diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index f31133a57082d202a4cc658cc6fb22bd6a95f801..b262e21353b61941748cfc4c08c4ff9015ecfb10 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -45,7 +45,7 @@ export default class State {
this.loading.next(true)
const structures = await getStructuresFromPdbId(pdbId)
- const struct = Symmetry.buildAssembly(structures[0], '1')
+ const struct = await Run(Symmetry.buildAssembly(structures[0], '1'))
// const structPointRepr = StructureRepresentation(Point)
// await Run(structPointRepr.create(struct))
diff --git a/src/apps/structure-info/index.ts b/src/apps/structure-info/index.ts
index 6f606817361e4b7afd05269a9d2335d0cb7c7289..5233f459b883ed17617f53fff9391cb95ba1a944 100644
--- a/src/apps/structure-info/index.ts
+++ b/src/apps/structure-info/index.ts
@@ -10,8 +10,9 @@ require('util.promisify').shim();
// import { Table } from 'mol-data/db'
import CIF from 'mol-io/reader/cif'
-import { Model } from 'mol-model/structure'
+import { Model, Structure, ElementSet, Unit, ElementGroup } from 'mol-model/structure'
import { Run, Progress } from 'mol-task'
+import { OrderedSet } from 'mol-data/int';
async function parseCif(data: string|Uint8Array) {
const comp = CIF.parse(data);
@@ -21,7 +22,8 @@ async function parseCif(data: string|Uint8Array) {
}
async function getPdb(pdb: string) {
- const data = await fetch(`https://files.rcsb.org/download/${pdb}.cif`)
+ //const data = await fetch(`https://files.rcsb.org/download/${pdb}.cif`)
+ const data = await fetch(`http://www.ebi.ac.uk/pdbe/static/entry/${pdb}_updated.cif`);
const parsed = await parseCif(await data.text())
return CIF.schema.mmCIF(parsed.result.blocks[0])
}
@@ -37,24 +39,40 @@ export function atomLabel(model: Model, aI: number) {
}
-function printBonds(model: Model) {
- // TODO: do bonds again
- // const { count, offset, neighbor } = Model.bonds(model)
- // for (let i = 0; i < count; ++i) {
- // const start = offset[i];
- // const end = offset[i + 1];
- // for (let bI = start; bI < end; bI++) {
- // console.log(`${atomLabel(model, i)} -- ${atomLabel(model, neighbor[bI])}`)
- // }
- // }
+function printBonds(structure: Structure) {
+ const { units, elements } = structure;
+ const unitIds = ElementSet.unitIndices(elements);
+
+ for (let i = 0, _i = OrderedSet.size(unitIds); i < _i; i++) {
+ const unit = units[OrderedSet.getAt(unitIds, i)];
+ const group = ElementSet.groupFromUnitIndex(elements, OrderedSet.getAt(unitIds, i));
+
+ const { count, offset, neighbor } = Unit.getGroupBonds(unit, group);
+ const { model } = unit;
+
+ if (!count) continue;
+
+ for (let j = 0; j < offset.length - 1; ++j) {
+ const start = offset[j];
+ const end = offset[j + 1];
+
+ if (end <= start) continue;
+
+ const aI = ElementGroup.getAt(group, j);
+ for (let _bI = start; _bI < end; _bI++) {
+ const bI = ElementGroup.getAt(group, neighbor[_bI])
+ console.log(`${atomLabel(model, aI)} -- ${atomLabel(model, bI)}`);
+ }
+ }
+ }
}
async function run(pdb: string) {
const mmcif = await getPdb(pdb)
const models = Model.create({ kind: 'mmCIF', data: mmcif });
- // const structure = Structure.ofModel(models[0])
+ const structure = Structure.ofModel(models[0])
// console.log(structure)
- printBonds(models[0])
+ printBonds(structure)
}
const parser = new argparse.ArgumentParser({
diff --git a/src/mol-geo/representation/structure/index.ts b/src/mol-geo/representation/structure/index.ts
index c2266895b070b890e93f5252d954c537c672cf82..092e2f7b7c8ab6b97cf9d6adfbbacaf28b31b3b6 100644
--- a/src/mol-geo/representation/structure/index.ts
+++ b/src/mol-geo/representation/structure/index.ts
@@ -40,10 +40,11 @@ export function StructureRepresentation<Props>(reprCtor: () => UnitsRepresentati
(a, b) => a.unit.model.id === b.unit.model.id && OrderedSet.areEqual(a.group.elements, b.group.elements)
);
- for (let i = 0, _i = ElementSet.unitCount(elements); i < _i; i++) {
- const group = ElementSet.unitGetByIndex(elements, i);
- const unitId = ElementSet.unitGetId(elements, i);
- uniqueGroups.add(unitId, { unit: units[unitId], group });
+ const unitIndices = ElementSet.unitIndices(elements);
+ for (let i = 0, _i = unitIndices.length; i < _i; i++) {
+ const unitIndex = unitIndices[i];
+ const group = ElementSet.groupFromUnitIndex(elements, unitIndex);
+ uniqueGroups.add(unitIndex, { unit: units[unitIndex], group });
}
for (let i = 0, _i = uniqueGroups.groups.length; i < _i; i++) {
@@ -53,24 +54,13 @@ export function StructureRepresentation<Props>(reprCtor: () => UnitsRepresentati
for (let j = 0, _j = group.length; j < _j; j++) {
groupUnits.push(units[group[j]])
}
- const elementGroup = ElementSet.unitGetByIndex(elements, group[0])
+ const elementGroup = ElementSet.groupFromUnitIndex(elements, group[0])
const repr = reprCtor()
unitReprs.push(repr)
await ctx.update({ message: 'Building units...', current: i, max: _i });
await ctx.runChild(repr.create(groupUnits, elementGroup, props));
renderObjects.push(...repr.renderObjects)
}
-
- // console.log(ElementSet.unitCount(elements))
- // console.log(uniqueGroups)
-
- // console.log({ elements, units })
-
- // const repr = reprCtor()
- // unitReprs.push(repr)
