diff --git a/src/mol-base/collections/integer/_spec/interval.spec.ts b/src/mol-base/collections/integer/_spec/interval.spec.ts
index cda22df8eaf9cde2c640ca6e2216b02dc1772dac..9aa97bdbd534c1a6c44111b39f2c7b3875be1a88 100644
--- a/src/mol-base/collections/integer/_spec/interval.spec.ts
+++ b/src/mol-base/collections/integer/_spec/interval.spec.ts
@@ -69,5 +69,8 @@ describe('interval', () => {
test('predIndexInt', Interval.findPredecessorIndexInInterval(r05, 0, Interval.ofRange(2, 3)), 2);
test('predIndexInt1', Interval.findPredecessorIndexInInterval(r05, 4, Interval.ofRange(2, 3)), 4);
+ test('predIndexInt2', Interval.findPredecessorIndex(Interval.ofRange(3, 10), 5), 2);
+ test('predIndexInt3', Interval.findPredecessorIndexInInterval(Interval.ofRange(3, 10), 5, Interval.ofRange(2, 6)), 2);
+
testI('findRange', Interval.findRange(r05, 2, 3), Interval.ofRange(2, 3));
});
\ No newline at end of file
diff --git a/src/mol-base/collections/integer/_spec/segmentation.spec.ts b/src/mol-base/collections/integer/_spec/segmentation.spec.ts
index 8732383fa97d9b242cac13dd23de64f6c365c3b9..6047b09c120c39712dbfa12e717b35795e6f4a41 100644
--- a/src/mol-base/collections/integer/_spec/segmentation.spec.ts
+++ b/src/mol-base/collections/integer/_spec/segmentation.spec.ts
@@ -11,7 +11,7 @@ import Segmentation from '../segmentation'
describe('segments', () => {
const data = OrderedSet.ofSortedArray([4, 9, 10, 11, 14, 15, 16]);
const segs = Segmentation.create([0, 4, 10, 12, 13, 15, 25]);
-
+
it('size', () => expect(Segmentation.count(segs)).toBe(6));
it('project', () => {
@@ -50,47 +50,68 @@ describe('segments', () => {
expect(count).toBe(4);
});
- // it('iteration range', () => {
- // const segs = Segmentation.create([0, 2, 4]);
- // const dataRange = OrderedSet.ofBounds(0, 4);
-
- // const it = Segmentation.transientSegments(segs, dataRange);
-
- // const t = Object.create(null);
- // let count = 0;
- // while (it.hasNext) {
- // count++;
- // const s = it.move();
- // for (let j = s.start; j < s.end; j++) {
- // const x = t[s.index];
- // const v = OrderedSet.getAt(dataRange, j);
- // if (!x) t[s.index] = [v];
- // else x[x.length] = v;
- // }
- // }
- // expect(count).toBe(2);
- // expect(t).toEqual({ 0: [0, 1], 1: [2, 3] });
- // });
-
- // it('iteration range 1', () => {
- // const segs = Segmentation.create([0, 2, 4]);
- // const dataRange = OrderedSet.ofBounds(0, 4);
-
- // const it = Segmentation.transientSegments(segs, dataRange, { index: 0, start: 2, end: 4 });
-
- // const t = Object.create(null);
- // let count = 0;
- // while (it.hasNext) {
- // count++;
- // const s = it.move();
- // for (let j = s.start; j < s.end; j++) {
- // const x = t[s.index];
- // const v = OrderedSet.getAt(dataRange, j);
- // if (!x) t[s.index] = [v];
- // else x[x.length] = v;
- // }
- // }
- // expect(count).toBe(1);
- // expect(t).toEqual({ 1: [2, 3] });
- // });
+ it('units', () => {
+ const data = OrderedSet.ofBounds(0, 4);
+ const segs = Segmentation.create([0, 1, 2, 3, 4]);
+ const it = Segmentation.transientSegments(segs, data, { index: 0, start: 2, end: 4 });
+
+ const t = Object.create(null);
+ let count = 0;
+ while (it.hasNext) {
+ count++;
+ const s = it.move();
+ for (let j = s.start; j < s.end; j++) {
+ const x = t[s.index];
+ const v = OrderedSet.getAt(data, j);
+ if (!x) t[s.index] = [v];
+ else x[x.length] = v;
+ }
+ }
+ expect(t).toEqual({ 2: [2], 3: [3] });
+ expect(count).toBe(2);
+ });
+
+ it('iteration range', () => {
+ const segs = Segmentation.create([0, 2, 4]);
+ const dataRange = OrderedSet.ofBounds(0, 4);
+
+ const it = Segmentation.transientSegments(segs, dataRange);
+
+ const t = Object.create(null);
+ let count = 0;
+ while (it.hasNext) {
+ count++;
+ const s = it.move();
