol-io/reader/gro/schema'
import Format from '../format'
import Model from '../model'
import * as Hierarchy from '../properties/hierarchy'
-import Conformation from '../properties/conformation'
+import AtomSiteConformation from '../properties/atom-site-conformation'
import CoarseGrained from '../properties/coarse-grained'
import findHierarchyKeys from '../utils/hierarchy-keys'
import { guessElement } from '../utils/guess-element'
@@ -77,7 +77,7 @@ function createHierarchyData(atomsData: Atoms, offsets: HierarchyOffsets): Hiera
return { atoms, residues, chains };
}
-function getConformation(atoms: Atoms): Conformation {
+function getConformation(atoms: Atoms): AtomSiteConformation {
return {
id: UUID.create(),
atomId: atoms.atomNumber,
@@ -105,7 +105,7 @@ function createModel(format: gro_Format, modelNum: number, previous?: Model): Mo
if (previous && isHierarchyDataEqual(previous.hierarchy, hierarchyData)) {
return {
...previous,
- conformation: getConformation(structure.atoms)
+ atomSiteConformation: getConformation(structure.atoms)
};
}
@@ -133,7 +133,7 @@ function createModel(format: gro_Format, modelNum: number, previous?: Model): Mo
hierarchy,
entities,
sequence: Sequence.fromHierarchy(hierarchy),
- conformation: getConformation(structure.atoms),
+ atomSiteConformation: getConformation(structure.atoms),
coarseGrained: CoarseGrained.Empty,
symmetry: { assemblies: [] },
atomCount: structure.atoms.count
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index d88ca8ac7..dddb04627 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -10,7 +10,7 @@ import { Interval, Segmentation } from 'mol-data/int'
import Format from '../format'
import Model from '../model'
import * as Hierarchy from '../properties/hierarchy'
-import Conformation from '../properties/conformation'
+import AtomSiteConformation from '../properties/atom-site-conformation'
import CoarseGrained from '../properties/coarse-grained'
import Symmetry from '../properties/symmetry'
import findHierarchyKeys from '../utils/hierarchy-keys'
@@ -67,7 +67,7 @@ function createHierarchyData({ data }: mmCIF_Format, bounds: Interval, offsets:
return { atoms, residues, chains };
}
-function getConformation({ data }: mmCIF_Format, bounds: Interval): Conformation {
+function getConformation({ data }: mmCIF_Format, bounds: Interval): AtomSiteConformation {
const start = Interval.start(bounds), end = Interval.end(bounds);
const { atom_site } = data;
return {
@@ -99,7 +99,7 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
if (previous && isHierarchyDataEqual(previous.hierarchy, hierarchyData)) {
return {
...previous,
- conformation: getConformation(format, bounds)
+ atomSiteConformation: getConformation(format, bounds)
};
}
@@ -121,7 +121,7 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
entities,
hierarchy,
sequence: getSequence(format.data, entities, hierarchy),
- conformation: getConformation(format, bounds),
+ atomSiteConformation: getConformation(format, bounds),
coarseGrained: CoarseGrained.Empty,
symmetry: getSymmetry(format),
atomCount: Interval.size(bounds)
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 9652cf5b1..e685af863 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -8,7 +8,7 @@ import UUID from 'mol-util/uuid'
import Format from './format'
import Sequence from './properties/sequence'
import Hierarchy from './properties/hierarchy'
-import Conformation from './properties/conformation'
+import AtomSiteConformation from './properties/atom-site-conformation'
import Symmetry from './properties/symmetry'
import CoarseGrained from './properties/coarse-grained'
import { Entities } from './properties/common';
@@ -32,7 +32,7 @@ interface Model extends Readonly<{
sequence: Sequence,
hierarchy: Hierarchy,
- conformation: Conformation,
+ atomSiteConformation: AtomSiteConformation,
symmetry: Symmetry,
coarseGrained: CoarseGrained,
diff --git a/src/mol-model/structure/model/properties/conformation.ts b/src/mol-model/structure/model/properties/atom-site-conformation.ts
similarity index 100%
rename from src/mol-model/structure/model/properties/conformation.ts
rename to src/mol-model/structure/model/properties/atom-site-conformation.ts
diff --git a/src/mol-model/structure/model/properties/coarse-grained.ts b/src/mol-model/structure/model/properties/coarse-grained.ts
index 730724114..5787428ee 100644
--- a/src/mol-model/structure/model/properties/coarse-grained.ts
+++ b/src/mol-model/structure/model/properties/coarse-grained.ts
@@ -9,13 +9,14 @@ import { Tensor } from 'mol-math/linear-algebra';
import { Column } from 'mol-data/db';
interface CoarseGrained {
+ isDefined: boolean,
modelList: mmCIF['ihm_model_list'],
- spheres: { [P in keyof CoarseGrained.Sphere]: Column<CoarseGrained.Sphere[P]> },
- gaussians: { [P in keyof CoarseGrained.Gaussian]: Column<CoarseGrained.Gaussian[P]> }