- // await ctx.update('Building units...');
- // await ctx.runChild(repr.create(units, elements, props));
- // renderObjects.push(...repr.renderObjects)
});
},
update(elements: ElementSet, props: RepresentationProps) {
diff --git a/src/mol-math/geometry.ts b/src/mol-math/geometry.ts
index f8134ddd0601834b1b8cbde0f79ef120664b041f..5754f04a380143ee983caaed3bea1b3d1028cc28 100644
--- a/src/mol-math/geometry.ts
+++ b/src/mol-math/geometry.ts
@@ -1,4 +1,4 @@
-/*
+/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
diff --git a/src/mol-math/geometry/_spec/lookup3d.spec.ts b/src/mol-math/geometry/_spec/lookup3d.spec.ts
index af2c30a463e8016d0efebf011cb47baffe8f8242..92760e92d874ac742f0cf8bc6f044f24f0916c06 100644
--- a/src/mol-math/geometry/_spec/lookup3d.spec.ts
+++ b/src/mol-math/geometry/_spec/lookup3d.spec.ts
@@ -1,8 +1,8 @@
-/*
-* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
-*
-* @author David Sehnal <david.sehnal@gmail.com>
-*/
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
import { GridLookup3D } from '../../geometry';
import { sortArray } from 'mol-data/util';
diff --git a/src/mol-math/geometry/common.ts b/src/mol-math/geometry/common.ts
index 195224635b1ef41049e0fafe83d8aa359186edd3..e203afdf228197b4b18a08bfd33ea0b50b4a455c 100644
--- a/src/mol-math/geometry/common.ts
+++ b/src/mol-math/geometry/common.ts
@@ -1,8 +1,8 @@
-/*
-* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
-*
-* @author David Sehnal <david.sehnal@gmail.com>
-*/
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
import { OrderedSet } from 'mol-data/int'
diff --git a/src/mol-math/geometry/lookup3d/common.ts b/src/mol-math/geometry/lookup3d/common.ts
index 0aa58601dcc7f61d3fdfc5eb13520f1037846177..874735b9ca2659be52324834350cc595f5bc5024 100644
--- a/src/mol-math/geometry/lookup3d/common.ts
+++ b/src/mol-math/geometry/lookup3d/common.ts
@@ -1,4 +1,4 @@
-/*
+/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
diff --git a/src/mol-math/geometry/lookup3d/grid.ts b/src/mol-math/geometry/lookup3d/grid.ts
index 6d168df2c935433c0330cf4bd26ba3e111892290..7abb47781969df8deb176c5e1f9918f3cf2b532d 100644
--- a/src/mol-math/geometry/lookup3d/grid.ts
+++ b/src/mol-math/geometry/lookup3d/grid.ts
@@ -1,4 +1,4 @@
-/*
+/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
diff --git a/src/mol-math/geometry/primitives/box3d.ts b/src/mol-math/geometry/primitives/box3d.ts
index 21a5795165779a10f5223e2b2ccf928d31018ad7..90b6b241c113c05083456013b2ed3d7b6eb5fbcc 100644
--- a/src/mol-math/geometry/primitives/box3d.ts
+++ b/src/mol-math/geometry/primitives/box3d.ts
@@ -1,4 +1,4 @@
-/*
+/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
diff --git a/src/mol-math/geometry/primitives/sphere3d.ts b/src/mol-math/geometry/primitives/sphere3d.ts
index bd74a09a2a1fd500a5b1708265be56b7fec88423..3e280da055a57333215ebda7b540d309b50280b1 100644
--- a/src/mol-math/geometry/primitives/sphere3d.ts
+++ b/src/mol-math/geometry/primitives/sphere3d.ts
@@ -1,4 +1,4 @@
-/*
+/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
diff --git a/src/mol-model/structure/_spec/atom-set.spec.ts b/src/mol-model/structure/_spec/atom-set.spec.ts
index 582e7798d261e4aa7ff7345836eae323105adace..60b208053c028b902523853e1a01d0587c0b027c 100644
--- a/src/mol-model/structure/_spec/atom-set.spec.ts
+++ b/src/mol-model/structure/_spec/atom-set.spec.ts
@@ -26,7 +26,7 @@ describe('atom set', () => {
expect(setToPairs(set)).toEqual([p(10, 11)]);
expect(ElementSet.elementHas(set, p(10, 11))).toBe(true);
expect(ElementSet.elementHas(set, p(11, 11))).toBe(false);
- expect(ElementSet.elementGetAt(set, 0)).toBe(p(10, 11));
+ expect(ElementSet.elementAt(set, 0)).toBe(p(10, 11));
expect(ElementSet.elementCount(set)).toBe(1);
});
@@ -35,7 +35,7 @@ describe('atom set', () => {
expect(setToPairs(set)).toEqual([p(10, 11)]);
expect(ElementSet.elementHas(set, p(10, 11))).toBe(true);
expect(ElementSet.elementHas(set, p(11, 11))).toBe(false);
- expect(ElementSet.elementGetAt(set, 0)).toBe(p(10, 11));
+ expect(ElementSet.elementAt(set, 0)).toBe(p(10, 11));
expect(ElementSet.elementCount(set)).toBe(1);
});
@@ -51,7 +51,7 @@ describe('atom set', () => {
expect(ElementSet.elementHas(set, p(3, 0))).toBe(true);
expect(ElementSet.elementHas(set, p(1, 7))).toBe(true);
for (let i = 0; i < ElementSet.elementCount(set); i++) {
- expect(Element.areEqual(ElementSet.elementGetAt(set, i), ret[i])).toBe(true);
+ expect(Element.areEqual(ElementSet.elementAt(set, i), ret[i])).toBe(true);
}
});
@@ -62,8 +62,8 @@ describe('atom set', () => {
gen.add(1, OrderedSet.ofSingleton(3));
const set = gen.getSet();
- expect(ElementSet.unitGetById(set, 0)).toBe(ElementSet.unitGetById(template, 0));
- expect(ElementSet.unitGetById(set, 1)).toBe(ElementSet.unitGetById(template, 1));
+ expect(ElementSet.groupFromUnitIndex(set, 0)).toBe(ElementSet.groupFromUnitIndex(template, 0));
+ expect(ElementSet.groupFromUnitIndex(set, 1)).toBe(ElementSet.groupFromUnitIndex(template, 1));
expect(set).toBe(template);
});
@@ -74,8 +74,8 @@ describe('atom set', () => {
gen.add(1, OrderedSet.ofSingleton(4));
const set = gen.getSet();
