From 4efaf1c28b3006e8b53ca25a3a5497a94ede911e Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Tue, 7 Nov 2017 17:31:40 +0100
Subject: [PATCH] Module refactoring
---
src/apps/cif2bcif/converter.ts | 2 +-
src/apps/cif2bcif/field-classifier.ts | 2 +-
src/apps/domain-annotation-server/mapping.ts | 2 +-
src/apps/domain-annotation-server/schemas.ts | 2 +-
src/apps/domain-annotation-server/utils.ts | 4 +--
src/mol-base/utils/uuid.ts | 19 ----------
.../_spec/equiv-index.spec.ts | 2 +-
.../_spec/iterators.spec.ts | 0
.../_spec/sort.spec.ts | 2 +-
.../database.ts => mol-data/db.ts} | 8 ++---
.../db}/_spec/table.spec.ts | 0
.../db}/column-helpers.ts | 0
.../database => mol-data/db}/column.ts | 2 +-
.../database => mol-data/db}/database.ts | 0
.../database => mol-data/db}/table.ts | 2 +-
src/mol-data/index.ts | 12 +++++++
.../integer.ts => mol-data/int.ts} | 12 +++----
.../int}/_spec/interval.spec.ts | 0
.../int}/_spec/linked-index.spec.ts | 0
.../int}/_spec/ordered-set.spec.ts | 0
.../int}/_spec/segmentation.spec.ts | 0
.../int}/_spec/sorted-array.spec.ts | 0
.../int}/_spec/tuple.spec.ts | 0
.../integer => mol-data/int}/impl/interval.ts | 0
.../int}/impl/ordered-set.ts | 0
.../int}/impl/segmentation.ts | 0
.../int}/impl/sorted-array.ts | 3 +-
.../integer => mol-data/int}/interval.ts | 0
.../integer => mol-data/int}/linked-index.ts | 0
.../integer => mol-data/int}/ordered-set.ts | 0
.../integer => mol-data/int}/segmentation.ts | 0
.../integer => mol-data/int}/sorted-array.ts | 0
.../integer => mol-data/int}/tuple.ts | 2 +-
.../collections => mol-data}/iterator.ts | 0
src/mol-data/util.ts | 15 ++++++++
.../util}/chunked-array.ts | 0
.../util}/equivalence-classes.ts | 0
.../util}/hash-functions.ts | 0
.../collections => mol-data/util}/hash-set.ts | 0
.../collections => mol-data/util}/sort.ts | 0
.../util}/unique-array.ts | 0
src/mol-io/common/binary-cif/array-encoder.ts | 2 +-
src/mol-io/reader/_spec/cif.spec.ts | 2 +-
src/mol-io/reader/_spec/column.spec.ts | 2 +-
src/mol-io/reader/cif/binary/field.ts | 2 +-
src/mol-io/reader/cif/binary/parser.ts | 2 +-
src/mol-io/reader/cif/data-model.ts | 4 +--
src/mol-io/reader/cif/schema.ts | 2 +-
src/mol-io/reader/cif/schema/dic.ts | 2 +-
src/mol-io/reader/cif/schema/mmcif.ts | 2 +-
src/mol-io/reader/cif/text/field.ts | 2 +-
src/mol-io/reader/cif/text/parser.ts | 2 +-
src/mol-io/reader/common/text/column/fixed.ts | 2 +-
src/mol-io/reader/common/text/column/token.ts | 2 +-
src/mol-io/reader/common/text/tokenizer.ts | 2 +-
src/mol-io/reader/gro/parser.ts | 4 +--
src/mol-io/reader/gro/schema.d.ts | 2 +-
src/mol-io/reader/mol2/schema.d.ts | 2 +-
src/mol-io/writer/cif/encoder.ts | 4 +--
src/mol-io/writer/cif/encoder/binary.ts | 4 +--
src/mol-io/writer/cif/encoder/text.ts | 4 +--
.../geometry/grid-lookup.ts | 0
src/{mol-base => mol-math}/geometry/sphere.ts | 0
.../geometry/transform.ts | 2 +-
src/{mol-base => mol-math}/graph/graph.ts | 0
src/mol-math/linear-algebra.ts | 8 +++++
.../linear-algebra/3d.ts} | 11 +++---
.../linear-algebra}/_spec/tensor.spec.ts | 4 +--
.../linear-algebra}/tensor.ts | 36 ++++++++++++++++---
src/{mol-data => mol-model}/sequence/TODO | 0
src/{mol-data => mol-model}/structure.ts | 0
.../structure/_spec/atom-set.spec.ts | 2 +-
.../structure/export/mmcif.ts | 4 +--
.../structure/model.ts | 0
.../structure/model/format.ts | 0
.../structure/model/formats/mmcif.ts | 10 +++---
.../structure/model/model.ts | 2 +-
.../structure/model/properties/computed.ts | 0
.../model/properties/conformation.ts | 4 +--
.../model/properties/format-specific.ts | 0
.../structure/model/properties/hierarchy.ts | 4 +--
.../structure/model/properties/transforms.ts | 0
.../structure/model/types.ts | 2 +-
.../structure/model/utils/hierarchy-keys.ts | 4 +--
.../structure/query.ts | 0
.../structure/query/generators.ts | 2 +-
.../structure/query/predicates.ts | 0
.../structure/query/properties.ts | 0
.../structure/query/query.ts | 0
.../structure/query/selection.ts | 4 +--
.../structure/structure.ts | 0
.../structure/structure/atom.ts | 2 +-
.../structure/structure/atom/set.ts | 2 +-
.../structure/structure/atom/set/builder.ts | 4 +--
.../structure/structure/atom/set/impl.ts | 6 ++--
.../structure/atom/set/properties.ts | 0
.../structure/structure/operator.ts | 2 +-
.../structure/structure/structure.ts | 4 +--
.../structure/structure/unit.ts | 2 +-
src/{mol-data => mol-model}/volume/TODO | 0
.../_spec/string-builder.spec.ts | 0
src/{mol-base/utils => mol-util}/bit-flags.ts | 0
src/{mol-base => mol-util}/computation.ts | 4 +--
src/mol-util/index.ts | 14 ++++++++
src/{mol-base/utils => mol-util}/scheduler.ts | 0
.../utils => mol-util}/string-builder.ts | 0
src/{mol-base/utils => mol-util}/time.ts | 0
src/mol-util/uuid.ts | 23 ++++++++++++
src/perf-tests/chunked-array-vs-native.ts | 2 +-
src/perf-tests/cif-encoder.ts | 2 +-
src/perf-tests/column.ts | 2 +-
src/perf-tests/iterators.ts | 2 +-
src/perf-tests/sets.ts | 4 +--
src/perf-tests/sort.ts | 2 +-
src/perf-tests/string-builder.ts | 2 +-
src/perf-tests/structure.ts | 6 ++--
src/script.ts | 4 +--
tsconfig.json | 8 +++--
118 files changed, 210 insertions(+), 127 deletions(-)
delete mode 100644 src/mol-base/utils/uuid.ts
rename src/{mol-base/collections => mol-data}/_spec/equiv-index.spec.ts (89%)
rename src/{mol-base/collections => mol-data}/_spec/iterators.spec.ts (100%)
rename src/{mol-base/collections => mol-data}/_spec/sort.spec.ts (98%)
rename src/{mol-base/collections/database.ts => mol-data/db.ts} (53%)
rename src/{mol-base/collections/database => mol-data/db}/_spec/table.spec.ts (100%)
rename src/{mol-base/collections/database => mol-data/db}/column-helpers.ts (100%)
rename src/{mol-base/collections/database => mol-data/db}/column.ts (99%)
rename src/{mol-base/collections/database => mol-data/db}/database.ts (100%)
rename src/{mol-base/collections/database => mol-data/db}/table.ts (99%)
create mode 100644 src/mol-data/index.ts
rename src/{mol-base/collections/integer.ts => mol-data/int.ts} (50%)
rename src/{mol-base/collections/integer => mol-data/int}/_spec/interval.spec.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/_spec/linked-index.spec.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/_spec/ordered-set.spec.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/_spec/segmentation.spec.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/_spec/sorted-array.spec.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/_spec/tuple.spec.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/impl/interval.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/impl/ordered-set.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/impl/segmentation.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/impl/sorted-array.ts (99%)
rename src/{mol-base/collections/integer => mol-data/int}/interval.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/linked-index.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/ordered-set.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/segmentation.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/sorted-array.ts (100%)
rename src/{mol-base/collections/integer => mol-data/int}/tuple.ts (98%)
rename src/{mol-base/collections => mol-data}/iterator.ts (100%)
create mode 100644 src/mol-data/util.ts
rename src/{mol-base/collections => mol-data/util}/chunked-array.ts (100%)
rename src/{mol-base/collections => mol-data/util}/equivalence-classes.ts (100%)
rename src/{mol-base/collections => mol-data/util}/hash-functions.ts (100%)
rename src/{mol-base/collections => mol-data/util}/hash-set.ts (100%)
rename src/{mol-base/collections => mol-data/util}/sort.ts (100%)
rename src/{mol-base/collections => mol-data/util}/unique-array.ts (100%)
rename src/{mol-base => mol-math}/geometry/grid-lookup.ts (100%)
