From 801e1ef035ff0de5c86640a23f896e7f25cbaf52 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 2 Nov 2017 15:42:19 +0100
Subject: [PATCH] more refactoring
---
src/mol-data/sequence/TODO | 0
src/mol-data/structure.ts | 13 -----
.../{ => structure}/_spec/atom-set.spec.ts | 2 +-
src/mol-data/{ => structure}/model.ts | 0
.../{ => structure}/model/builders/mmcif.ts | 9 ++-
.../{ => structure}/model/constants.ts | 2 +-
.../{ => structure}/model/data-format.ts | 2 +-
src/mol-data/{ => structure}/model/model.ts | 2 +-
.../model/properties/computed.ts | 0
.../model/properties/conformation.ts | 4 +-
.../model/properties/format-specific.ts | 0
.../model/properties/hierarchy.ts | 8 +--
.../model/properties/transforms.ts | 0
.../model/utils/hierarchy-keys.ts | 4 +-
src/mol-data/{ => structure}/query.ts | 0
.../{ => structure}/query/generators.ts | 2 +-
.../{ => structure}/query/properties.ts | 0
src/mol-data/{ => structure}/query/query.ts | 0
.../{ => structure}/query/selection.ts | 4 +-
src/mol-data/structure/structure.ts | 57 ++----------------
.../structure/{ => structure}/atom.ts | 2 +-
.../structure/{ => structure}/atom/set.ts | 2 +-
.../{ => structure}/atom/set/builder.ts | 4 +-
.../{ => structure}/atom/set/impl.ts | 6 +-
.../{ => structure}/atom/set/properties.ts | 0
.../structure/{ => structure}/operator.ts | 2 +-
src/mol-data/structure/structure/structure.ts | 58 +++++++++++++++++++
.../structure/{ => structure}/unit.ts | 0
src/mol-data/volume/TODO | 0
src/perf-tests/sets.ts | 2 +-
src/perf-tests/structure.ts | 6 +-
src/script.ts | 2 +-
32 files changed, 96 insertions(+), 97 deletions(-)
create mode 100644 src/mol-data/sequence/TODO
delete mode 100644 src/mol-data/structure.ts
rename src/mol-data/{ => structure}/_spec/atom-set.spec.ts (99%)
rename src/mol-data/{ => structure}/model.ts (100%)
rename src/mol-data/{ => structure}/model/builders/mmcif.ts (94%)
rename src/mol-data/{ => structure}/model/constants.ts (99%)
rename src/mol-data/{ => structure}/model/data-format.ts (77%)
rename src/mol-data/{ => structure}/model/model.ts (94%)
rename src/mol-data/{ => structure}/model/properties/computed.ts (100%)
rename src/mol-data/{ => structure}/model/properties/conformation.ts (86%)
rename src/mol-data/{ => structure}/model/properties/format-specific.ts (100%)
rename src/mol-data/{ => structure}/model/properties/hierarchy.ts (91%)
rename src/mol-data/{ => structure}/model/properties/transforms.ts (100%)
rename src/mol-data/{ => structure}/model/utils/hierarchy-keys.ts (96%)
rename src/mol-data/{ => structure}/query.ts (100%)
rename src/mol-data/{ => structure}/query/generators.ts (97%)
rename src/mol-data/{ => structure}/query/properties.ts (100%)
rename src/mol-data/{ => structure}/query/query.ts (100%)
rename src/mol-data/{ => structure}/query/selection.ts (96%)
rename src/mol-data/structure/{ => structure}/atom.ts (95%)
rename src/mol-data/structure/{ => structure}/atom/set.ts (96%)
rename src/mol-data/structure/{ => structure}/atom/set/builder.ts (93%)
rename src/mol-data/structure/{ => structure}/atom/set/impl.ts (98%)
rename src/mol-data/structure/{ => structure}/atom/set/properties.ts (100%)
rename src/mol-data/structure/{ => structure}/operator.ts (91%)
create mode 100644 src/mol-data/structure/structure/structure.ts
rename src/mol-data/structure/{ => structure}/unit.ts (100%)
create mode 100644 src/mol-data/volume/TODO
diff --git a/src/mol-data/sequence/TODO b/src/mol-data/sequence/TODO
new file mode 100644
index 000000000..e69de29bb
diff --git a/src/mol-data/structure.ts b/src/mol-data/structure.ts
deleted file mode 100644
index cc8bf49f3..000000000
--- a/src/mol-data/structure.ts
+++ /dev/null
@@ -1,13 +0,0 @@
-/**
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import Atom from './structure/atom'