- expect(ElementSet.unitGetById(set, 0)).toBe(ElementSet.unitGetById(template, 0));
- expect(ElementSet.unitGetById(set, 1) === ElementSet.unitGetById(template, 1)).toBe(false);
+ expect(ElementSet.groupFromUnitIndex(set, 0)).toBe(ElementSet.groupFromUnitIndex(template, 0));
+ expect(ElementSet.groupFromUnitIndex(set, 1) === ElementSet.groupFromUnitIndex(template, 1)).toBe(false);
expect(set === template).toBe(false);
});
@@ -89,9 +89,9 @@ describe('atom set', () => {
const u0 = ElementSet.union([p01, p02, p06], template);
const u1 = ElementSet.union([p01, p02, p06, p13], template);
- expect(ElementSet.unitGetById(u0, 0)).toBe(ElementSet.unitGetById(template, 0));
- expect(ElementSet.unitGetById(u1, 0)).toBe(ElementSet.unitGetById(template, 0));
- expect(ElementSet.unitGetById(u1, 1)).toBe(ElementSet.unitGetById(template, 1));
+ expect(ElementSet.groupFromUnitIndex(u0, 0)).toBe(ElementSet.groupFromUnitIndex(template, 0));
+ expect(ElementSet.groupFromUnitIndex(u1, 0)).toBe(ElementSet.groupFromUnitIndex(template, 0));
+ expect(ElementSet.groupFromUnitIndex(u1, 1)).toBe(ElementSet.groupFromUnitIndex(template, 1));
expect(u1).toBe(template);
});
@@ -108,7 +108,7 @@ describe('atom set', () => {
}
const ms = gen.getSet();
for (let i = 0; i < control.length; i++) {
- expect(Element.areEqual(ElementSet.elementGetAt(ms, i), control[i])).toBe(true);
+ expect(Element.areEqual(ElementSet.elementAt(ms, i), control[i])).toBe(true);
}
for (let i = 0; i < control.length; i++) {
diff --git a/src/mol-model/structure/model/formats/mmcif/assembly.ts b/src/mol-model/structure/model/formats/mmcif/assembly.ts
index a03ff07ae39d81a905646fdbaabb044861cda526..2315133d4cb83c7219207a9690f5b55ca148db9b 100644
--- a/src/mol-model/structure/model/formats/mmcif/assembly.ts
+++ b/src/mol-model/structure/model/formats/mmcif/assembly.ts
@@ -8,7 +8,7 @@ import { Mat4, Tensor } from 'mol-math/linear-algebra'
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import Format from '../../format'
import { Assembly, OperatorGroup, OperatorGroups } from '../../properties/symmetry'
-import { Queries as Q } from '../../../query'
+import { Queries as Q, Query } from '../../../query'
import mmCIF_Format = Format.mmCIF
@@ -57,10 +57,10 @@ function operatorGroupsProvider(generators: Generator[], matrices: Matrices): ()
const operatorList = parseOperatorList(gen.expression);
const operatorNames = expandOperators(operatorList);
const operators = getAssemblyOperators(matrices, operatorNames, operatorOffset);
- const selector = Q.generators.atoms({ chainTest: Q.pred.and(
+ const selector = Query(Q.generators.atoms({ chainTest: Q.pred.and(
Q.pred.eq(Q.props.unit.operator_name, SymmetryOperator.DefaultName),
Q.pred.inSet(Q.props.chain.label_asym_id, gen.asymIds)
- )});
+ )}));
groups[groups.length] = { selector, operators };
operatorOffset += operators.length;
}
diff --git a/src/mol-model/structure/model/formats/mmcif/bonds.ts b/src/mol-model/structure/model/formats/mmcif/bonds.ts
index 2a123a82d881f882362c9aaf27f2f001cb957964..139a7a8117647b2e14ff66dd0c9c5ea9f04bcbaf 100644
--- a/src/mol-model/structure/model/formats/mmcif/bonds.ts
+++ b/src/mol-model/structure/model/formats/mmcif/bonds.ts
@@ -6,12 +6,12 @@
*/
import Model from '../../model'
-import Bonds from '../../properties/bonds'
import { BondType } from '../../types'
import { findEntityIdByAsymId, findAtomIndexByLabelName } from './util'
import { Column } from 'mol-data/db'
+import { GroupBonds } from '../../../structure/element/properties/bonds/group-data';
-export class StructConn implements Bonds.StructConn {
+export class StructConn implements GroupBonds.StructConn {
private _residuePairIndex: Map<string, StructConn.Entry[]> | undefined = void 0;
private _atomIndex: Map<number, StructConn.Entry[]> | undefined = void 0;
@@ -71,7 +71,7 @@ export class StructConn implements Bonds.StructConn {
}
export namespace StructConn {
- export interface Entry extends Bonds.StructConnEntry {
+ export interface Entry extends GroupBonds.StructConnEntry {
distance: number,
order: number,
flags: number,
@@ -181,7 +181,7 @@ export namespace StructConn {
}
}
-export class ComponentBondInfo implements Bonds.ComponentBondInfo {
+export class ComponentBondInfo implements GroupBonds.ComponentBondInfo {
entries: Map<string, ComponentBondInfo.Entry> = new Map();
newEntry(id: string) {
@@ -192,7 +192,7 @@ export class ComponentBondInfo implements Bonds.ComponentBondInfo {
}
export namespace ComponentBondInfo {
- export class Entry implements Bonds.ComponentBondInfoEntry {
+ export class Entry implements GroupBonds.ComponentBondInfoEntry {
map: Map<string, Map<string, { order: number, flags: number }>> = new Map();
add(a: string, b: string, order: number, flags: number, swap = true) {
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 99a3877aa1b99b03eb46d3d12aacabf58cffef1b..e7f0fe0a8b85b9bf3b0b32f869bdf970ccb87f55 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -14,7 +14,6 @@ import CoarseGrained from './properties/coarse-grained'
import from_gro from './formats/gro'
import from_mmCIF from './formats/mmcif'
-
/**
* Interface to the "source data" of the molecule.