rename src/{mol-base => mol-math}/geometry/sphere.ts (100%)
rename src/{mol-base => mol-math}/geometry/transform.ts (91%)
rename src/{mol-base => mol-math}/graph/graph.ts (100%)
create mode 100644 src/mol-math/linear-algebra.ts
rename src/{mol-base/math/linear-algebra-3d.ts => mol-math/linear-algebra/3d.ts} (98%)
rename src/{mol-base/math => mol-math/linear-algebra}/_spec/tensor.spec.ts (98%)
rename src/{mol-base/math => mol-math/linear-algebra}/tensor.ts (82%)
rename src/{mol-data => mol-model}/sequence/TODO (100%)
rename src/{mol-data => mol-model}/structure.ts (100%)
rename src/{mol-data => mol-model}/structure/_spec/atom-set.spec.ts (99%)
rename src/{mol-data => mol-model}/structure/export/mmcif.ts (98%)
rename src/{mol-data => mol-model}/structure/model.ts (100%)
rename src/{mol-data => mol-model}/structure/model/format.ts (100%)
rename src/{mol-data => mol-model}/structure/model/formats/mmcif.ts (96%)
rename src/{mol-data => mol-model}/structure/model/model.ts (95%)
rename src/{mol-data => mol-model}/structure/model/properties/computed.ts (100%)
rename src/{mol-data => mol-model}/structure/model/properties/conformation.ts (88%)
rename src/{mol-data => mol-model}/structure/model/properties/format-specific.ts (100%)
rename src/{mol-data => mol-model}/structure/model/properties/hierarchy.ts (95%)
rename src/{mol-data => mol-model}/structure/model/properties/transforms.ts (100%)
rename src/{mol-data => mol-model}/structure/model/types.ts (99%)
rename src/{mol-data => mol-model}/structure/model/utils/hierarchy-keys.ts (97%)
rename src/{mol-data => mol-model}/structure/query.ts (100%)
rename src/{mol-data => mol-model}/structure/query/generators.ts (99%)
rename src/{mol-data => mol-model}/structure/query/predicates.ts (100%)
rename src/{mol-data => mol-model}/structure/query/properties.ts (100%)
rename src/{mol-data => mol-model}/structure/query/query.ts (100%)
rename src/{mol-data => mol-model}/structure/query/selection.ts (97%)
rename src/{mol-data => mol-model}/structure/structure.ts (100%)
rename src/{mol-data => mol-model}/structure/structure/atom.ts (96%)
rename src/{mol-data => mol-model}/structure/structure/atom/set.ts (96%)
rename src/{mol-data => mol-model}/structure/structure/atom/set/builder.ts (95%)
rename src/{mol-data => mol-model}/structure/structure/atom/set/impl.ts (99%)
rename src/{mol-data => mol-model}/structure/structure/atom/set/properties.ts (100%)
rename src/{mol-data => mol-model}/structure/structure/operator.ts (91%)
rename src/{mol-data => mol-model}/structure/structure/structure.ts (95%)
rename src/{mol-data => mol-model}/structure/structure/unit.ts (98%)
rename src/{mol-data => mol-model}/volume/TODO (100%)
rename src/{mol-base/utils => mol-util}/_spec/string-builder.spec.ts (100%)
rename src/{mol-base/utils => mol-util}/bit-flags.ts (100%)
rename src/{mol-base => mol-util}/computation.ts (99%)
create mode 100644 src/mol-util/index.ts
rename src/{mol-base/utils => mol-util}/scheduler.ts (100%)
rename src/{mol-base/utils => mol-util}/string-builder.ts (100%)
rename src/{mol-base/utils => mol-util}/time.ts (100%)
create mode 100644 src/mol-util/uuid.ts
diff --git a/src/apps/cif2bcif/converter.ts b/src/apps/cif2bcif/converter.ts
index 5083500e4..b663a301e 100644
--- a/src/apps/cif2bcif/converter.ts
+++ b/src/apps/cif2bcif/converter.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Iterator from 'mol-base/collections/iterator'
+import Iterator from 'mol-data/iterator'
import CIF, { Category } from 'mol-io/reader/cif'
import * as Encoder from 'mol-io/writer/cif'
import * as fs from 'fs'
diff --git a/src/apps/cif2bcif/field-classifier.ts b/src/apps/cif2bcif/field-classifier.ts
index 0fe447382..145cdc6f9 100644
--- a/src/apps/cif2bcif/field-classifier.ts
+++ b/src/apps/cif2bcif/field-classifier.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-base/collections/database'
+import { Column } from 'mol-data/db'
import { Field } from 'mol-io/reader/cif/data-model'
import { FieldDefinition, FieldType } from 'mol-io/writer/cif/encoder'
diff --git a/src/apps/domain-annotation-server/mapping.ts b/src/apps/domain-annotation-server/mapping.ts
index 419e4c270..da87d9b46 100644
--- a/src/apps/domain-annotation-server/mapping.ts
+++ b/src/apps/domain-annotation-server/mapping.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Table } from 'mol-base/collections/database'
+import { Table } from 'mol-data/db'
import { CIFEncoder, create as createEncoder } from 'mol-io/writer/cif'
import * as S from './schemas'
import { getCategoryInstanceProvider } from './utils'
diff --git a/src/apps/domain-annotation-server/schemas.ts b/src/apps/domain-annotation-server/schemas.ts
index 90bbcba97..e6caffdac 100644
--- a/src/apps/domain-annotation-server/schemas.ts
+++ b/src/apps/domain-annotation-server/schemas.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-base/collections/database'
+import { Column } from 'mol-data/db'
import Type = Column.Schema
diff --git a/src/apps/domain-annotation-server/utils.ts b/src/apps/domain-annotation-server/utils.ts
index 767de8fa4..7c3e91b2a 100644
--- a/src/apps/domain-annotation-server/utils.ts
+++ b/src/apps/domain-annotation-server/utils.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Table } from 'mol-base/collections/database'
-import Iterator from 'mol-base/collections/iterator'
+import { Table } from 'mol-data/db'
+import Iterator from 'mol-data/iterator'
import * as Encoder from 'mol-io/writer/cif'
function columnValue(k: string) {
diff --git a/src/mol-base/utils/uuid.ts b/src/mol-base/utils/uuid.ts
deleted file mode 100644
index 29c7d24de..000000000
--- a/src/mol-base/utils/uuid.ts
+++ /dev/null
@@ -1,19 +0,0 @@
-/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import now from './time'
-
-export default interface UUID extends String { '@type': 'uuid' }
-
-export function newUUID(): UUID {
- let d = (+new Date()) + now();
- const uuid = 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'.replace(/[xy]/g, function(c) {
- const r = (d + Math.random()*16)%16 | 0;
- d = Math.floor(d/16);
- return (c==='x' ? r : (r&0x3|0x8)).toString(16);
- });
- return uuid as any;
-}
\ No newline at end of file
diff --git a/src/mol-base/collections/_spec/equiv-index.spec.ts b/src/mol-data/_spec/equiv-index.spec.ts
similarity index 89%
rename from src/mol-base/collections/_spec/equiv-index.spec.ts
rename to src/mol-data/_spec/equiv-index.spec.ts
index d2d0a2856..9083c0145 100644
--- a/src/mol-base/collections/_spec/equiv-index.spec.ts
+++ b/src/mol-data/_spec/equiv-index.spec.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import EquivalenceClasses from '../equivalence-classes'
+import EquivalenceClasses from '../util/equivalence-classes'
describe('equiv-classes', () => {
it('integer mod classes', () => {
diff --git a/src/mol-base/collections/_spec/iterators.spec.ts b/src/mol-data/_spec/iterators.spec.ts
similarity index 100%
rename from src/mol-base/collections/_spec/iterators.spec.ts
rename to src/mol-data/_spec/iterators.spec.ts
diff --git a/src/mol-base/collections/_spec/sort.spec.ts b/src/mol-data/_spec/sort.spec.ts
similarity index 98%
rename from src/mol-base/collections/_spec/sort.spec.ts
rename to src/mol-data/_spec/sort.spec.ts
index 4bccb03cb..9d2a122cc 100644
--- a/src/mol-base/collections/_spec/sort.spec.ts
+++ b/src/mol-data/_spec/sort.spec.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import * as Sort from '../sort'
+import * as Sort from '../util/sort'
function shuffle<T>(data: T, len: number, clone: (s: T) => T, swap: Sort.Swapper = Sort.arraySwap) {
const a = clone(data);
diff --git a/src/mol-base/collections/database.ts b/src/mol-data/db.ts
similarity index 53%
rename from src/mol-base/collections/database.ts
rename to src/mol-data/db.ts