-import AtomSet from './structure/atom/set'
-import Structure from './structure/structure'
-import Operator from './structure/operator'
-import Unit from './structure/unit'
-
-export { Atom, AtomSet, Structure, Operator, Unit }
\ No newline at end of file
diff --git a/src/mol-data/_spec/atom-set.spec.ts b/src/mol-data/structure/_spec/atom-set.spec.ts
similarity index 99%
rename from src/mol-data/_spec/atom-set.spec.ts
rename to src/mol-data/structure/_spec/atom-set.spec.ts
index 62e5ea804..2ca79d8f9 100644
--- a/src/mol-data/_spec/atom-set.spec.ts
+++ b/src/mol-data/structure/_spec/atom-set.spec.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { OrderedSet } from '../../mol-base/collections/integer'
+import { OrderedSet } from '../../../mol-base/collections/integer'
import AtomSet from '../structure/atom/set'
import Atom from '../structure/atom'
diff --git a/src/mol-data/model.ts b/src/mol-data/structure/model.ts
similarity index 100%
rename from src/mol-data/model.ts
rename to src/mol-data/structure/model.ts
diff --git a/src/mol-data/model/builders/mmcif.ts b/src/mol-data/structure/model/builders/mmcif.ts
similarity index 94%
rename from src/mol-data/model/builders/mmcif.ts
rename to src/mol-data/structure/model/builders/mmcif.ts
index 4d92bbc56..3fa96b038 100644
--- a/src/mol-data/model/builders/mmcif.ts
+++ b/src/mol-data/structure/model/builders/mmcif.ts
@@ -5,12 +5,11 @@
*/
import { mmCIF } from '../data-format'
-//import { Frame as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
import Model from '../model'
-import Column from '../../../mol-base/collections/column'
-import Table from '../../../mol-base/collections/table'
-import { Interval, Segmentation } from '../../../mol-base/collections/integer'
-import { newUUID } from '../../../mol-base/utils/uuid'
+import Column from '../../../../mol-base/collections/column'
+import Table from '../../../../mol-base/collections/table'
+import { Interval, Segmentation } from '../../../../mol-base/collections/integer'
+import { newUUID } from '../../../../mol-base/utils/uuid'
import * as Hierarchy from '../properties/hierarchy'
import Conformation from '../properties/conformation'
import findHierarchyKeys from '../utils/hierarchy-keys'
diff --git a/src/mol-data/model/constants.ts b/src/mol-data/structure/model/constants.ts
similarity index 99%
rename from src/mol-data/model/constants.ts
rename to src/mol-data/structure/model/constants.ts
index 5db57c733..48c863c7f 100644
--- a/src/mol-data/model/constants.ts
+++ b/src/mol-data/structure/model/constants.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import BitFlags from '../../mol-base/utils/bit-flags'
+import BitFlags from '../../../mol-base/utils/bit-flags'
export const enum EntityType {
Unknown = 'unknown',
diff --git a/src/mol-data/model/data-format.ts b/src/mol-data/structure/model/data-format.ts
similarity index 77%
rename from src/mol-data/model/data-format.ts
rename to src/mol-data/structure/model/data-format.ts
index 128136b86..c5c4aa2e7 100644
--- a/src/mol-data/model/data-format.ts
+++ b/src/mol-data/structure/model/data-format.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Frame as mmCIF_Frame } from '../../mol-io/reader/cif/schema/mmcif'
+import { Frame as mmCIF_Frame } from '../../../mol-io/reader/cif/schema/mmcif'
export interface mmCIF { kind: 'mmCIF', data: mmCIF_Frame }
diff --git a/src/mol-data/model/model.ts b/src/mol-data/structure/model/model.ts
similarity index 94%
rename from src/mol-data/model/model.ts
rename to src/mol-data/structure/model/model.ts
index 12c5fe73a..b2dbf68fc 100644
--- a/src/mol-data/model/model.ts
+++ b/src/mol-data/structure/model/model.ts
@@ -7,7 +7,7 @@
import DataFormat from './data-format'
import HierarchyProperties from './properties/hierarchy'