*
diff --git a/src/mol-model/structure/model/utils/compute-bonds.ts b/src/mol-model/structure/model/utils/compute-bonds.ts
deleted file mode 100644
index 6db9047fd2017f7c78e20f7325069e7759e989d1..0000000000000000000000000000000000000000
--- a/src/mol-model/structure/model/utils/compute-bonds.ts
+++ /dev/null
@@ -1,253 +0,0 @@
-// /**
-// * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.
-// *
-// * @author David Sehnal <david.sehnal@gmail.com>
-// */
-
-// import Mask from 'mol-util/mask'
-// import Model from '../model'
-// import { BondType, ElementSymbol } from '../types'
-// import Bonds from '../properties/bonds'
-// import { StructConn, ComponentBondInfo } from '../formats/mmcif/bonds'
-
-// export interface BondComputationParameters {
-// maxHbondLength: number,
-// forceCompute: boolean
-// }
-
-// // H,D,T are all mapped to H
-// const __ElementIndex: { [e: string]: number | undefined } = { 'H': 0, 'h': 0, 'D': 0, 'd': 0, 'T': 0, 't': 0, 'He': 2, 'HE': 2, 'he': 2, 'Li': 3, 'LI': 3, 'li': 3, 'Be': 4, 'BE': 4, 'be': 4, 'B': 5, 'b': 5, 'C': 6, 'c': 6, 'N': 7, 'n': 7, 'O': 8, 'o': 8, 'F': 9, 'f': 9, 'Ne': 10, 'NE': 10, 'ne': 10, 'Na': 11, 'NA': 11, 'na': 11, 'Mg': 12, 'MG': 12, 'mg': 12, 'Al': 13, 'AL': 13, 'al': 13, 'Si': 14, 'SI': 14, 'si': 14, 'P': 15, 'p': 15, 'S': 16, 's': 16, 'Cl': 17, 'CL': 17, 'cl': 17, 'Ar': 18, 'AR': 18, 'ar': 18, 'K': 19, 'k': 19, 'Ca': 20, 'CA': 20, 'ca': 20, 'Sc': 21, 'SC': 21, 'sc': 21, 'Ti': 22, 'TI': 22, 'ti': 22, 'V': 23, 'v': 23, 'Cr': 24, 'CR': 24, 'cr': 24, 'Mn': 25, 'MN': 25, 'mn': 25, 'Fe': 26, 'FE': 26, 'fe': 26, 'Co': 27, 'CO': 27, 'co': 27, 'Ni': 28, 'NI': 28, 'ni': 28, 'Cu': 29, 'CU': 29, 'cu': 29, 'Zn': 30, 'ZN': 30, 'zn': 30, 'Ga': 31, 'GA': 31, 'ga': 31, 'Ge': 32, 'GE': 32, 'ge': 32, 'As': 33, 'AS': 33, 'as': 33, 'Se': 34, 'SE': 34, 'se': 34, 'Br': 35, 'BR': 35, 'br': 35, 'Kr': 36, 'KR': 36, 'kr': 36, 'Rb': 37, 'RB': 37, 'rb': 37, 'Sr': 38, 'SR': 38, 'sr': 38, 'Y': 39, 'y': 39, 'Zr': 40, 'ZR': 40, 'zr': 40, 'Nb': 41, 'NB': 41, 'nb': 41, 'Mo': 42, 'MO': 42, 'mo': 42, 'Tc': 43, 'TC': 43, 'tc': 43, 'Ru': 44, 'RU': 44, 'ru': 44, 'Rh': 45, 'RH': 45, 'rh': 45, 'Pd': 46, 'PD': 46, 'pd': 46, 'Ag': 47, 'AG': 47, 'ag': 47, 'Cd': 48, 'CD': 48, 'cd': 48, 'In': 49, 'IN': 49, 'in': 49, 'Sn': 50, 'SN': 50, 'sn': 50, 'Sb': 51, 'SB': 51, 'sb': 51, 'Te': 52, 'TE': 52, 'te': 52, 'I': 53, 'i': 53, 'Xe': 54, 'XE': 54, 'xe': 54, 'Cs': 55, 'CS': 55, 'cs': 55, 'Ba': 56, 'BA': 56, 'ba': 56, 'La': 57, 'LA': 57, 'la': 57, 'Ce': 58, 'CE': 58, 'ce': 58, 'Pr': 59, 'PR': 59, 'pr': 59, 'Nd': 60, 'ND': 60, 'nd': 60, 'Pm': 61, 'PM': 61, 'pm': 61, 'Sm': 62, 'SM': 62, 'sm': 62, 'Eu': 63, 'EU': 63, 'eu': 63, 'Gd': 64, 'GD': 64, 'gd': 64, 'Tb': 65, 'TB': 65, 'tb': 65, 'Dy': 66, 'DY': 66, 'dy': 66, 'Ho': 67, 'HO': 67, 'ho': 67, 'Er': 68, 'ER': 68, 'er': 68, 'Tm': 69, 'TM': 69, 'tm': 69, 'Yb': 70, 'YB': 70, 'yb': 70, 'Lu': 71, 'LU': 71, 'lu': 71, 'Hf': 72, 'HF': 72, 'hf': 72, 'Ta': 73, 'TA': 73, 'ta': 73, 'W': 74, 'w': 74, 'Re': 75, 'RE': 75, 're': 75, 'Os': 76, 'OS': 76, 'os': 76, 'Ir': 77, 'IR': 77, 'ir': 77, 'Pt': 78, 'PT': 78, 'pt': 78, 'Au': 79, 'AU': 79, 'au': 79, 'Hg': 80, 'HG': 80, 'hg': 80, 'Tl': 81, 'TL': 81, 'tl': 81, 'Pb': 82, 'PB': 82, 'pb': 82, 'Bi': 83, 'BI': 83, 'bi': 83, 'Po': 84, 'PO': 84, 'po': 84, 'At': 85, 'AT': 85, 'at': 85, 'Rn': 86, 'RN': 86, 'rn': 86, 'Fr': 87, 'FR': 87, 'fr': 87, 'Ra': 88, 'RA': 88, 'ra': 88, 'Ac': 89, 'AC': 89, 'ac': 89, 'Th': 90, 'TH': 90, 'th': 90, 'Pa': 91, 'PA': 91, 'pa': 91, 'U': 92, 'u': 92, 'Np': 93, 'NP': 93, 'np': 93, 'Pu': 94, 'PU': 94, 'pu': 94, 'Am': 95, 'AM': 95, 'am': 95, 'Cm': 96, 'CM': 96, 'cm': 96, 'Bk': 97, 'BK': 97, 'bk': 97, 'Cf': 98, 'CF': 98, 'cf': 98, 'Es': 99, 'ES': 99, 'es': 99, 'Fm': 100, 'FM': 100, 'fm': 100, 'Md': 101, 'MD': 101, 'md': 101, 'No': 102, 'NO': 102, 'no': 102, 'Lr': 103, 'LR': 103, 'lr': 103, 'Rf': 104, 'RF': 104, 'rf': 104, 'Db': 105, 'DB': 105, 'db': 105, 'Sg': 106, 'SG': 106, 'sg': 106, 'Bh': 107, 'BH': 107, 'bh': 107, 'Hs': 108, 'HS': 108, 'hs': 108, 'Mt': 109, 'MT': 109, 'mt': 109 };
-
-// const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 1.9, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
-
-// const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.3, 35: 1.3, 44: 1.05, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.55, 113: 1.59, 114: 1.36, 129: 1.45, 144: 1.6, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
-
-// const __DefaultBondingRadius = 2.001;