index 78818f8d8..367b533a0 100644
--- a/src/mol-base/collections/database.ts
+++ b/src/mol-data/db.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Database from './database/database'
-import Table from './database/table'
-import Column from './database/column'
-import * as ColumnHelpers from './database/column-helpers'
+import Database from './db/database'
+import Table from './db/table'
+import Column from './db/column'
+import * as ColumnHelpers from './db/column-helpers'
export { Database, Table, Column, ColumnHelpers }
\ No newline at end of file
diff --git a/src/mol-base/collections/database/_spec/table.spec.ts b/src/mol-data/db/_spec/table.spec.ts
similarity index 100%
rename from src/mol-base/collections/database/_spec/table.spec.ts
rename to src/mol-data/db/_spec/table.spec.ts
diff --git a/src/mol-base/collections/database/column-helpers.ts b/src/mol-data/db/column-helpers.ts
similarity index 100%
rename from src/mol-base/collections/database/column-helpers.ts
rename to src/mol-data/db/column-helpers.ts
diff --git a/src/mol-base/collections/database/column.ts b/src/mol-data/db/column.ts
similarity index 99%
rename from src/mol-base/collections/database/column.ts
rename to src/mol-data/db/column.ts
index 4a373652b..484411e6f 100644
--- a/src/mol-base/collections/database/column.ts
+++ b/src/mol-data/db/column.ts
@@ -5,7 +5,7 @@
*/
import * as ColumnHelpers from './column-helpers'
-import Tensors from '../../math/tensor'
+import { Tensor as Tensors } from 'mol-math/linear-algebra'
interface Column<T> {
readonly '@type': Column.Type,
diff --git a/src/mol-base/collections/database/database.ts b/src/mol-data/db/database.ts
similarity index 100%
rename from src/mol-base/collections/database/database.ts
rename to src/mol-data/db/database.ts
diff --git a/src/mol-base/collections/database/table.ts b/src/mol-data/db/table.ts
similarity index 99%
rename from src/mol-base/collections/database/table.ts
rename to src/mol-data/db/table.ts
index a7178bc1c..65b7bd172 100644
--- a/src/mol-base/collections/database/table.ts
+++ b/src/mol-data/db/table.ts
@@ -5,7 +5,7 @@
*/
import Column from './column'
-import { sortArray } from '../sort'
+import { sortArray } from '../util/sort'
/** A collection of columns */
type Table<Schema extends Table.Schema> = {
diff --git a/src/mol-data/index.ts b/src/mol-data/index.ts
new file mode 100644
index 000000000..1db90c26e
--- /dev/null
+++ b/src/mol-data/index.ts
@@ -0,0 +1,12 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as DB from './db'
+import * as Int from './int'
+import Iterator from './iterator'
+import * as Util from './util'
+
+export { DB, Int, Iterator, Util }
\ No newline at end of file
diff --git a/src/mol-base/collections/integer.ts b/src/mol-data/int.ts
similarity index 50%
rename from src/mol-base/collections/integer.ts
rename to src/mol-data/int.ts
index 1abd46acc..54c2795bb 100644
--- a/src/mol-base/collections/integer.ts
+++ b/src/mol-data/int.ts
@@ -4,12 +4,12 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Interval from './integer/interval'
-import OrderedSet from './integer/ordered-set'
-import Segmentation from './integer/segmentation'
-import SortedArray from './integer/sorted-array'
-import Tuple from './integer/tuple'
-import LinkedIndex from './integer/linked-index'
+import Interval from './int/interval'
+import OrderedSet from './int/ordered-set'
+import Segmentation from './int/segmentation'
+import SortedArray from './int/sorted-array'
+import Tuple from './int/tuple'
+import LinkedIndex from './int/linked-index'
import Iterator from './iterator'
export { Interval, OrderedSet, Segmentation, SortedArray, Tuple, LinkedIndex, Iterator }
\ No newline at end of file
diff --git a/src/mol-base/collections/integer/_spec/interval.spec.ts b/src/mol-data/int/_spec/interval.spec.ts
similarity index 100%
rename from src/mol-base/collections/integer/_spec/interval.spec.ts
rename to src/mol-data/int/_spec/interval.spec.ts
diff --git a/src/mol-base/collections/integer/_spec/linked-index.spec.ts b/src/mol-data/int/_spec/linked-index.spec.ts
similarity index 100%
rename from src/mol-base/collections/integer/_spec/linked-index.spec.ts
rename to src/mol-data/int/_spec/linked-index.spec.ts
diff --git a/src/mol-base/collections/integer/_spec/ordered-set.spec.ts b/src/mol-data/int/_spec/ordered-set.spec.ts
similarity index 100%
rename from src/mol-base/collections/integer/_spec/ordered-set.spec.ts
rename to src/mol-data/int/_spec/ordered-set.spec.ts
diff --git a/src/mol-base/collections/integer/_spec/segmentation.spec.ts b/src/mol-data/int/_spec/segmentation.spec.ts
similarity index 100%
rename from src/mol-base/collections/integer/_spec/segmentation.spec.ts
rename to src/mol-data/int/_spec/segmentation.spec.ts
diff --git a/src/mol-base/collections/integer/_spec/sorted-array.spec.ts b/src/mol-data/int/_spec/sorted-array.spec.ts
similarity index 100%
rename from src/mol-base/collections/integer/_spec/sorted-array.spec.ts
rename to src/mol-data/int/_spec/sorted-array.spec.ts
diff --git a/src/mol-base/collections/integer/_spec/tuple.spec.ts b/src/mol-data/int/_spec/tuple.spec.ts
similarity index 100%
rename from src/mol-base/collections/integer/_spec/tuple.spec.ts
rename to src/mol-data/int/_spec/tuple.spec.ts
diff --git a/src/mol-base/collections/integer/impl/interval.ts b/src/mol-data/int/impl/interval.ts
similarity index 100%
rename from src/mol-base/collections/integer/impl/interval.ts
rename to src/mol-data/int/impl/interval.ts
diff --git a/src/mol-base/collections/integer/impl/ordered-set.ts b/src/mol-data/int/impl/ordered-set.ts
similarity index 100%
rename from src/mol-base/collections/integer/impl/ordered-set.ts
rename to src/mol-data/int/impl/ordered-set.ts
diff --git a/src/mol-base/collections/integer/impl/segmentation.ts b/src/mol-data/int/impl/segmentation.ts
similarity index 100%
rename from src/mol-base/collections/integer/impl/segmentation.ts
rename to src/mol-data/int/impl/segmentation.ts
diff --git a/src/mol-base/collections/integer/impl/sorted-array.ts b/src/mol-data/int/impl/sorted-array.ts
similarity index 99%
rename from src/mol-base/collections/integer/impl/sorted-array.ts
rename to src/mol-data/int/impl/sorted-array.ts
index fe0d90565..f3147c708 100644
--- a/src/mol-base/collections/integer/impl/sorted-array.ts
+++ b/src/mol-data/int/impl/sorted-array.ts
@@ -4,8 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { sortArray } from '../../sort'
-import { hash3, hash4 } from '../../hash-functions'
+import { sortArray, hash3, hash4 } from '../../util'
import Interval from '../interval'
type Nums = ArrayLike<number>
diff --git a/src/mol-base/collections/integer/interval.ts b/src/mol-data/int/interval.ts
similarity index 100%
rename from src/mol-base/collections/integer/interval.ts
rename to src/mol-data/int/interval.ts
diff --git a/src/mol-base/collections/integer/linked-index.ts b/src/mol-data/int/linked-index.ts
similarity index 100%
rename from src/mol-base/collections/integer/linked-index.ts
rename to src/mol-data/int/linked-index.ts
diff --git a/src/mol-base/collections/integer/ordered-set.ts b/src/mol-data/int/ordered-set.ts
similarity index 100%
rename from src/mol-base/collections/integer/ordered-set.ts
rename to src/mol-data/int/ordered-set.ts
diff --git a/src/mol-base/collections/integer/segmentation.ts b/src/mol-data/int/segmentation.ts
similarity index 100%
rename from src/mol-base/collections/integer/segmentation.ts
rename to src/mol-data/int/segmentation.ts
diff --git a/src/mol-base/collections/integer/sorted-array.ts b/src/mol-data/int/sorted-array.ts
similarity index 100%
rename from src/mol-base/collections/integer/sorted-array.ts
rename to src/mol-data/int/sorted-array.ts
diff --git a/src/mol-base/collections/integer/tuple.ts b/src/mol-data/int/tuple.ts