import ConformationProperties from './properties/conformation'
-import UUID from '../../mol-base/utils/uuid'
+import UUID from '../../../mol-base/utils/uuid'
import buildMmCIF from './builders/mmcif'
diff --git a/src/mol-data/model/properties/computed.ts b/src/mol-data/structure/model/properties/computed.ts
similarity index 100%
rename from src/mol-data/model/properties/computed.ts
rename to src/mol-data/structure/model/properties/computed.ts
diff --git a/src/mol-data/model/properties/conformation.ts b/src/mol-data/structure/model/properties/conformation.ts
similarity index 86%
rename from src/mol-data/model/properties/conformation.ts
rename to src/mol-data/structure/model/properties/conformation.ts
index 7ea3c5243..a80739667 100644
--- a/src/mol-data/model/properties/conformation.ts
+++ b/src/mol-data/structure/model/properties/conformation.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column from '../../../mol-base/collections/column'
-import UUID from '../../../mol-base/utils/uuid'
+import Column from '../../../../mol-base/collections/column'
+import UUID from '../../../../mol-base/utils/uuid'
interface Conformation {
id: UUID,
diff --git a/src/mol-data/model/properties/format-specific.ts b/src/mol-data/structure/model/properties/format-specific.ts
similarity index 100%
rename from src/mol-data/model/properties/format-specific.ts
rename to src/mol-data/structure/model/properties/format-specific.ts
diff --git a/src/mol-data/model/properties/hierarchy.ts b/src/mol-data/structure/model/properties/hierarchy.ts
similarity index 91%
rename from src/mol-data/model/properties/hierarchy.ts
rename to src/mol-data/structure/model/properties/hierarchy.ts
index e86fc8983..dceb055c4 100644
--- a/src/mol-data/model/properties/hierarchy.ts
+++ b/src/mol-data/structure/model/properties/hierarchy.ts
@@ -4,10 +4,10 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column from '../../../mol-base/collections/column'
-import Table from '../../../mol-base/collections/table'
-import { Segmentation } from '../../../mol-base/collections/integer'
-import { Schema as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
+import Column from '../../../../mol-base/collections/column'
+import Table from '../../../../mol-base/collections/table'
+import { Segmentation } from '../../../../mol-base/collections/integer'
+import { Schema as mmCIF } from '../../../../mol-io/reader/cif/schema/mmcif'
const _esCache = Object.create(null);
export interface ElementSymbol extends String { '@type': 'element-symbol' }
diff --git a/src/mol-data/model/properties/transforms.ts b/src/mol-data/structure/model/properties/transforms.ts
similarity index 100%
rename from src/mol-data/model/properties/transforms.ts
rename to src/mol-data/structure/model/properties/transforms.ts
diff --git a/src/mol-data/model/utils/hierarchy-keys.ts b/src/mol-data/structure/model/utils/hierarchy-keys.ts
similarity index 96%
rename from src/mol-data/model/utils/hierarchy-keys.ts
rename to src/mol-data/structure/model/utils/hierarchy-keys.ts
index 6bc5a4a8c..b99cec069 100644
--- a/src/mol-data/model/utils/hierarchy-keys.ts
+++ b/src/mol-data/structure/model/utils/hierarchy-keys.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Column from '../../../mol-base/collections/column'
+import Column from '../../../../mol-base/collections/column'
import { Data, Segments, Keys } from '../properties/hierarchy'
-import { Interval, Segmentation } from '../../../mol-base/collections/integer'
+import { Interval, Segmentation } from '../../../../mol-base/collections/integer'
function getResidueId(comp_id: string, seq_id: number, ins_code: string) {
return `${comp_id} ${seq_id} ${ins_code}`;
diff --git a/src/mol-data/query.ts b/src/mol-data/structure/query.ts
similarity index 100%
rename from src/mol-data/query.ts