-
-// const MetalsSet = (function () {
-// const metals = ['LI', 'NA', 'K', 'RB', 'CS', 'FR', 'BE', 'MG', 'CA', 'SR', 'BA', 'RA', 'AL', 'GA', 'IN', 'SN', 'TL', 'PB', 'BI', 'SC', 'TI', 'V', 'CR', 'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', 'Y', 'ZR', 'NB', 'MO', 'TC', 'RU', 'RH', 'PD', 'AG', 'CD', 'LA', 'HF', 'TA', 'W', 'RE', 'OS', 'IR', 'PT', 'AU', 'HG', 'AC', 'RF', 'DB', 'SG', 'BH', 'HS', 'MT', 'CE', 'PR', 'ND', 'PM', 'SM', 'EU', 'GD', 'TB', 'DY', 'HO', 'ER', 'TM', 'YB', 'LU', 'TH', 'PA', 'U', 'NP', 'PU', 'AM', 'CM', 'BK', 'CF', 'ES', 'FM', 'MD', 'NO', 'LR'];
-// const set = new Set<number>();
-// for (const m of metals) {
-// set.add(__ElementIndex[m]!);
-// }
-// return set;
-// })();
-
-// function pair(a: number, b: number) {
-// if (a < b) return (a + b) * (a + b + 1) / 2 + b;
-// else return (a + b) * (a + b + 1) / 2 + a;
-// }
-
-// function idx(e: ElementSymbol) {
-// const i = __ElementIndex[e as any as string];
-// if (i === void 0) return -1;
-// return i;
-// }
-
-// function pairThreshold(i: number, j: number) {
-// if (i < 0 || j < 0) return -1;
-// const r = __ElementPairThresholds[pair(i, j)];
-// if (r === void 0) return -1;
-// return r;
-// }
-
-// function threshold(i: number) {
-// if (i < 0) return __DefaultBondingRadius;
-// const r = __ElementBondThresholds[i];
-// if (r === void 0) return __DefaultBondingRadius;
-// return r;
-// }
-
-// const H_ID = __ElementIndex['H']!;
-// function isHydrogen(i: number) {
-// return i === H_ID;
-// }
-
-// function computePerAtomBonds(atomA: number[], atomB: number[], _order: number[], _flags: number[], atomCount: number) {
-// const bucketSizes = new Int32Array(atomCount);
-// const bucketOffsets = new Int32Array(atomCount + 1) as any as number[];
-// const bucketFill = new Int32Array(atomCount);
-
-// for (const i of atomA) bucketSizes[i]++;
-// for (const i of atomB) bucketSizes[i]++;
-
-// let offset = 0;
-// for (let i = 0; i < atomCount; i++) {
-// bucketOffsets[i] = offset;
-// offset += bucketSizes[i];
-// }
-// bucketOffsets[atomCount] = offset;
-
-// const neighbor = new Int32Array(offset) as any as number[];
-// const flags = new Uint16Array(offset) as any as number[];
-// const order = new Int8Array(offset) as any as number[];
-
-// for (let i = 0, _i = atomA.length; i < _i; i++) {
-// const a = atomA[i], b = atomB[i], f = _flags[i], o = _order[i];
-
-// const oa = bucketOffsets[a] + bucketFill[a];
-// const ob = bucketOffsets[b] + bucketFill[b];
-
-// neighbor[oa] = b;
-// flags[oa] = f;
-// order[oa] = o;
-// bucketFill[a]++;
-
-// neighbor[ob] = a;
-// flags[ob] = f;
-// order[ob] = o;
-// bucketFill[b]++;
-// }
-
-// return {
-// offsets: bucketOffsets,
-// neighbor,
-// flags,
-// order
-// };
-// }
-
-// function _computeBonds(model: Model, params: BondComputationParameters): Bonds {
-// const MAX_RADIUS = 3;
-
-// const { x, y, z } = model.conformation;
-// const { atomCount } = model;
-// const { residueKey } = model.hierarchy
-// const { type_symbol, label_atom_id, label_alt_id } = model.hierarchy.atoms;
-// const { label_comp_id } = model.hierarchy.residues;
-// const query3d = Model.spatialLookup(model).find(Mask.always(atomCount));
-
-// const structConn = model.sourceData.kind === 'mmCIF' ? StructConn.create(model) : void 0
-// const component = model.sourceData.kind === 'mmCIF' ? ComponentBondInfo.create(model) : void 0
-
-// const atomA: number[] = [];
-// const atomB: number[] = [];
-// const flags: number[] = [];
-// const order: number[] = [];
-
-// let lastResidue = -1;
-// let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
-
-// for (let aI = 0; aI < atomCount; aI++) {
-// const raI = residueKey.value(aI);
-// // const rowA = dataIndex[aI]; // TODO
-// const rowA = aI;
-
-// if (!params.forceCompute && raI !== lastResidue) {
-// const resn = label_comp_id.value(rowA)!;
-// if (!!component && component.entries.has(resn)) {
-// componentMap = component.entries.get(resn)!.map;
-// } else {
-// componentMap = void 0;
-// }
-// }
-// lastResidue = raI;
-
-// const componentPairs = componentMap ? componentMap.get(label_atom_id.value(rowA)) : void 0;
-
-// const aeI = idx(type_symbol.value(rowA)!);
-
-// const { indices, count, squaredDistances } = query3d(x[aI], y[aI], z[aI], MAX_RADIUS);
-// const isHa = isHydrogen(aeI);
-// const thresholdA = threshold(aeI);
-// const altA = label_alt_id.value(rowA);
-// const metalA = MetalsSet.has(aeI);