+ for (let j = s.start; j < s.end; j++) {
+ const x = t[s.index];
+ const v = OrderedSet.getAt(dataRange, j);
+ if (!x) t[s.index] = [v];
+ else x[x.length] = v;
+ }
+ }
+ expect(count).toBe(2);
+ expect(t).toEqual({ 0: [0, 1], 1: [2, 3] });
+ });
+
+ it('iteration range 1', () => {
+ const segs = Segmentation.create([0, 2, 4]);
+ const dataRange = OrderedSet.ofBounds(0, 4);
+
+ const it = Segmentation.transientSegments(segs, dataRange, { index: 0, start: 2, end: 4 });
+
+ const t = Object.create(null);
+ let count = 0;
+ while (it.hasNext) {
+ count++;
+ const s = it.move();
+ for (let j = s.start; j < s.end; j++) {
+ const x = t[s.index];
+ const v = OrderedSet.getAt(dataRange, j);
+ if (!x) t[s.index] = [v];
+ else x[x.length] = v;
+ }
+ }
+ expect(count).toBe(1);
+ expect(t).toEqual({ 1: [2, 3] });
+ });
});
diff --git a/src/mol-base/collections/integer/impl/interval.ts b/src/mol-base/collections/integer/impl/interval.ts
index 00354c32edac05cfc6d65a8e4d971775059de110..3a265b8b266bdf81bd1cf841377c4140039770fb 100644
--- a/src/mol-base/collections/integer/impl/interval.ts
+++ b/src/mol-base/collections/integer/impl/interval.ts
@@ -43,11 +43,12 @@ export function findPredecessorIndex(int: Tuple, v: number) {
}
export function findPredecessorIndexInInterval(int: Tuple, v: number, bounds: Tuple) {
- const bS = start(bounds)
- if (v <= bS) return bS;
+ const bS = start(bounds);
+ const s = start(int);
+ if (v <= bS + s) return bS;
const bE = end(bounds);
- if (v >= bE) return bE;
- return v - start(int);
+ if (v >= bE + s) return bE;
+ return v - s;
}
export function findRange(int: Tuple, min: number, max: number) {
diff --git a/src/mol-base/collections/integer/impl/segmentation.ts b/src/mol-base/collections/integer/impl/segmentation.ts
index 1da81db5d999b298122e8488d6e0f4425e80b425..f9b7d6f4230aca4c34c4f8f638620677d648a8ef 100644
--- a/src/mol-base/collections/integer/impl/segmentation.ts
+++ b/src/mol-base/collections/integer/impl/segmentation.ts
@@ -91,6 +91,7 @@ export class SegmentIterator implements Iterator<Segs.Segment> {
const max = OrderedSet.getAt(this.set, sMax);
this.segmentMin = this.getSegmentIndex(min);
this.segmentMax = this.getSegmentIndex(max);
+
this.hasNext = this.segmentMax >= this.segmentMin && Interval.size(this.setRange) > 0;
}
diff --git a/src/mol-data/structure.ts b/src/mol-data/structure.ts
new file mode 100644
index 0000000000000000000000000000000000000000..5542ea39939397d841b9449c0c4ce19352b722d9
--- /dev/null
+++ b/src/mol-data/structure.ts
@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export * from './structure/model'
+export * from './structure/structure'
+export * from './structure/query'
\ No newline at end of file
diff --git a/src/mol-data/structure/model.ts b/src/mol-data/structure/model.ts
index 70d5c31f2380055c388c5a0c07b08d417d8a4f05..1fd76534768b57ae6fa2386a6befaa78d1ea32e2 100644
--- a/src/mol-data/structure/model.ts
+++ b/src/mol-data/structure/model.ts
@@ -5,7 +5,7 @@
*/
import Model from './model/model'
-import ModelDataFormat from './model/data-format'
-import * as ModelConstants from './model/constants'
+import * as Constants from './model/constants'
+import Format from './model/format'
-export { Model, ModelConstants, ModelDataFormat }
\ No newline at end of file
+export { Model, Constants, Format }
\ No newline at end of file
diff --git a/src/mol-data/structure/model/data-format.ts b/src/mol-data/structure/model/format.ts
similarity index 53%
rename from src/mol-data/structure/model/data-format.ts
rename to src/mol-data/structure/model/format.ts
index a12b0a5d08d4f16361cf325a14ffdb9f041e1d01..e1878bbdb8ded54aff9da4db4882fa1cebc02363 100644
--- a/src/mol-data/structure/model/data-format.ts