+ spheres: CoarseGrained.Spheres,
+ gaussians: CoarseGrained.Gaussians
}
namespace CoarseGrained {
- export const Empty: CoarseGrained = { } as any;
+ export const Empty: CoarseGrained = { isDefined: false } as any;
interface Site {
// index to the Model.hierarchy.entities table
@@ -40,6 +41,9 @@ namespace CoarseGrained {
weight: number,
covarianceMatrix: Tensor.Data
}
+
+ export type Spheres = { count: number} & { [P in keyof Sphere]: Column<Sphere[P]> }
+ export type Gaussians = { count: number} & { [P in keyof Gaussian]: Column<Gaussian[P]> }
}
export default CoarseGrained;
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/hierarchy.ts b/src/mol-model/structure/model/properties/hierarchy.ts
index 8987e070d..d25903d95 100644
--- a/src/mol-model/structure/model/properties/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/hierarchy.ts
@@ -40,15 +40,10 @@ export const ChainsSchema = {
export type ChainsSchema = typeof ChainsSchema
export interface Chains extends Table<ChainsSchema> { }
-// export const EntitySchema = mmCIF['entity']
-// export type EntitySchema = typeof EntitySchema
-// export interface Entities extends Table<EntitySchema> { }
-
export interface Data {
atoms: Atoms,
residues: Residues,
- chains: Chains,
- //entities: Entities
+ chains: Chains
}
export interface Segments {
diff --git a/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts b/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
index fb078c889..a75540509 100644
--- a/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
+++ b/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
@@ -110,7 +110,7 @@ function computePerAtomBonds(atomA: number[], atomB: number[], _order: number[],
function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondComputationParameters): GroupBonds {
const MAX_RADIUS = 3;
- const { x, y, z } = unit.model.conformation;
+ const { x, y, z } = unit.model.atomSiteConformation;
const atomCount = ElementGroup.size(atoms);
const { residueIndex } = unit;
const { type_symbol, label_atom_id, label_alt_id } = unit.model.hierarchy.atoms;
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 2109cc10b..201002b58 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -47,7 +47,7 @@ namespace Unit {
// Reference some commonly accessed things for faster access.
readonly residueIndex: ArrayLike<number>,
readonly chainIndex: ArrayLike<number>,
- readonly conformation: Model['conformation']
+ readonly conformation: Model['atomSiteConformation']
}
// Coarse grained representations.
@@ -58,7 +58,7 @@ namespace Unit {
export function createAtomic(model: Model, operator: SymmetryOperator, fullGroup: ElementGroup): Unit {
const h = model.hierarchy;
- const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, model.conformation);
+ const { invariantPosition, position, x, y, z } = SymmetryOperator.createMapping(operator, model.atomSiteConformation);
return {
model,
@@ -68,7 +68,7 @@ namespace Unit {
residueIndex: h.residueSegments.segmentMap,
chainIndex: h.chainSegments.segmentMap,
hierarchy: model.hierarchy,
- conformation: model.conformation,
+ conformation: model.atomSiteConformation,
invariantPosition,
position,
x, y, z
@@ -89,7 +89,7 @@ namespace Unit {
export function getLookup3d(unit: Unit, group: ElementGroup) {
if (group.__lookup3d__) return group.__lookup3d__;
if (Unit.isAtomic(unit)) {
- const { x, y, z } = unit.model.conformation;
+ const { x, y, z } = unit.model.atomSiteConformation;
group.__lookup3d__ = GridLookup3D({ x, y, z, indices: group.elements });
return group.__lookup3d__;
}
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 57a23cec6..1e0a9b972 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -356,11 +356,11 @@ export namespace PropertyAccess {
// return;
console.log('bs', baseline(models[0]));
- console.log('sp', sumProperty(structures[0], l => l.unit.model.conformation.atomId.value(l.element)));
- console.log(sumPropertySegmented(structures[0], l => l.unit.model.conformation.atomId.value(l.element)));
+ console.log('sp', sumProperty(structures[0], l => l.unit.model.atomSiteConformation.atomId.value(l.element)));
+ console.log(sumPropertySegmented(structures[0], l => l.unit.model.atomSiteConformation.atomId.value(l.element)));
//console.log(sumPropertySegmentedMutable(structures[0], l => l.unit.model.conformation.atomId.value(l.element));
- console.log(sumPropertyAtomSetIt(structures[0], l => l.unit.model.conformation.atomId.value(l.element)));
+ console.log(sumPropertyAtomSetIt(structures[0], l => l.unit.model.atomSiteConformation.atomId.value(l.element)));
//console.log(sumProperty(structures[0], Property.cachedAtomColumn(m => m.conformation.atomId)));
//console.log(sumDirect(structures[0]));
//console.log('r', sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])));
--
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