-// const structConnEntries = params.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
-
-// for (let ni = 0; ni < count; ni++) {
-// const bI = indices[ni];
-// if (bI <= aI) continue;
-
-// // const rowB = dataIndex[bI]; // TODO
-// const rowB = bI;
-
-// const altB = label_alt_id.value(rowB);
-// if (altA && altB && altA !== altB) continue;
-
-// const beI = idx(type_symbol.value(rowB)!);
-// const isMetal = metalA || MetalsSet.has(beI);
-
-// const rbI = residueKey.value(bI);
-// // handle "component dictionary" bonds.
-// if (raI === rbI && componentPairs) {
-// const e = componentPairs.get(label_atom_id.value(rowB)!);
-// if (e) {
-// atomA[atomA.length] = aI;
-// atomB[atomB.length] = bI;
-// order[order.length] = e.order;
-// let flag = e.flags;
-// if (isMetal) {
-// if (flag | BondType.Flag.Covalent) flag ^= BondType.Flag.Covalent;
-// flag |= BondType.Flag.MetallicCoordination;
-// }
-// flags[flags.length] = flag;
-// }
-// continue;
-// }
-
-// const isHb = isHydrogen(beI);
-// if (isHa && isHb) continue;
-
-// const dist = Math.sqrt(squaredDistances[ni]);
-// if (dist === 0) continue;
-
-// // handle "struct conn" bonds.
-// if (structConnEntries && structConnEntries.length) {
-// let added = false;
-// for (const se of structConnEntries) {
-// for (const p of se.partners) {
-// if (p.atomIndex === bI) {
-// atomA[atomA.length] = aI;
-// atomB[atomB.length] = bI;
-// flags[flags.length] = se.flags;
-// order[order.length] = se.order;
-// added = true;
-// break;
-// }
-// }
-// if (added) break;
-// }
-// if (added) continue;
-// }
-
-// if (isHa || isHb) {
-// if (dist < params.maxHbondLength) {
-// atomA[atomA.length] = aI;
-// atomB[atomB.length] = bI;
-// order[order.length] = 1;
-// flags[flags.length] = BondType.Flag.Covalent | BondType.Flag.Computed; // TODO: check if correct
-// }
-// continue;
-// }
-
-// const thresholdAB = pairThreshold(aeI, beI);
-// const pairingThreshold = thresholdAB > 0
-// ? thresholdAB
-// : beI < 0 ? thresholdA : Math.max(thresholdA, threshold(beI));
-
-
-// if (dist <= pairingThreshold) {
-// atomA[atomA.length] = aI;
-// atomB[atomB.length] = bI;
-// order[order.length] = 1;
-// flags[flags.length] = (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed;
-// }
-// }
-// }
-
-// const bonds = computePerAtomBonds(atomA, atomB, order, flags, atomCount);
-// return {
-// offset: bonds.offsets,
-// neighbor: bonds.neighbor,
-// flags: bonds.flags,
-// order: bonds.order,
-// count: atomA.length
-// };
-// }
-
-// export default function computeBonds(model: Model, params?: Partial<BondComputationParameters>) {
-// return _computeBonds(model, {
-// maxHbondLength: (params && params.maxHbondLength) || 1.15,
-// forceCompute: !!(params && params.forceCompute),
-// });
-// }
\ No newline at end of file
diff --git a/src/mol-model/structure/query/generators.ts b/src/mol-model/structure/query/generators.ts
index 53fff73ed4b567bdb202ba72a2b6a02b42df34fb..56beedae592d85f6436c39ba1593fc9f77a17e35 100644
--- a/src/mol-model/structure/query/generators.ts
+++ b/src/mol-model/structure/query/generators.ts
@@ -10,7 +10,7 @@ import P from './properties'
import { Structure, ElementSet, Element } from '../structure'
import { OrderedSet, Segmentation } from 'mol-data/int'
-export const all: Query = s => Selection.Singletons(s, s.elements);
+export const all: Query.Provider = async (s, ctx) => Selection.Singletons(s, s.elements);
export interface AtomQueryParams {
entityTest: Element.Predicate,
@@ -27,7 +27,7 @@ export interface AtomGroupsQueryParams extends AtomQueryParams {
export function residues(params?: Partial<AtomQueryParams>) { return atoms({ ...params, groupBy: P.residue.key }); }
export function chains(params?: Partial<AtomQueryParams>) { return atoms({ ...params, groupBy: P.chain.key }); }
-export function atoms(params?: Partial<AtomGroupsQueryParams>): Query {
+export function atoms(params?: Partial<AtomGroupsQueryParams>): Query.Provider {
if (!params || (!params.atomTest && !params.residueTest && !params.chainTest && !params.entityTest && !params.groupBy)) return all;
if (!!params.atomTest && !params.residueTest && !params.chainTest && !params.entityTest && !params.groupBy) return atomGroupsLinear(params.atomTest);
@@ -43,17 +43,17 @@ export function atoms(params?: Partial<AtomGroupsQueryParams>): Query {
return atomGroupsGrouped(normalized);
}
-function atomGroupsLinear(atomTest: Element.Predicate): Query {
- return structure => {
+function atomGroupsLinear(atomTest: Element.Predicate): Query.Provider {