+++ b/src/mol-data/structure/model/format.ts
@@ -4,11 +4,13 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Database as mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif'
-
-export interface mmCIF { kind: 'mmCIF', data: mmCIF_Database }
+import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif'
type Format =
- | mmCIF
+ | Format.mmCIF
+
+namespace Format {
+ export interface mmCIF { kind: 'mmCIF', data: mmCIF_Database }
+}
export default Format
\ No newline at end of file
diff --git a/src/mol-data/structure/model/builders/mmcif.ts b/src/mol-data/structure/model/formats/mmcif.ts
similarity index 89%
rename from src/mol-data/structure/model/builders/mmcif.ts
rename to src/mol-data/structure/model/formats/mmcif.ts
index 6e38b03a3f821d026d7acd48ca2ff6d868121f16..5f6cf3c9c6ebace88b2b45f2600cfa38889a6963 100644
--- a/src/mol-data/structure/model/builders/mmcif.ts
+++ b/src/mol-data/structure/model/formats/mmcif.ts
@@ -4,16 +4,18 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { mmCIF } from '../data-format'
+import Format from '../format'
import Model from '../model'
+import * as Hierarchy from '../properties/hierarchy'
+import Conformation from '../properties/conformation'
import { Column, Table } from 'mol-base/collections/database'
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'
-function findModelBounds({ data }: mmCIF, startIndex: number) {
+import mmCIF_Format = Format.mmCIF
+
+function findModelBounds({ data }: mmCIF_Format, startIndex: number) {
const num = data.atom_site.pdbx_PDB_model_num;
const atomCount = num.rowCount;
if (!num.isDefined) return Interval.ofBounds(startIndex, atomCount);
@@ -22,7 +24,7 @@ function findModelBounds({ data }: mmCIF, startIndex: number) {
return Interval.ofBounds(startIndex, endIndex);
}
-function findHierarchyOffsets({ data }: mmCIF, bounds: Interval) {
+function findHierarchyOffsets({ data }: mmCIF_Format, bounds: Interval) {
const start = Interval.start(bounds), end = Interval.end(bounds);
const residues = [start], chains = [start];
@@ -37,12 +39,11 @@ function findHierarchyOffsets({ data }: mmCIF, bounds: Interval) {
if (newResidue) residues[residues.length] = i;
if (newChain) chains[chains.length] = i;
- }
-
+ }
return { residues, chains };
}
-function createHierarchyData({ data }: mmCIF, bounds: Interval, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): Hierarchy.Data {
+function createHierarchyData({ data }: mmCIF_Format, bounds: Interval, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): Hierarchy.Data {
const { atom_site } = data;
const start = Interval.start(bounds), end = Interval.end(bounds);
const atoms = Table.ofColumns(Hierarchy.AtomsSchema, {
@@ -60,7 +61,7 @@ function createHierarchyData({ data }: mmCIF, bounds: Interval, offsets: { resid
return { atoms, residues, chains, entities: data.entity };
}
-function getConformation({ data }: mmCIF, bounds: Interval): Conformation {
+function getConformation({ data }: mmCIF_Format, bounds: Interval): Conformation {
const start = Interval.start(bounds), end = Interval.end(bounds);
const { atom_site } = data;
return {
@@ -81,7 +82,7 @@ function isHierarchyDataEqual(a: Hierarchy.Hierarchy, b: Hierarchy.Data) {
&& Table.areEqual(a.atoms as Table<Hierarchy.AtomsSchema>, b.atoms as Table<Hierarchy.AtomsSchema>)
}
-function createModel(format: mmCIF, bounds: Interval, previous?: Model): Model {
+function createModel(format: mmCIF_Format, bounds: Interval, previous?: Model): Model {
const hierarchyOffsets = findHierarchyOffsets(format, bounds);
const hierarchyData = createHierarchyData(format, bounds, hierarchyOffsets);
@@ -97,7 +98,6 @@ function createModel(format: mmCIF, bounds: Interval, previous?: Model): Model {
chainSegments: Segmentation.ofOffsets(hierarchyOffsets.chains, bounds),