rename to src/mol-data/structure/query.ts
diff --git a/src/mol-data/query/generators.ts b/src/mol-data/structure/query/generators.ts
similarity index 97%
rename from src/mol-data/query/generators.ts
rename to src/mol-data/structure/query/generators.ts
index d90d9c3b9..a647260f6 100644
--- a/src/mol-data/query/generators.ts
+++ b/src/mol-data/structure/query/generators.ts
@@ -8,7 +8,7 @@ import Query from './query'
//import Selection from './selection'
import * as P from './properties'
import { AtomSet, Atom } from '../structure'
-import { OrderedSet } from '../../mol-base/collections/integer'
+import { OrderedSet } from '../../../mol-base/collections/integer'
export interface AtomGroupsSpec {
entityTest: Atom.Predicate,
diff --git a/src/mol-data/query/properties.ts b/src/mol-data/structure/query/properties.ts
similarity index 100%
rename from src/mol-data/query/properties.ts
rename to src/mol-data/structure/query/properties.ts
diff --git a/src/mol-data/query/query.ts b/src/mol-data/structure/query/query.ts
similarity index 100%
rename from src/mol-data/query/query.ts
rename to src/mol-data/structure/query/query.ts
diff --git a/src/mol-data/query/selection.ts b/src/mol-data/structure/query/selection.ts
similarity index 96%
rename from src/mol-data/query/selection.ts
rename to src/mol-data/structure/query/selection.ts
index d2ef57dff..8e46f0f36 100644
--- a/src/mol-data/query/selection.ts
+++ b/src/mol-data/structure/query/selection.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Iterator from '../../mol-base/collections/iterator'
-import HashSet from '../../mol-base/collections/hash-set'
+import Iterator from '../../../mol-base/collections/iterator'
+import HashSet from '../../../mol-base/collections/hash-set'
import { Structure, Atom, AtomSet } from '../structure'
type Selection =
diff --git a/src/mol-data/structure/structure.ts b/src/mol-data/structure/structure.ts
index cc995ad2c..cc8bf49f3 100644
--- a/src/mol-data/structure/structure.ts
+++ b/src/mol-data/structure/structure.ts
@@ -4,55 +4,10 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Model } from '../model'
-import Unit from './unit'
-import Operator from './operator'
-import AtomSet from './atom/set'
-import { OrderedSet } from '../../mol-base/collections/integer'
+import Atom from './structure/atom'
+import AtomSet from './structure/atom/set'
+import Structure from './structure/structure'
+import Operator from './structure/operator'
+import Unit from './structure/unit'
-interface Structure extends Readonly<{
- units: { readonly [id: number]: Unit },
- atoms: AtomSet
-}> { }
-
-namespace Structure {
- export const Empty = { units: {}, atoms: AtomSet.Empty };
-
- export function ofModel(model: Model): Structure {
- const chains = model.hierarchy.chainSegments;
- const builder = Builder();
-
- for (let c = 0; c < chains.count; c++) {
- const unit = Unit.create(model, Operator.Identity);
- builder.addUnit(unit);
- builder.addAtoms(unit.id, OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
- }
-
- return builder.getStructure();
- }
-
- export interface Builder {
- addUnit(unit: Unit): void,
- addAtoms(unitId: number, atoms: OrderedSet): void,
- getStructure(): Structure,
- readonly atomCount: number
- }
-
- class BuilderImpl implements Builder {
- private units = Object.create(null);
- private atoms = Object.create(null);
- atomCount = 0;
-
- addUnit(unit: Unit) { this.units[unit.id] = unit; }
- addAtoms(unitId: number, atoms: OrderedSet) { this.atoms[unitId] = atoms; this.atomCount += OrderedSet.size(atoms); }
- getStructure(): Structure { return this.atomCount > 0 ? { units: this.units, atoms: AtomSet.create(this.atoms) } : Empty; }
- }
-
- export function Builder(): Builder { return new BuilderImpl(); }
-
-
- // TODO: "lift" atom set operators?