+ return async (structure, ctx) => {
const { elements, units } = structure;
- const unitIds = ElementSet.unitIds(elements);
+ const unitIds = ElementSet.unitIndices(elements);
const l = Element.Location();
const builder = ElementSet.LinearBuilder(elements);
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unitId = unitIds[i];
l.unit = units[unitId];
- const set = ElementSet.unitGetByIndex(elements, i).elements;
+ const set = ElementSet.groupAt(elements, i).elements;
builder.beginUnit();
for (let j = 0, _j = OrderedSet.size(set); j < _j; j++) {
@@ -61,16 +61,18 @@ function atomGroupsLinear(atomTest: Element.Predicate): Query {
if (atomTest(l)) builder.addToUnit(l.element);
}
builder.commitUnit(unitId);
+
+ if (ctx.shouldUpdate) await ctx.update({ message: 'Atom Groups', current: 0, max: unitIds.length });
}
return Selection.Singletons(structure, builder.getSet());
};
}
-function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: AtomGroupsQueryParams): Query {
- return structure => {
+function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: AtomGroupsQueryParams): Query.Provider {
+ return async (structure, ctx) => {
const { elements, units } = structure;
- const unitIds = ElementSet.unitIds(elements);
+ const unitIds = ElementSet.unitIndices(elements);
const l = Element.Location();
const builder = ElementSet.LinearBuilder(elements);
@@ -78,7 +80,7 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
const unitId = unitIds[i];
const unit = units[unitId];
l.unit = unit;
- const set = ElementSet.unitGetByIndex(elements, i).elements;
+ const set = ElementSet.groupAt(elements, i).elements;
builder.beginUnit();
const chainsIt = Segmentation.transientSegments(unit.hierarchy.chainSegments, set);
@@ -104,6 +106,8 @@ function atomGroupsSegmented({ entityTest, chainTest, residueTest, atomTest }: A
}
}
builder.commitUnit(unitId);
+
+ if (ctx.shouldUpdate) await ctx.update({ message: 'Atom Groups', current: 0, max: unitIds.length });
}
return Selection.Singletons(structure, builder.getSet());
@@ -157,10 +161,10 @@ class LinearGroupingBuilder {
constructor(private structure: Structure) { }
}
-function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, groupBy }: AtomGroupsQueryParams): Query {
- return structure => {
+function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, groupBy }: AtomGroupsQueryParams): Query.Provider {
+ return async (structure, ctx) => {
const { elements, units } = structure;
- const unitIds = ElementSet.unitIds(elements);
+ const unitIds = ElementSet.unitIndices(elements);
const l = Element.Location();
const builder = new LinearGroupingBuilder(structure);
@@ -168,7 +172,7 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
const unitId = unitIds[i];
const unit = units[unitId];
l.unit = unit;
- const set = ElementSet.unitGetByIndex(elements, i).elements;
+ const set = ElementSet.groupAt(elements, i).elements;
const chainsIt = Segmentation.transientSegments(unit.hierarchy.chainSegments, set);
const residuesIt = Segmentation.transientSegments(unit.hierarchy.residueSegments, set);
@@ -192,6 +196,8 @@ function atomGroupsGrouped({ entityTest, chainTest, residueTest, atomTest, group
}
}
}
+
+ if (ctx.shouldUpdate) await ctx.update({ message: 'Atom Groups', current: 0, max: unitIds.length });
}
return builder.getSelection();
diff --git a/src/mol-model/structure/query/query.ts b/src/mol-model/structure/query/query.ts
index 001f1e0e79b3082011d3b60baecfa2a67e88befa..e8620e337b1b10f137b295adc148c43d57133166 100644
--- a/src/mol-model/structure/query/query.ts
+++ b/src/mol-model/structure/query/query.ts
@@ -4,10 +4,21 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
+import { Task, RuntimeContext } from 'mol-task'
import { Structure } from '../structure'
import Selection from './selection'
// TODO: Query { (s: Structure): Computation<Selection> }
-interface Query { (s: Structure): Selection }
+interface Query { (s: Structure): Task<Selection>, provider: Query.Provider }
+function Query(q: Query.Provider): Query {
+ const ret = (s => Task.create('Query', ctx => q(s, ctx))) as Query;
+ ret.provider = q;
+ return ret;
+}
+
+namespace Query {
+ export interface Provider { (s: Structure, ctx: RuntimeContext): Promise<Selection> }
+}
+
export default Query
\ No newline at end of file
diff --git a/src/mol-model/structure/query/selection.ts b/src/mol-model/structure/query/selection.ts
index fb4f43f7dc10673043445fdacd30f8a0890ac183..f9f516710817ea7ae9d8c042457a7f81e2f53a2d 100644