}
const hierarchyKeys = findHierarchyKeys(hierarchyData, hierarchySegments);
-
return {
id: newUUID(),
sourceData: format,
@@ -108,7 +108,7 @@ function createModel(format: mmCIF, bounds: Interval, previous?: Model): Model {
};
}
-function buildModels(format: mmCIF): ReadonlyArray<Model> {
+function buildModels(format: mmCIF_Format): ReadonlyArray<Model> {
const models: Model[] = [];
const atomCount = format.data.atom_site._rowCount;
diff --git a/src/mol-data/structure/model/model.ts b/src/mol-data/structure/model/model.ts
index 4eef29c376e5abbae13be178c3a3d0760219906f..9cdfd3787284c68adbc86da838b55debbbec2bfd 100644
--- a/src/mol-data/structure/model/model.ts
+++ b/src/mol-data/structure/model/model.ts
@@ -4,12 +4,12 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import DataFormat from './data-format'
+import UUID from 'mol-base/utils/uuid'
+import Format from './format'
import HierarchyProperties from './properties/hierarchy'
import ConformationProperties from './properties/conformation'
-import UUID from 'mol-base/utils/uuid'
+import from_mmCIF from './formats/mmcif'
-import buildMmCIF from './builders/mmcif'
/**
* Interface to the "source data" of the molecule.
@@ -21,7 +21,7 @@ interface Model extends Readonly<{
modelNum: number,
- sourceData: DataFormat,
+ sourceData: Format,
hierarchy: HierarchyProperties,
conformation: ConformationProperties,
@@ -30,9 +30,9 @@ interface Model extends Readonly<{
}> { }
namespace Model {
- export function create(format: DataFormat) {
+ export function create(format: Format) {
switch (format.kind) {
- case 'mmCIF': return buildMmCIF(format);
+ case 'mmCIF': return from_mmCIF(format);
}
}
}
diff --git a/src/mol-data/structure/model/properties/hierarchy.ts b/src/mol-data/structure/model/properties/hierarchy.ts
index 9f6c0d81e3b7a065bdcf4ff49112a9a4149bb3a3..365c3943a09743ee4ecb4c4f2a27bb4a0391290b 100644
--- a/src/mol-data/structure/model/properties/hierarchy.ts
+++ b/src/mol-data/structure/model/properties/hierarchy.ts
@@ -6,7 +6,7 @@
import { Column, Table } from 'mol-base/collections/database'
import { Segmentation } from 'mol-base/collections/integer'
-import { Schema as mmCIF } from 'mol-io/reader/cif/schema/mmcif'
+import { mmCIF_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/structure/query.ts b/src/mol-data/structure/query.ts
index a228f7bb6f3a032c1a57f53e29a61307d9120ee5..4a8bf6150e5b28990211f94ea72ea9a5e1cb7559 100644
--- a/src/mol-data/structure/query.ts
+++ b/src/mol-data/structure/query.ts
@@ -9,4 +9,9 @@ import Query from './query/query'
import * as generators from './query/generators'
import * as props from './query/properties'
-export { Selection, Query, generators, props }
\ No newline at end of file
+export const Queries = {
+ generators,
+ props
+}
+
+export { Selection, Query }
\ No newline at end of file
diff --git a/src/mol-data/structure/query/generators.ts b/src/mol-data/structure/query/generators.ts
index 0ea357af41ea38d9829b2f02f4d6a8a4be77a7f9..eb6cb540346d750af3826f70c31d76fe3d32078b 100644
--- a/src/mol-data/structure/query/generators.ts
+++ b/src/mol-data/structure/query/generators.ts
@@ -5,10 +5,9 @@
*/
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, Segmentation } from 'mol-base/collections/integer'
export interface AtomGroupsSpec {
entityTest: Atom.Predicate,
@@ -62,16 +61,49 @@ function atomGroupsLinear(atomTest: Atom.Predicate): Query {
function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: AtomGroupsSpec): Query {
return structure => {
+ const { atoms, units } = structure;
+ const unitIds = AtomSet.unitIds(atoms);
+ const l = Atom.Location();
+ const builder = AtomSet.Builder(atoms);
+ for (let i = 0, _i = unitIds.length; i < _i; i++) {