similarity index 98%
rename from src/mol-base/collections/integer/tuple.ts
rename to src/mol-data/int/tuple.ts
index 86cf4ea6b..7967f45cf 100644
--- a/src/mol-base/collections/integer/tuple.ts
+++ b/src/mol-data/int/tuple.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { hash2 } from '../hash-functions'
+import { hash2 } from '../util'
/**
* Represents a pair of two integers as a double,
diff --git a/src/mol-base/collections/iterator.ts b/src/mol-data/iterator.ts
similarity index 100%
rename from src/mol-base/collections/iterator.ts
rename to src/mol-data/iterator.ts
diff --git a/src/mol-data/util.ts b/src/mol-data/util.ts
new file mode 100644
index 000000000..ab0c73fcf
--- /dev/null
+++ b/src/mol-data/util.ts
@@ -0,0 +1,15 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import ChunkedArray from './util/chunked-array'
+import EquivalenceClasses from './util/chunked-array'
+import HashSet from './util/hash-set'
+import UniqueArray from './util/unique-array'
+
+export * from './util/hash-functions'
+export * from './util/sort'
+
+export { ChunkedArray, EquivalenceClasses, HashSet, UniqueArray }
\ No newline at end of file
diff --git a/src/mol-base/collections/chunked-array.ts b/src/mol-data/util/chunked-array.ts
similarity index 100%
rename from src/mol-base/collections/chunked-array.ts
rename to src/mol-data/util/chunked-array.ts
diff --git a/src/mol-base/collections/equivalence-classes.ts b/src/mol-data/util/equivalence-classes.ts
similarity index 100%
rename from src/mol-base/collections/equivalence-classes.ts
rename to src/mol-data/util/equivalence-classes.ts
diff --git a/src/mol-base/collections/hash-functions.ts b/src/mol-data/util/hash-functions.ts
similarity index 100%
rename from src/mol-base/collections/hash-functions.ts
rename to src/mol-data/util/hash-functions.ts
diff --git a/src/mol-base/collections/hash-set.ts b/src/mol-data/util/hash-set.ts
similarity index 100%
rename from src/mol-base/collections/hash-set.ts
rename to src/mol-data/util/hash-set.ts
diff --git a/src/mol-base/collections/sort.ts b/src/mol-data/util/sort.ts
similarity index 100%
rename from src/mol-base/collections/sort.ts
rename to src/mol-data/util/sort.ts
diff --git a/src/mol-base/collections/unique-array.ts b/src/mol-data/util/unique-array.ts
similarity index 100%
rename from src/mol-base/collections/unique-array.ts
rename to src/mol-data/util/unique-array.ts
diff --git a/src/mol-io/common/binary-cif/array-encoder.ts b/src/mol-io/common/binary-cif/array-encoder.ts
index 13f70f180..344171b8a 100644
--- a/src/mol-io/common/binary-cif/array-encoder.ts
+++ b/src/mol-io/common/binary-cif/array-encoder.ts
@@ -7,7 +7,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import ChunkedArray from 'mol-base/collections/chunked-array'
+import ChunkedArray from 'mol-data/util/chunked-array'
import { Encoding, EncodedData } from './encoding'
export interface ArrayEncoder {
diff --git a/src/mol-io/reader/_spec/cif.spec.ts b/src/mol-io/reader/_spec/cif.spec.ts
index 856e1e16f..90fae982a 100644
--- a/src/mol-io/reader/_spec/cif.spec.ts
+++ b/src/mol-io/reader/_spec/cif.spec.ts
@@ -7,7 +7,7 @@
import * as Data from '../cif/data-model'
import TextField from '../cif/text/field'
import * as Schema from '../cif/schema'
-import { Column } from 'mol-base/collections/database'
+import { Column } from 'mol-data/db'
const columnData = `123abc`;
diff --git a/src/mol-io/reader/_spec/column.spec.ts b/src/mol-io/reader/_spec/column.spec.ts
index f7df7dfc8..e9e31ca99 100644
--- a/src/mol-io/reader/_spec/column.spec.ts
+++ b/src/mol-io/reader/_spec/column.spec.ts
@@ -7,7 +7,7 @@
import FixedColumn from '../common/text/column/fixed'
import TokenColumn from '../common/text/column/token'
-import { Column, ColumnHelpers } from 'mol-base/collections/database'
+import { Column, ColumnHelpers } from 'mol-data/db'
const lines = [
'1.123 abc',
diff --git a/src/mol-io/reader/cif/binary/field.ts b/src/mol-io/reader/cif/binary/field.ts
index 5847e0ab3..89e2c47af 100644
--- a/src/mol-io/reader/cif/binary/field.ts
+++ b/src/mol-io/reader/cif/binary/field.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, ColumnHelpers } from 'mol-base/collections/database'
+import { Column, ColumnHelpers } from 'mol-data/db'
import * as Data from '../data-model'
import { EncodedColumn, decode } from '../../../common/binary-cif'
import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../../common/text/number-parser'
diff --git a/src/mol-io/reader/cif/binary/parser.ts b/src/mol-io/reader/cif/binary/parser.ts
index c72a9f438..4f1b705eb 100644
--- a/src/mol-io/reader/cif/binary/parser.ts
+++ b/src/mol-io/reader/cif/binary/parser.ts
@@ -9,7 +9,7 @@ import { EncodedCategory, EncodedFile } from '../../../common/binary-cif'
import Field from './field'
import Result from '../../result'
import decodeMsgPack from '../../../common/msgpack/decode'
-import Computation from 'mol-base/computation'
+import Computation from 'mol-util/computation'
function checkVersions(min: number[], current: number[]) {
for (let i = 0; i < 2; i++) {
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index 75805537f..417692342 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-base/collections/database'
-import Tensor from 'mol-base/math/tensor'
+import { Column } from 'mol-data/db'
+import { Tensor } from 'mol-math/linear-algebra'
export interface File {
readonly name?: string,
diff --git a/src/mol-io/reader/cif/schema.ts b/src/mol-io/reader/cif/schema.ts
index 441f4082c..ef0b3f5e2 100644
--- a/src/mol-io/reader/cif/schema.ts
+++ b/src/mol-io/reader/cif/schema.ts
@@ -5,7 +5,7 @@
*/
import * as Data from './data-model'
-import { Database, Table, Column, ColumnHelpers } from 'mol-base/collections/database'
+import { Database, Table, Column, ColumnHelpers } from 'mol-data/db'
export function toDatabase<Schema extends Database.Schema, Frame extends Database<Schema> = Database<Schema>>(schema: Schema, frame: Data.Frame): Frame {
return createDatabase(schema, frame) as Frame;
diff --git a/src/mol-io/reader/cif/schema/dic.ts b/src/mol-io/reader/cif/schema/dic.ts
index f9a934abd..48a73dd51 100644
--- a/src/mol-io/reader/cif/schema/dic.ts
+++ b/src/mol-io/reader/cif/schema/dic.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Database, Column } from 'mol-base/collections/database'
+import { Database, Column } from 'mol-data/db'
import Schema = Column.Schema
import FP = Schema.FP
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 59b31c101..5fec25ce3 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Database, Column } from 'mol-base/collections/database'
+import { Database, Column } from 'mol-data/db'
import Schema = Column.Schema
import FP = Schema.FP
diff --git a/src/mol-io/reader/cif/text/field.ts b/src/mol-io/reader/cif/text/field.ts
index 1628da3e4..6d1888494 100644
--- a/src/mol-io/reader/cif/text/field.ts
+++ b/src/mol-io/reader/cif/text/field.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, ColumnHelpers } from 'mol-base/collections/database'
+import { Column, ColumnHelpers } from 'mol-data/db'
import * as TokenColumn from '../../common/text/column/token'
import { Tokens } from '../../common/text/tokenizer'
import * as Data from '../data-model'
diff --git a/src/mol-io/reader/cif/text/parser.ts b/src/mol-io/reader/cif/text/parser.ts
index 0a3f13c24..064b014a9 100644
--- a/src/mol-io/reader/cif/text/parser.ts
+++ b/src/mol-io/reader/cif/text/parser.ts
@@ -26,7 +26,7 @@ import * as Data from '../data-model'
import Field from './field'
import { Tokens, TokenBuilder } from '../../common/text/tokenizer'
import Result from '../../result'
-import Computation from 'mol-base/computation'
+import Computation from 'mol-util/computation'
/**
* Types of supported mmCIF tokens.