- // TODO: "diff"
-}
-
-export default Structure
\ No newline at end of file
+export { Atom, AtomSet, Structure, Operator, Unit }
\ No newline at end of file
diff --git a/src/mol-data/structure/atom.ts b/src/mol-data/structure/structure/atom.ts
similarity index 95%
rename from src/mol-data/structure/atom.ts
rename to src/mol-data/structure/structure/atom.ts
index 34a38d169..ddce507fd 100644
--- a/src/mol-data/structure/atom.ts
+++ b/src/mol-data/structure/structure/atom.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Tuple } from '../../mol-base/collections/integer'
+import { Tuple } from '../../../mol-base/collections/integer'
import Unit from './unit'
import Structure from './structure'
diff --git a/src/mol-data/structure/atom/set.ts b/src/mol-data/structure/structure/atom/set.ts
similarity index 96%
rename from src/mol-data/structure/atom/set.ts
rename to src/mol-data/structure/structure/atom/set.ts
index 92a04dc70..25a77f423 100644
--- a/src/mol-data/structure/atom/set.ts
+++ b/src/mol-data/structure/structure/atom/set.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { OrderedSet, SortedArray, Iterator } from '../../../mol-base/collections/integer'
+import { OrderedSet, SortedArray, Iterator } from '../../../../mol-base/collections/integer'
import Atom from '../atom'
import * as Impl from './set/impl'
import createBuilder from './set/builder'
diff --git a/src/mol-data/structure/atom/set/builder.ts b/src/mol-data/structure/structure/atom/set/builder.ts
similarity index 93%
rename from src/mol-data/structure/atom/set/builder.ts
rename to src/mol-data/structure/structure/atom/set/builder.ts
index a1940c367..1e6c4beda 100644
--- a/src/mol-data/structure/atom/set/builder.ts
+++ b/src/mol-data/structure/structure/atom/set/builder.ts
@@ -5,8 +5,8 @@
*/
import AtomSet from '../set'
-import { OrderedSet } from '../../../../mol-base/collections/integer'
-import { sortArray } from '../../../../mol-base/collections/sort'
+import { OrderedSet } from '../../../../../mol-base/collections/integer'
+import { sortArray } from '../../../../../mol-base/collections/sort'
class Builder {
private keys: number[] = [];
diff --git a/src/mol-data/structure/atom/set/impl.ts b/src/mol-data/structure/structure/atom/set/impl.ts
similarity index 98%
rename from src/mol-data/structure/atom/set/impl.ts
rename to src/mol-data/structure/structure/atom/set/impl.ts
index fab4133aa..7f2f2d15f 100644
--- a/src/mol-data/structure/atom/set/impl.ts
+++ b/src/mol-data/structure/structure/atom/set/impl.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { SortedArray, Interval, Iterator, OrderedSet } from '../../../../mol-base/collections/integer'
-import { sortArray } from '../../../../mol-base/collections/sort'
-import { hash1 } from '../../../../mol-base/collections/hash-functions'
+import { SortedArray, Interval, Iterator, OrderedSet } from '../../../../../mol-base/collections/integer'
+import { sortArray } from '../../../../../mol-base/collections/sort'
+import { hash1 } from '../../../../../mol-base/collections/hash-functions'
import Atom from '../../atom'
/** Long and painful implementation starts here */
diff --git a/src/mol-data/structure/atom/set/properties.ts b/src/mol-data/structure/structure/atom/set/properties.ts
similarity index 100%
rename from src/mol-data/structure/atom/set/properties.ts
rename to src/mol-data/structure/structure/atom/set/properties.ts
diff --git a/src/mol-data/structure/operator.ts b/src/mol-data/structure/structure/operator.ts
similarity index 91%
rename from src/mol-data/structure/operator.ts
rename to src/mol-data/structure/structure/operator.ts
index 484dd7590..363331f27 100644
--- a/src/mol-data/structure/operator.ts
+++ b/src/mol-data/structure/structure/operator.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Mat4 } from '../../mol-base/math/linear-algebra'
+import { Mat4 } from '../../../mol-base/math/linear-algebra'