+ const unitId = unitIds[i];
+ const unit = units[unitId];
+ l.unit = unit;
+ const set = AtomSet.unitGetByIndex(atoms, i);
- throw 'nyi'
+ builder.beginUnit();
+ const chainsIt = Segmentation.transientSegments(unit.hierarchy.chainSegments, set);
+ const residues = unit.hierarchy.residueSegments;
+ while (chainsIt.hasNext) {
+ const chainSegment = chainsIt.move();
+ l.atom = OrderedSet.getAt(set, chainSegment.start);
+ // test entity and chain
+ if (!entityTest(l) || !chainTest(l)) continue;
+
+ const residuesIt = Segmentation.transientSegments(residues, set, chainSegment);
+ while (residuesIt.hasNext) {
+ const residueSegment = residuesIt.move();
+ l.atom = OrderedSet.getAt(set, residueSegment.start);
+
+ // test residue
+ if (!residueTest(l)) continue;
+
+ for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
+ l.atom = OrderedSet.getAt(set, j);
+ if (atomTest(l)) builder.addToUnit(l.atom);
+ }
+ }
+ }
+ builder.commitUnit(unitId);
+ }
+
+ return { units, atoms: builder.getSet() };
};
}
function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, groupBy }: AtomGroupsSpec): Query {
return structure => {
-
-
throw 'nyi'
};
}
diff --git a/src/mol-data/structure/query/properties.ts b/src/mol-data/structure/query/properties.ts
index 808cb4dbfdfc00b53c9d622bd06e6d698c87b522..18bf1d5cb4451ad4313b88da93e192da254d1951 100644
--- a/src/mol-data/structure/query/properties.ts
+++ b/src/mol-data/structure/query/properties.ts
@@ -17,7 +17,8 @@ export const atom = {
}
export const residue = {
- auth_seq_id: Atom.property(l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom]))
+ auth_seq_id: Atom.property(l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])),
+ auth_comp_id: Atom.property(l => l.unit.hierarchy.residues.auth_comp_id.value(l.unit.residueIndex[l.atom]))
}
export const chain = {
diff --git a/src/mol-data/structure/structure/structure.ts b/src/mol-data/structure/structure/structure.ts
index 4b2cf5daa305ede7c0e0abd76efd440ce76e713c..14c10d4c7d893893aa38998caf92f5a2426d7c58 100644
--- a/src/mol-data/structure/structure/structure.ts
+++ b/src/mol-data/structure/structure/structure.ts
@@ -4,7 +4,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-import { Model } from '../model'
+import { Model, Format } from '../model'
import Unit from './unit'
import Operator from './operator'
import AtomSet from './atom/set'
@@ -18,6 +18,11 @@ interface Structure extends Readonly<{
namespace Structure {
export const Empty = { units: {}, atoms: AtomSet.Empty };
+ export function ofData(format: Format) {
+ const models = Model.create(format);
+ return models.map(ofModel);
+ }
+
export function ofModel(model: Model): Structure {
const chains = model.hierarchy.chainSegments;
const builder = Builder();
diff --git a/src/mol-io/reader/cif.ts b/src/mol-io/reader/cif.ts
index 8b22eec8c103d76da655d3605b3372f111ff70d5..1a57f99fe09e4860b1cbf8d75f64f7ddab5c4014 100644
--- a/src/mol-io/reader/cif.ts
+++ b/src/mol-io/reader/cif.ts
@@ -8,7 +8,7 @@ import parseText from './cif/text/parser'
import parseBinary from './cif/binary/parser'
import { Frame } from './cif/data-model'
import { toDatabase } from './cif/schema'
-import { Schema as mmCIF_Schema, Database as mmCIF_Database } from './cif/schema/mmcif'
+import { mmCIF_Schema, mmCIF_Database } from './cif/schema/mmcif'
export default {
parseText,
diff --git a/src/mol-io/reader/cif/schema/dic.ts b/src/mol-io/reader/cif/schema/dic.ts
index fc6c0dd02a90772141bba8ef5a844c266f417a61..712a667f4e12b7c0b09860dbdd557ab6bf726444 100644
--- a/src/mol-io/reader/cif/schema/dic.ts
+++ b/src/mol-io/reader/cif/schema/dic.ts
@@ -60,7 +60,7 @@ const item_units_conversion = {
// TODO save frame dic schema
-export const Schema = {
+export const CIFDictionary_Schema = {