diff --git a/src/mol-io/reader/common/text/column/fixed.ts b/src/mol-io/reader/common/text/column/fixed.ts
index d279f3f2e..5b094506a 100644
--- a/src/mol-io/reader/common/text/column/fixed.ts
+++ b/src/mol-io/reader/common/text/column/fixed.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, ColumnHelpers } from 'mol-base/collections/database'
+import { Column, ColumnHelpers } from 'mol-data/db'
import { trimStr, Tokens } from '../tokenizer'
import { parseIntSkipLeadingWhitespace, parseFloatSkipLeadingWhitespace } from '../number-parser'
diff --git a/src/mol-io/reader/common/text/column/token.ts b/src/mol-io/reader/common/text/column/token.ts
index e4dd79fe3..21d8afd06 100644
--- a/src/mol-io/reader/common/text/column/token.ts
+++ b/src/mol-io/reader/common/text/column/token.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, ColumnHelpers } from 'mol-base/collections/database'
+import { Column, ColumnHelpers } from 'mol-data/db'
import { Tokens } from '../tokenizer'
import { parseInt as fastParseInt, parseFloat as fastParseFloat } from '../number-parser'
diff --git a/src/mol-io/reader/common/text/tokenizer.ts b/src/mol-io/reader/common/text/tokenizer.ts
index d8ddc0746..55b310e5d 100644
--- a/src/mol-io/reader/common/text/tokenizer.ts
+++ b/src/mol-io/reader/common/text/tokenizer.ts
@@ -6,7 +6,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import Computation from 'mol-base/computation'
+import Computation from 'mol-util/computation'
export interface Tokenizer {
data: string,
diff --git a/src/mol-io/reader/gro/parser.ts b/src/mol-io/reader/gro/parser.ts
index 531a8b275..47e7ea192 100644
--- a/src/mol-io/reader/gro/parser.ts
+++ b/src/mol-io/reader/gro/parser.ts
@@ -5,12 +5,12 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-base/collections/database'
+import { Column } from 'mol-data/db'
import Tokenizer from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed'
import * as Schema from './schema'
import Result from '../result'
-import Computation from 'mol-base/computation'
+import Computation from 'mol-util/computation'
interface State {
tokenizer: Tokenizer,
diff --git a/src/mol-io/reader/gro/schema.d.ts b/src/mol-io/reader/gro/schema.d.ts
index bd871b6ff..9a0b1ca55 100644
--- a/src/mol-io/reader/gro/schema.d.ts
+++ b/src/mol-io/reader/gro/schema.d.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-base/collections/database'
+import { Column } from 'mol-data/db'
export interface Header {
title: string,
diff --git a/src/mol-io/reader/mol2/schema.d.ts b/src/mol-io/reader/mol2/schema.d.ts
index fbf458ce8..374b52d0d 100644
--- a/src/mol-io/reader/mol2/schema.d.ts
+++ b/src/mol-io/reader/mol2/schema.d.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Column } from 'mol-base/collections/database'
+import { Column } from 'mol-data/db'
// Full format http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
// there are many records but for now ignore (pass over) all but the following
diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index ed7b05418..548adbf99 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Iterator from 'mol-base/collections/iterator'
-import { Column } from 'mol-base/collections/database'
+import Iterator from 'mol-data/iterator'
+import { Column } from 'mol-data/db'
import Encoder from '../encoder'
// TODO: support for "coordinate fields", make "coordinate precision" a parameter of the encoder
diff --git a/src/mol-io/writer/cif/encoder/binary.ts b/src/mol-io/writer/cif/encoder/binary.ts
index 54968e5fb..581795963 100644
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -6,8 +6,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Iterator from 'mol-base/collections/iterator'
-import { Column } from 'mol-base/collections/database'
+import Iterator from 'mol-data/iterator'
+import { Column } from 'mol-data/db'
import encodeMsgPack from '../../../common/msgpack/encode'
import {
EncodedColumn, EncodedData, EncodedFile, EncodedDataBlock, EncodedCategory, ArrayEncoder, ArrayEncoding as E, VERSION
diff --git a/src/mol-io/writer/cif/encoder/text.ts b/src/mol-io/writer/cif/encoder/text.ts
index b07a54853..ef51b6424 100644
--- a/src/mol-io/writer/cif/encoder/text.ts
+++ b/src/mol-io/writer/cif/encoder/text.ts
@@ -6,8 +6,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-base/collections/database'
-import StringBuilder from 'mol-base/utils/string-builder'
+import { Column } from 'mol-data/db'
+import StringBuilder from 'mol-util/string-builder'
import * as Enc from '../encoder'
import Writer from '../../writer'
diff --git a/src/mol-base/geometry/grid-lookup.ts b/src/mol-math/geometry/grid-lookup.ts
similarity index 100%
rename from src/mol-base/geometry/grid-lookup.ts
rename to src/mol-math/geometry/grid-lookup.ts
diff --git a/src/mol-base/geometry/sphere.ts b/src/mol-math/geometry/sphere.ts
similarity index 100%
rename from src/mol-base/geometry/sphere.ts
rename to src/mol-math/geometry/sphere.ts
diff --git a/src/mol-base/geometry/transform.ts b/src/mol-math/geometry/transform.ts
similarity index 91%
rename from src/mol-base/geometry/transform.ts
rename to src/mol-math/geometry/transform.ts
index 4eb1d64c6..cf9aaa6d9 100644
--- a/src/mol-base/geometry/transform.ts
+++ b/src/mol-math/geometry/transform.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Mat4 } from '../math/linear-algebra-3d'
+import { Mat4 } from '../linear-algebra/3d'
interface Transform extends Readonly<{
transform: Mat4,
diff --git a/src/mol-base/graph/graph.ts b/src/mol-math/graph/graph.ts
similarity index 100%
rename from src/mol-base/graph/graph.ts
rename to src/mol-math/graph/graph.ts
diff --git a/src/mol-math/linear-algebra.ts b/src/mol-math/linear-algebra.ts
new file mode 100644
index 000000000..20ffdc270
--- /dev/null
+++ b/src/mol-math/linear-algebra.ts
@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export * from './linear-algebra/3d'
+export * from './linear-algebra/tensor'
\ No newline at end of file
diff --git a/src/mol-base/math/linear-algebra-3d.ts b/src/mol-math/linear-algebra/3d.ts
similarity index 98%
rename from src/mol-base/math/linear-algebra-3d.ts
rename to src/mol-math/linear-algebra/3d.ts
index 0f998a126..fccdb52b7 100644
--- a/src/mol-base/math/linear-algebra-3d.ts
+++ b/src/mol-math/linear-algebra/3d.ts
@@ -77,7 +77,7 @@ export namespace Mat4 {
mat[15] = 1;
return mat;
}
-
+
export function ofRows(rows: number[][]): Mat4 {
const out = zero();
for (let i = 0; i < 4; i++) {
@@ -89,11 +89,14 @@ export namespace Mat4 {
return out;
}
+ const _id = identity();
+ export function isIdentity(m: Mat4, eps?: number) {
+ return areEqual(m, _id, typeof eps === 'undefined' ? EPSILON.Value : eps);
+ }
+
export function areEqual(a: Mat4, b: Mat4, eps: number) {
for (let i = 0; i < 16; i++) {
- if (Math.abs(a[i] - b[i]) > eps) {
- return false;
- }
+ if (Math.abs(a[i] - b[i]) > eps) return false;
}
return true;
}
diff --git a/src/mol-base/math/_spec/tensor.spec.ts b/src/mol-math/linear-algebra/_spec/tensor.spec.ts
similarity index 98%
rename from src/mol-base/math/_spec/tensor.spec.ts
rename to src/mol-math/linear-algebra/_spec/tensor.spec.ts
index 0d4541121..7a1780d1d 100644
--- a/src/mol-base/math/_spec/tensor.spec.ts
+++ b/src/mol-math/linear-algebra/_spec/tensor.spec.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import T from '../tensor'
-import { Mat4 } from '../linear-algebra-3d'
+import { Tensor as T } from '../tensor'
+import { Mat4 } from '../3d'
describe('tensor', () => {
it('vector', () => {
diff --git a/src/mol-base/math/tensor.ts b/src/mol-math/linear-algebra/tensor.ts
similarity index 82%
rename from src/mol-base/math/tensor.ts
rename to src/mol-math/linear-algebra/tensor.ts
index d77c82b05..e5a872b9e 100644
--- a/src/mol-base/math/tensor.ts
+++ b/src/mol-math/linear-algebra/tensor.ts
@@ -4,9 +4,11 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-interface Tensor extends Array<number> { '@type': 'tensor' }
+import { Mat4, Vec3, Vec4 } from './3d'
-namespace Tensor {
+export interface Tensor extends Array<number> { '@type': 'tensor' }