interface Operator extends Readonly<{
name: string,
diff --git a/src/mol-data/structure/structure/structure.ts b/src/mol-data/structure/structure/structure.ts
new file mode 100644
index 000000000..31e001a27
--- /dev/null
+++ b/src/mol-data/structure/structure/structure.ts
@@ -0,0 +1,58 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Model } from '../model'
+import Unit from './unit'
+import Operator from './operator'
+import AtomSet from './atom/set'
+import { OrderedSet } from '../../../mol-base/collections/integer'
+
+interface Structure extends Readonly<{
+ units: { readonly [id: number]: Unit },
+ atoms: AtomSet
+}> { }
+
+namespace Structure {
+ export const Empty = { units: {}, atoms: AtomSet.Empty };
+
+ export function ofModel(model: Model): Structure {
+ const chains = model.hierarchy.chainSegments;
+ const builder = Builder();
+
+ for (let c = 0; c < chains.count; c++) {
+ const unit = Unit.create(model, Operator.Identity);
+ builder.addUnit(unit);
+ builder.addAtoms(unit.id, OrderedSet.ofBounds(chains.segments[c], chains.segments[c + 1]));
+ }
+
+ return builder.getStructure();
+ }
+
+ export interface Builder {
+ addUnit(unit: Unit): void,
+ addAtoms(unitId: number, atoms: OrderedSet): void,
+ getStructure(): Structure,
+ readonly atomCount: number
+ }
+
+ class BuilderImpl implements Builder {
+ private units = Object.create(null);
+ private atoms = Object.create(null);
+ atomCount = 0;
+
+ addUnit(unit: Unit) { this.units[unit.id] = unit; }
+ addAtoms(unitId: number, atoms: OrderedSet) { this.atoms[unitId] = atoms; this.atomCount += OrderedSet.size(atoms); }
+ getStructure(): Structure { return this.atomCount > 0 ? { units: this.units, atoms: AtomSet.create(this.atoms) } : Empty; }
+ }
+
+ export function Builder(): Builder { return new BuilderImpl(); }
+
+
+ // TODO: "lift" atom set operators?
+ // TODO: "diff"
+}
+
+export default Structure
\ No newline at end of file
diff --git a/src/mol-data/structure/unit.ts b/src/mol-data/structure/structure/unit.ts
similarity index 100%
rename from src/mol-data/structure/unit.ts
rename to src/mol-data/structure/structure/unit.ts
diff --git a/src/mol-data/volume/TODO b/src/mol-data/volume/TODO
new file mode 100644
index 000000000..e69de29bb
diff --git a/src/perf-tests/sets.ts b/src/perf-tests/sets.ts
index e4f067085..b499ae2a3 100644
--- a/src/perf-tests/sets.ts
+++ b/src/perf-tests/sets.ts
@@ -1,6 +1,6 @@
import * as B from 'benchmark'
import { Tuple, Segmentation, OrderedSet as OrdSet } from '../mol-base/collections/integer'
-import { AtomSet } from '../mol-data/structure'
+import { AtomSet } from '../mol-data/structure/structure'
export namespace Iteration {
const U = 1000, V = 2500;
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index b066edf91..7da905f45 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -10,9 +10,9 @@ import * as util from 'util'
import * as fs from 'fs'
import CIF from '../mol-io/reader/cif'
-import { Model } from '../mol-data/Model'
-import { Structure, Atom, AtomSet } from '../mol-data/structure'
-import * as Q from '../mol-data/query'
+import { Model } from '../mol-data/structure/model'
+import { Structure, Atom, AtomSet } from '../mol-data/structure/structure'
+import * as Q from '../mol-data/structure/query'
import { OrderedSet as OrdSet, Segmentation } from '../mol-base/collections/integer'
require('util.promisify').shim();
diff --git a/src/script.ts b/src/script.ts
index e42be6c0b..7408e72ea 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -17,7 +17,7 @@ import CIF from './mol-io/reader/cif'
import Computation from './mol-base/computation'
-import buildModels from './mol-data/model/builders/mmcif'
+import buildModels from './mol-data/structure/model/builders/mmcif'
// import { toTypedFrame as applySchema } from './reader/cif/schema'
import { generateSchema } from './mol-io/reader/cif/schema/utils'
--
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