datablock,
dictionary,
dictionary_history,
@@ -71,5 +71,5 @@ export const Schema = {
item_units_conversion
}
-export type Schema = typeof Schema;
-export interface Database extends Database.Tables<typeof Schema> { }
\ No newline at end of file
+export type CIFDictionary_Schema = typeof CIFDictionary_Schema;
+export interface CIFDictionary_Database extends Database.Tables<CIFDictionary_Schema> { }
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 9682fef280ee359fa0ef22f0122ec81912ec8795..9f478aa5c0aa07b1c5548b34f1523ed0d807a040 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -228,7 +228,7 @@ const atom_site = {
pdbx_PDB_model_num: int
}
-export const Schema = {
+export const mmCIF_Schema = {
entry,
entity,
exptl,
@@ -246,5 +246,5 @@ export const Schema = {
atom_site
};
-export type Schema = typeof Schema;
-export interface Database extends Database<typeof Schema> { }
\ No newline at end of file
+export type mmCIF_Schema = typeof mmCIF_Schema;
+export interface mmCIF_Database extends Database<mmCIF_Schema> { }
\ No newline at end of file
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index 23bd4e97a79049230c7c0e17d3d9da30127a3a79..34d5126ac3b557a8b408f68a60910c33bc92e657 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -10,9 +10,7 @@ import * as util from 'util'
import * as fs from 'fs'
import CIF from 'mol-io/reader/cif'
-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 { Structure, Model, Queries as Q, Atom, AtomSet } from 'mol-data/structure'
import { OrderedSet as OrdSet, Segmentation } from 'mol-base/collections/integer'
require('util.promisify').shim();
@@ -92,6 +90,7 @@ export namespace PropertyAccess {
let s = 0;
+ let vA = 0, cC = 0, rC = 0;
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unit = units[unitIds[i]];
l.unit = unit;
@@ -100,18 +99,26 @@ export namespace PropertyAccess {
const chainsIt = Segmentation.transientSegments(unit.hierarchy.chainSegments, set);
const residues = unit.hierarchy.residueSegments;
while (chainsIt.hasNext) {
+ cC++;
+
const chainSegment = chainsIt.move();
const residuesIt = Segmentation.transientSegments(residues, set, chainSegment);
while (residuesIt.hasNext) {
+ rC++;
const residueSegment = residuesIt.move();
+ // l.atom = OrdSet.getAt(set, residueSegment.start);
+ // console.log(unit.hierarchy.residues.auth_comp_id.value(unit.residueIndex[l.atom]), l.atom, OrdSet.getAt(set, residueSegment.end))
for (let j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
l.atom = OrdSet.getAt(set, j);
+ vA++;
s += p(l);
}
}
}
}
+ console.log('seg atom count', vA, cC, rC);
+
return s;
}
@@ -228,8 +235,8 @@ export namespace PropertyAccess {
// }
export async function run() {
- const { structures, models } = await readCIF('./examples/1cbs_full.bcif');
- //const { structures, models } = await readCIF('e:/test/quick/1jj2_full.bcif');
+ //const { structures, models } = await readCIF('./examples/1cbs_full.bcif');
+ const { structures, models } = await readCIF('e:/test/quick/1jj2_full.bcif');
//const { structures, models } = await readCIF('e:/test/quick/3j3q_updated.cif');
console.log('parsed');
@@ -237,6 +244,7 @@ export namespace PropertyAccess {
console.log(baseline(models[0]));
console.log(sumProperty(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)));
console.log(sumPropertySegmented(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)));
+
//console.log(sumPropertySegmentedMutable(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)));
console.log(sumPropertyAtomSetIt(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)));
//console.log(sumProperty(structures[0], Property.cachedAtomColumn(m => m.conformation.atomId)));
@@ -245,25 +253,33 @@ export namespace PropertyAccess {