+
+export namespace Tensor {
export type ArrayCtor = { new (size: number): ArrayLike<number> }
export interface Space {
@@ -47,6 +49,32 @@ namespace Tensor {
export function ColumnMajorMatrix(rows: number, cols: number, ctor?: ArrayCtor) { return Space([rows, cols], [1, 0], ctor); }
export function RowMajorMatrix(rows: number, cols: number, ctor?: ArrayCtor) { return Space([rows, cols], [0, 1], ctor); }
+ export function toMat4(space: Space, data: Tensor): Mat4 {
+ if (space.rank !== 2) throw new Error('Invalid tensor rank');
+ const mat = Mat4.zero();
+ const d0 = Math.min(4, space.dimensions[0]), d1 = Math.min(4, space.dimensions[1]);
+ for (let i = 0; i < d0; i++) {
+ for (let j = 0; j < d1; j++) Mat4.setValue(mat, i, j, space.get(data, i, j));
+ }
+ return mat;
+ }
+
+ export function toVec3(space: Space, data: Tensor): Vec3 {
+ if (space.rank !== 1) throw new Error('Invalid tensor rank');
+ const vec = Vec3.zero();
+ const d0 = Math.min(3, space.dimensions[0]);
+ for (let i = 0; i < d0; i++) vec[i] = data[i];
+ return vec;
+ }
+
+ export function toVec4(space: Space, data: Tensor): Vec4 {
+ if (space.rank !== 1) throw new Error('Invalid tensor rank');
+ const vec = Vec4.zero();
+ const d0 = Math.min(4, space.dimensions[0]);
+ for (let i = 0; i < d0; i++) vec[i] = data[i];
+ return vec;
+ }
+
function accessors(layout: Layout): { get: Space['get'], set: Space['set'] } {
const { dimensions, axisOrderFastToSlow: ao } = layout;
switch (dimensions.length) {
@@ -113,6 +141,4 @@ namespace Tensor {
}
return o;
}
-}
-
-export default Tensor
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-data/sequence/TODO b/src/mol-model/sequence/TODO
similarity index 100%
rename from src/mol-data/sequence/TODO
rename to src/mol-model/sequence/TODO
diff --git a/src/mol-data/structure.ts b/src/mol-model/structure.ts
similarity index 100%
rename from src/mol-data/structure.ts
rename to src/mol-model/structure.ts
diff --git a/src/mol-data/structure/_spec/atom-set.spec.ts b/src/mol-model/structure/_spec/atom-set.spec.ts
similarity index 99%
rename from src/mol-data/structure/_spec/atom-set.spec.ts
rename to src/mol-model/structure/_spec/atom-set.spec.ts
index 03ca32556..d77dd5e86 100644
--- a/src/mol-data/structure/_spec/atom-set.spec.ts
+++ b/src/mol-model/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-data/int'
import AtomSet from '../structure/atom/set'
import Atom from '../structure/atom'
diff --git a/src/mol-data/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
similarity index 98%
rename from src/mol-data/structure/export/mmcif.ts
rename to src/mol-model/structure/export/mmcif.ts
index 64d86d66c..c5cf31063 100644
--- a/src/mol-data/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, Table } from 'mol-base/collections/database'
-import Iterator from 'mol-base/collections/iterator'
+import { Column, Table } from 'mol-data/db'
+import Iterator from 'mol-data/iterator'
import * as Encoder from 'mol-io/writer/cif'
//import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif'
import { Structure, Atom, AtomSet } from '../structure'
diff --git a/src/mol-data/structure/model.ts b/src/mol-model/structure/model.ts
similarity index 100%
rename from src/mol-data/structure/model.ts
rename to src/mol-model/structure/model.ts
diff --git a/src/mol-data/structure/model/format.ts b/src/mol-model/structure/model/format.ts
similarity index 100%
rename from src/mol-data/structure/model/format.ts
rename to src/mol-model/structure/model/format.ts
diff --git a/src/mol-data/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
similarity index 96%
rename from src/mol-data/structure/model/formats/mmcif.ts
rename to src/mol-model/structure/model/formats/mmcif.ts
index 7c0d947e6..24b91ee40 100644
--- a/src/mol-data/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { newUUID } from 'mol-base/utils/uuid'
-import { Column, Table } from 'mol-base/collections/database'
-import { Interval, Segmentation } from 'mol-base/collections/integer'
+import UUID from 'mol-util/uuid'
+import { Column, Table } from 'mol-data/db'
+import { Interval, Segmentation } from 'mol-data/int'
import Format from '../format'
import Model from '../model'
import * as Hierarchy from '../properties/hierarchy'
@@ -66,7 +66,7 @@ function getConformation({ data }: mmCIF_Format, bounds: Interval): Conformation
const start = Interval.start(bounds), end = Interval.end(bounds);
const { atom_site } = data;
return {
- id: newUUID(),
+ id: UUID.create(),
atomId: Column.window(atom_site.id, start, end),
occupancy: Column.window(atom_site.occupancy, start, end),
B_iso_or_equiv: Column.window(atom_site.B_iso_or_equiv, start, end),
@@ -100,7 +100,7 @@ function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model):
}
const hierarchyKeys = findHierarchyKeys(hierarchyData, hierarchySegments);
return {
- id: newUUID(),
+ id: UUID.create(),
sourceData: format,
modelNum: format.data.atom_site.pdbx_PDB_model_num.value(Interval.start(bounds)),
hierarchy: { ...hierarchyData, ...hierarchyKeys, ...hierarchySegments },
diff --git a/src/mol-data/structure/model/model.ts b/src/mol-model/structure/model/model.ts
similarity index 95%
rename from src/mol-data/structure/model/model.ts
rename to src/mol-model/structure/model/model.ts
index c393d2452..c7a33db54 100644
--- a/src/mol-data/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import UUID from 'mol-base/utils/uuid'
+import UUID from 'mol-util/uuid'
import Format from './format'
import HierarchyProperties from './properties/hierarchy'
import ConformationProperties from './properties/conformation'
diff --git a/src/mol-data/structure/model/properties/computed.ts b/src/mol-model/structure/model/properties/computed.ts
similarity index 100%
rename from src/mol-data/structure/model/properties/computed.ts
rename to src/mol-model/structure/model/properties/computed.ts
diff --git a/src/mol-data/structure/model/properties/conformation.ts b/src/mol-model/structure/model/properties/conformation.ts
similarity index 88%
rename from src/mol-data/structure/model/properties/conformation.ts
rename to src/mol-model/structure/model/properties/conformation.ts
index c53ab0844..66a975d62 100644
--- a/src/mol-data/structure/model/properties/conformation.ts
+++ b/src/mol-model/structure/model/properties/conformation.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-base/collections/database'
-import UUID from 'mol-base/utils/uuid'
+import { Column } from 'mol-data/db'
+import UUID from 'mol-util/uuid'
interface Conformation {
id: UUID,
diff --git a/src/mol-data/structure/model/properties/format-specific.ts b/src/mol-model/structure/model/properties/format-specific.ts
similarity index 100%
rename from src/mol-data/structure/model/properties/format-specific.ts
rename to src/mol-model/structure/model/properties/format-specific.ts
diff --git a/src/mol-data/structure/model/properties/hierarchy.ts b/src/mol-model/structure/model/properties/hierarchy.ts
similarity index 95%
rename from src/mol-data/structure/model/properties/hierarchy.ts
rename to src/mol-model/structure/model/properties/hierarchy.ts
index a19de7fd5..f3bec187d 100644
--- a/src/mol-data/structure/model/properties/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/hierarchy.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column, Table } from 'mol-base/collections/database'
-import { Segmentation } from 'mol-base/collections/integer'
+import { Column, Table } from 'mol-data/db'
+import { Segmentation } from 'mol-data/int'
import { mmCIF_Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
import { ElementSymbol} from '../types'
diff --git a/src/mol-data/structure/model/properties/transforms.ts b/src/mol-model/structure/model/properties/transforms.ts
similarity index 100%
rename from src/mol-data/structure/model/properties/transforms.ts
rename to src/mol-model/structure/model/properties/transforms.ts
diff --git a/src/mol-data/structure/model/types.ts b/src/mol-model/structure/model/types.ts
similarity index 99%
rename from src/mol-data/structure/model/types.ts