//const authSeqId = Atom.property(l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom]));
- const auth_seq_id = Q.props.residue.auth_seq_id;
- const q = Q.generators.atomGroups({ atomTest: l => auth_seq_id(l) < 3 });
- const qr = q(structures[0]);
- console.log(qr);
+ //const auth_seq_id = Q.props.residue.auth_seq_id;
+ const auth_comp_id = Q.props.residue.auth_comp_id;
+ //const auth_asym_id = Q.props.chain.auth_asym_id;
+ //const set = new Set(['A', 'B', 'C', 'D']);
+ //const q = Q.generators.atomGroups({ atomTest: l => auth_seq_id(l) < 3 });
+ const q = Q.generators.atomGroups({ atomTest: l => auth_comp_id(l) === 'ALA' });
+ const q1 = Q.generators.atomGroups({ residueTest: l => auth_comp_id(l) === 'ALA' });
+ //const q2 = Q.generators.atomGroups({ chainTest: l => set.has(auth_asym_id(l)), residueTest: l => auth_comp_id(l) === 'ALA' });
+ q(structures[0]);
+ q1(structures[0]);
+ //console.log(q1(structures[0]));
//const col = models[0].conformation.atomId.value;
const suite = new B.Suite();
suite
+ .add('test q', () => q1(structures[0]))
//.add('test int', () => sumProperty(structures[0], l => col(l.atom)))
- .add('sum residue', () => sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])))
+ // .add('sum residue', () => sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])))
- .add('baseline', () => baseline(models[0]))
- .add('direct', () => sumDirect(structures[0]))
+ // .add('baseline', () => baseline(models[0]))
+ // .add('direct', () => sumDirect(structures[0]))
//.add('normal int', () => sumProperty(structures[0], l => l.unit.model.conformation.atomId.value(l.atom)))
//.add('atom set it int', () => sumPropertyAtomSetIt(structures[0], l => l.unit.conformation.atomId.value(l.atom)))
// .add('segmented faster int', () => sumPropertySegmented(structures[0], l => l.unit.conformation.atomId.value(l.atom)))
// .add('faster int', () => sumProperty(structures[0], l => l.unit.conformation.atomId.value(l.atom)))
- .add('segmented faster _x', () => sumPropertySegmented(structures[0], l => l.unit.conformation.__x[l.atom]))
- .add('faster _x', () => sumProperty(structures[0], l => l.unit.conformation.__x[l.atom] + l.unit.conformation.__y[l.atom] + l.unit.conformation.__z[l.atom]))
+ //.add('segmented faster _x', () => sumPropertySegmented(structures[0], l => l.unit.conformation.__x[l.atom]))
+ //.add('faster _x', () => sumProperty(structures[0], l => l.unit.conformation.__x[l.atom] + l.unit.conformation.__y[l.atom] + l.unit.conformation.__z[l.atom]))
//.add('segmented mut faster int', () => sumPropertySegmentedMutable(structures[0], l => l.unit.conformation.atomId.value(l.atom)))
//.add('normal shortcut int', () => sumProperty(structures[0], l => l.conformation.atomId.value(l.atom)))
//.add('cached int', () => sumProperty(structures[0], Property.cachedAtomColumn(m => m.conformation.atomId)))
diff --git a/src/script.ts b/src/script.ts
index 55a43f4b352d9bf37ddd6b140518443eca89c051..8207880be1ce4cd3bcea5794b6aca404a0c59a03 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/structure/model/builders/mmcif'
+import { Model } from 'mol-data/structure/model'
// import { toTypedFrame as applySchema } from './reader/cif/schema'
import { generateSchema } from 'mol-io/reader/cif/schema/utils'
@@ -115,11 +115,11 @@ async function runCIF(input: string | Uint8Array) {
console.log(mmcif.pdbx_struct_oper_list.matrix.value(0));
console.time('createModels');
- const models = buildModels({ kind: 'mmCIF', data: mmcif });
+ const models = Model.create({ kind: 'mmCIF', data: mmcif });
console.timeEnd('createModels');
for (let i = 0; i < models.length; i++) {
- console.log(models[i].id);
+ console.log(models[i].id, models[i].conformation.id);
}
// console.log(models[0].hierarchy.isMonotonous);