rename to src/mol-model/structure/model/types.ts
index 4a90f04c9..d105c1f81 100644
--- a/src/mol-data/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import BitFlags from 'mol-base/utils/bit-flags'
+import BitFlags from 'mol-util/bit-flags'
const _esCache = (function () {
const cache = Object.create(null);
diff --git a/src/mol-data/structure/model/utils/hierarchy-keys.ts b/src/mol-model/structure/model/utils/hierarchy-keys.ts
similarity index 97%
rename from src/mol-data/structure/model/utils/hierarchy-keys.ts
rename to src/mol-model/structure/model/utils/hierarchy-keys.ts
index cc0f4821a..c09484245 100644
--- a/src/mol-data/structure/model/utils/hierarchy-keys.ts
+++ b/src/mol-model/structure/model/utils/hierarchy-keys.ts
@@ -4,9 +4,9 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Column } from 'mol-base/collections/database'
+import { Column } from 'mol-data/db'
import { Data, Segments, Keys } from '../properties/hierarchy'
-import { Interval, Segmentation } from 'mol-base/collections/integer'
+import { Interval, Segmentation } from 'mol-data/int'
function getResidueId(comp_id: string, seq_id: number, ins_code: string) {
return `${comp_id} ${seq_id} ${ins_code}`;
diff --git a/src/mol-data/structure/query.ts b/src/mol-model/structure/query.ts
similarity index 100%
rename from src/mol-data/structure/query.ts
rename to src/mol-model/structure/query.ts
diff --git a/src/mol-data/structure/query/generators.ts b/src/mol-model/structure/query/generators.ts
similarity index 99%
rename from src/mol-data/structure/query/generators.ts
rename to src/mol-model/structure/query/generators.ts
index 5846eee6b..12d43abc4 100644
--- a/src/mol-data/structure/query/generators.ts
+++ b/src/mol-model/structure/query/generators.ts
@@ -8,7 +8,7 @@ import Query from './query'
import Selection from './selection'
import P from './properties'
import { Structure, AtomSet, Atom } from '../structure'
-import { OrderedSet, Segmentation } from 'mol-base/collections/integer'
+import { OrderedSet, Segmentation } from 'mol-data/int'
export const all: Query = s => s;
diff --git a/src/mol-data/structure/query/predicates.ts b/src/mol-model/structure/query/predicates.ts
similarity index 100%
rename from src/mol-data/structure/query/predicates.ts
rename to src/mol-model/structure/query/predicates.ts
diff --git a/src/mol-data/structure/query/properties.ts b/src/mol-model/structure/query/properties.ts
similarity index 100%
rename from src/mol-data/structure/query/properties.ts
rename to src/mol-model/structure/query/properties.ts
diff --git a/src/mol-data/structure/query/query.ts b/src/mol-model/structure/query/query.ts
similarity index 100%
rename from src/mol-data/structure/query/query.ts
rename to src/mol-model/structure/query/query.ts
diff --git a/src/mol-data/structure/query/selection.ts b/src/mol-model/structure/query/selection.ts
similarity index 97%
rename from src/mol-data/structure/query/selection.ts
rename to src/mol-model/structure/query/selection.ts
index 57700f931..8504e4252 100644
--- a/src/mol-data/structure/query/selection.ts
+++ b/src/mol-model/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-data/iterator'
+import HashSet from 'mol-data/util/hash-set'
import { Structure, Atom, AtomSet } from '../structure'
type Selection =
diff --git a/src/mol-data/structure/structure.ts b/src/mol-model/structure/structure.ts
similarity index 100%
rename from src/mol-data/structure/structure.ts
rename to src/mol-model/structure/structure.ts
diff --git a/src/mol-data/structure/structure/atom.ts b/src/mol-model/structure/structure/atom.ts
similarity index 96%
rename from src/mol-data/structure/structure/atom.ts
rename to src/mol-model/structure/structure/atom.ts
index ef57e121f..217bbb1eb 100644
--- a/src/mol-data/structure/structure/atom.ts
+++ b/src/mol-model/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-data/int'
import Unit from './unit'
import Structure from './structure'
diff --git a/src/mol-data/structure/structure/atom/set.ts b/src/mol-model/structure/structure/atom/set.ts
similarity index 96%
rename from src/mol-data/structure/structure/atom/set.ts
rename to src/mol-model/structure/structure/atom/set.ts
index 6abe38108..3ce250e24 100644
--- a/src/mol-data/structure/structure/atom/set.ts
+++ b/src/mol-model/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-data/int'
import Atom from '../atom'
import * as Impl from './set/impl'
import createBuilder, { Builder as AtomSetBuilder } from './set/builder'
diff --git a/src/mol-data/structure/structure/atom/set/builder.ts b/src/mol-model/structure/structure/atom/set/builder.ts
similarity index 95%
rename from src/mol-data/structure/structure/atom/set/builder.ts
rename to src/mol-model/structure/structure/atom/set/builder.ts
index bf756939e..fdda1a1c5 100644
--- a/src/mol-data/structure/structure/atom/set/builder.ts
+++ b/src/mol-model/structure/structure/atom/set/builder.ts
@@ -6,8 +6,8 @@
import AtomSet from '../set'
import Atom from '../../atom'
-import { OrderedSet } from 'mol-base/collections/integer'
-import { sortArray } from 'mol-base/collections/sort'
+import { OrderedSet } from 'mol-data/int'
+import { sortArray } from 'mol-data/util/sort'
export class Builder {
private keys: number[] = [];
diff --git a/src/mol-data/structure/structure/atom/set/impl.ts b/src/mol-model/structure/structure/atom/set/impl.ts
similarity index 99%
rename from src/mol-data/structure/structure/atom/set/impl.ts
rename to src/mol-model/structure/structure/atom/set/impl.ts
index 8c0f2bcd4..f60658f1f 100644
--- a/src/mol-data/structure/structure/atom/set/impl.ts
+++ b/src/mol-model/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-data/int'
+import { sortArray } from 'mol-data/util/sort'
+import { hash1 } from 'mol-data/util/hash-functions'
import Atom from '../../atom'
/** Long and painful implementation starts here */
diff --git a/src/mol-data/structure/structure/atom/set/properties.ts b/src/mol-model/structure/structure/atom/set/properties.ts
similarity index 100%
rename from src/mol-data/structure/structure/atom/set/properties.ts
rename to src/mol-model/structure/structure/atom/set/properties.ts
diff --git a/src/mol-data/structure/structure/operator.ts b/src/mol-model/structure/structure/operator.ts
similarity index 91%
rename from src/mol-data/structure/structure/operator.ts
rename to src/mol-model/structure/structure/operator.ts
index e6fc2fd2f..10ba47cb8 100644
--- a/src/mol-data/structure/structure/operator.ts
+++ b/src/mol-model/structure/structure/operator.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Mat4 } from 'mol-base/math/linear-algebra-3d'
+import { Mat4 } from 'mol-math/linear-algebra'
interface Operator extends Readonly<{
name: string,
diff --git a/src/mol-data/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
similarity index 95%
rename from src/mol-data/structure/structure/structure.ts
rename to src/mol-model/structure/structure/structure.ts
index 9b6c64720..0d09fa4db 100644
--- a/src/mol-data/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -4,8 +4,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { OrderedSet, Iterator } from 'mol-base/collections/integer'
-import UniqueArray from 'mol-base/collections/unique-array'
+import { OrderedSet, Iterator } from 'mol-data/int'
+import UniqueArray from 'mol-data/util/unique-array'
import { Model, Format } from '../model'
import Unit from './unit'
import Operator from './operator'
diff --git a/src/mol-data/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
similarity index 98%
rename from src/mol-data/structure/structure/unit.ts
rename to src/mol-model/structure/structure/unit.ts
index b58145ca2..c819836d9 100644
--- a/src/mol-data/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -6,7 +6,7 @@
import { Model } from '../model'
import Operator from './operator'
-import { Vec3, Mat4 } from 'mol-base/math/linear-algebra-3d'
+import { Vec3, Mat4 } from 'mol-math/linear-algebra'
interface Unit extends Readonly<{
// Structure-level unique identifier of the unit.
diff --git a/src/mol-data/volume/TODO b/src/mol-model/volume/TODO
similarity index 100%
rename from src/mol-data/volume/TODO
rename to src/mol-model/volume/TODO
diff --git a/src/mol-base/utils/_spec/string-builder.spec.ts b/src/mol-util/_spec/string-builder.spec.ts
similarity index 100%
rename from src/mol-base/utils/_spec/string-builder.spec.ts
rename to src/mol-util/_spec/string-builder.spec.ts
diff --git a/src/mol-base/utils/bit-flags.ts b/src/mol-util/bit-flags.ts
similarity index 100%
rename from src/mol-base/utils/bit-flags.ts
rename to src/mol-util/bit-flags.ts
diff --git a/src/mol-base/computation.ts b/src/mol-util/computation.ts
similarity index 99%
rename from src/mol-base/computation.ts
rename to src/mol-util/computation.ts
index d81b970a9..6bafb7a99 100644
--- a/src/mol-base/computation.ts
+++ b/src/mol-util/computation.ts
@@ -5,8 +5,8 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Scheduler from './utils/scheduler'
-import timeNow from './utils/time'
+import Scheduler from './scheduler'
+import timeNow from './time'
interface Computation<A> {
(ctx?: Computation.Context): Promise<A>
diff --git a/src/mol-util/index.ts b/src/mol-util/index.ts
new file mode 100644
index 000000000..18a0aa3cd
--- /dev/null
+++ b/src/mol-util/index.ts
@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import BitFlags from './bit-flags'
+import Computation from './computation'
+import Scheduler from './scheduler'
+import StringBuilder from './string-builder'
+import Time from './time'
+import UUID from './uuid'
+
+export { BitFlags, Computation, Scheduler, StringBuilder, Time, UUID }
\ No newline at end of file
diff --git a/src/mol-base/utils/scheduler.ts b/src/mol-util/scheduler.ts
similarity index 100%
rename from src/mol-base/utils/scheduler.ts
rename to src/mol-util/scheduler.ts
diff --git a/src/mol-base/utils/string-builder.ts b/src/mol-util/string-builder.ts
similarity index 100%
rename from src/mol-base/utils/string-builder.ts
rename to src/mol-util/string-builder.ts
diff --git a/src/mol-base/utils/time.ts b/src/mol-util/time.ts
similarity index 100%
rename from src/mol-base/utils/time.ts
rename to src/mol-util/time.ts
diff --git a/src/mol-util/uuid.ts b/src/mol-util/uuid.ts
new file mode 100644
index 000000000..471d34969
--- /dev/null
+++ b/src/mol-util/uuid.ts
@@ -0,0 +1,23 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import now from './time'
+
+interface UUID extends String { '@type': 'uuid' }
+
+namespace UUID {
+ export function create(): UUID {
+ let d = (+new Date()) + now();
+ const uuid = 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'.replace(/[xy]/g, function(c) {
+ const r = (d + Math.random()*16)%16 | 0;
+ d = Math.floor(d/16);
+ return (c==='x' ? r : (r&0x3|0x8)).toString(16);
+ });
+ return uuid as any;
+ }
+}
+
+export default UUID;
\ No newline at end of file
diff --git a/src/perf-tests/chunked-array-vs-native.ts b/src/perf-tests/chunked-array-vs-native.ts
index 80fc3ff31..1b145425d 100644
--- a/src/perf-tests/chunked-array-vs-native.ts
+++ b/src/perf-tests/chunked-array-vs-native.ts
@@ -1,5 +1,5 @@
import * as B from 'benchmark'
-import ChunkedArray from 'mol-base/collections/chunked-array'
+import ChunkedArray from 'mol-data/util/chunked-array'
function testNative(size: number) {
const xs = new Array(size);
diff --git a/src/perf-tests/cif-encoder.ts b/src/perf-tests/cif-encoder.ts
index 2b1193e3e..5f2250825 100644
--- a/src/perf-tests/cif-encoder.ts
+++ b/src/perf-tests/cif-encoder.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import Iterator from 'mol-base/collections/iterator'
+import Iterator from 'mol-data/iterator'
import * as Enc from 'mol-io/writer/cif'
const category1: Enc.CategoryDefinition<number> = {
diff --git a/src/perf-tests/column.ts b/src/perf-tests/column.ts
index 0232e28e0..88ad89b35 100644
--- a/src/perf-tests/column.ts
+++ b/src/perf-tests/column.ts
@@ -1,5 +1,5 @@
import * as B from 'benchmark'
-import { Column as C } from 'mol-base/collections/database'
+import { Column as C } from 'mol-data/db'
export namespace Column {
function createData(n: number) {
diff --git a/src/perf-tests/iterators.ts b/src/perf-tests/iterators.ts
index c98036308..a08ad0fc5 100644
--- a/src/perf-tests/iterators.ts
+++ b/src/perf-tests/iterators.ts
@@ -1,5 +1,5 @@
import * as B from 'benchmark'
-import It from 'mol-base/collections/iterator'
+import It from 'mol-data/iterator'
function createData(n: number) {
const data = [];//new Int32Array(n);
diff --git a/src/perf-tests/sets.ts b/src/perf-tests/sets.ts
index 76d8c03c7..699c9037c 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/structure'
+import { Tuple, Segmentation, OrderedSet as OrdSet } from 'mol-data/int'
+import { AtomSet } from 'mol-model/structure'
export namespace Iteration {
const U = 1000, V = 2500;
diff --git a/src/perf-tests/sort.ts b/src/perf-tests/sort.ts
index d4461e91e..2c136f83e 100644
--- a/src/perf-tests/sort.ts
+++ b/src/perf-tests/sort.ts
@@ -1,5 +1,5 @@
import * as B from 'benchmark'
-import * as Sort from 'mol-base/collections/sort'
+import * as Sort from 'mol-data/util'
function shuffle(a: number[]) {
for (let i = a.length - 1; i > 0; i--) {
diff --git a/src/perf-tests/string-builder.ts b/src/perf-tests/string-builder.ts
index 41b269c50..fa73eb600 100644
--- a/src/perf-tests/string-builder.ts
+++ b/src/perf-tests/string-builder.ts
@@ -1,5 +1,5 @@
import * as B from 'benchmark'
-import SB from 'mol-base/utils/string-builder'
+import SB from 'mol-util/string-builder'
export namespace Test {
function createData(n: number) {
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 801a98c79..62c780e59 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -10,10 +10,10 @@ import * as util from 'util'
import * as fs from 'fs'
import CIF from 'mol-io/reader/cif'
-import { Structure, Model, Queries as Q, Atom, AtomSet, Selection } from 'mol-data/structure'
-import { OrderedSet as OrdSet, Segmentation } from 'mol-base/collections/integer'
+import { Structure, Model, Queries as Q, Atom, AtomSet, Selection } from 'mol-model/structure'
+import { OrderedSet as OrdSet, Segmentation } from 'mol-data/int'
-import to_mmCIF from 'mol-data/structure/export/mmcif'
+import to_mmCIF from 'mol-model/structure/export/mmcif'
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
diff --git a/src/script.ts b/src/script.ts
index 05b1c962b..03c5d970a 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -15,9 +15,9 @@ const writeFileAsync = util.promisify(fs.writeFile);
import Gro from 'mol-io/reader/gro/parser'
import CIF from 'mol-io/reader/cif'
-import Computation from 'mol-base/computation'
+import Computation from 'mol-util/computation'
-import { Model } from 'mol-data/structure/model'
+import { Model } from 'mol-model/structure'
// import { toTypedFrame as applySchema } from './reader/cif/schema'
import { generateSchema } from 'mol-io/reader/cif/schema/utils'
diff --git a/tsconfig.json b/tsconfig.json
index d25a81888..c90e01741 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -13,9 +13,11 @@
"outDir": "build/node_modules",
"baseUrl": "src",
"paths": {
- "mol-base": ["./mol-base"],
- "mol-data": ["./mol-data"],
- "mol-io": ["./mol-io"]
+ "mol-util": ["./mol-util", "./mol-util/index.ts"],
+ "mol-data": ["./mol-data", "./mol-data/index.ts"],
+ "mol-math": ["./mol-math"],
+ "mol-io": ["./mol-io"],
+ "mol-model": ["./mol-model"]
}
},
"include": [ "**/*" ]
--
GitLab