--- a/src/mol-model/structure/query/selection.ts
+++ b/src/mol-model/structure/query/selection.ts
@@ -35,7 +35,7 @@ namespace Selection {
export function getAt(sel: Selection, i: number): Structure {
if (isSingleton(sel)) {
- const atom = ElementSet.elementGetAt(sel.set, i);
+ const atom = ElementSet.elementAt(sel.set, i);
return Structure.create(sel.structure.units, ElementSet.singleton(atom, sel.structure.elements));
}
return Structure.create(sel.structure.units, sel.sets[i]);
diff --git a/src/mol-model/structure/structure/element/group.ts b/src/mol-model/structure/structure/element/group.ts
index ec7544470f6cf9c29a19ad606a83f904adf61934..e89b3d37e87b6611a0630fe4978fe1218ceaa76b 100644
--- a/src/mol-model/structure/structure/element/group.ts
+++ b/src/mol-model/structure/structure/element/group.ts
@@ -5,15 +5,17 @@
*/
import { OrderedSet } from 'mol-data/int'
-import { Lookup3D, GridLookup3D } from 'mol-math/geometry';
+import { Lookup3D } from 'mol-math/geometry'
import Unit from '../unit'
+import { GroupBonds } from './properties/bonds/group-data';
interface ElementGroup {
elements: OrderedSet,
// Unique identifier of the group, usable as partial key for various "caches".
key: number,
- __lookup3d__?: Lookup3D
+ __lookup3d__?: Lookup3D,
+ __bonds__?: GroupBonds
}
namespace ElementGroup {
@@ -64,17 +66,6 @@ namespace ElementGroup {
return createNew(set);
}
- export function getLookup3d(unit: Unit, group: ElementGroup) {
- if (group.__lookup3d__) return group.__lookup3d__;
- if (Unit.isAtomic(unit)) {
- const { x, y, z } = unit.model.conformation;
- group.__lookup3d__ = GridLookup3D({ x, y, z, indices: group.elements });
- return group.__lookup3d__;
- }
-
- throw 'not implemented';
- }
-
let _id = 0;
function nextKey() {
const ret = _id;
diff --git a/src/mol-model/structure/structure/element/impl/set.ts b/src/mol-model/structure/structure/element/impl/set.ts
index cae6746058e0c0ecd8925fc326586c71cf2e09cb..2aaf3182e5f1ea62f0c313357d3b48d6b8a5dd4c 100644
--- a/src/mol-model/structure/structure/element/impl/set.ts
+++ b/src/mol-model/structure/structure/element/impl/set.ts
@@ -9,10 +9,19 @@ import { sortArray } from 'mol-data/util/sort'
import { hash1 } from 'mol-data/util/hash-functions'
import Element from '../../element'
import ElementGroup from '../group'
+import { ElementSetLookup3D } from '../../util/lookup3d'
+import Structure from '../../structure';
/** Long and painful implementation starts here */
-export type ElementSetImpl = { groups: IntMap<ElementGroup>, offsets: Int32Array, hashCode: number, keys: SortedArray }
+export type ElementSetImpl = {
+ groups: IntMap<ElementGroup>,
+ offsets: Int32Array,
+ hashCode: number,
+ keys: SortedArray,
+
+ __lookup3d__?: ElementSetLookup3D
+}
export const Empty: ElementSetImpl = { groups: IntMap.Empty, offsets: new Int32Array(1), hashCode: 0, keys: SortedArray.Empty };
@@ -270,6 +279,13 @@ export function Generator() {
return new AtomSetGenerator();
}
+export function getLookup3d(s: Structure) {
+ const set = s.elements as any as ElementSetImpl;
+ if (set.__lookup3d__) return set.__lookup3d__;
+ set.__lookup3d__ = ElementSetLookup3D.create(s);
+ return set.__lookup3d__;
+}
+
/** When adding groups, compare them to existing ones. If they all match, return the whole original set. */
class ChildGenerator {
private keys: number[] = [];
diff --git a/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts b/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
new file mode 100644
index 0000000000000000000000000000000000000000..fb078c889fb924c543659b995eb6b6eea3e28eba
--- /dev/null
+++ b/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
@@ -0,0 +1,253 @@
+/**
+ * Copyright (c) 2017 MolQL contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { BondType, ElementSymbol } from '../../../../model/types'
+import { GroupBonds } from './group-data'
+import { StructConn, ComponentBondInfo } from '../../../../model/formats/mmcif/bonds'
+import Unit from '../../../unit';
+import ElementGroup from '../../group';
+
+export interface BondComputationParameters {
+ maxHbondLength: number,
+ forceCompute: boolean
+}
+
+// H,D,T are all mapped to H
+const __ElementIndex: { [e: string]: number | undefined } = { 'H': 0, 'h': 0, 'D': 0, 'd': 0, 'T': 0, 't': 0, 'He': 2, 'HE': 2, 'he': 2, 'Li': 3, 'LI': 3, 'li': 3, 'Be': 4, 'BE': 4, 'be': 4, 'B': 5, 'b': 5, 'C': 6, 'c': 6, 'N': 7, 'n': 7, 'O': 8, 'o': 8, 'F': 9, 'f': 9, 'Ne': 10, 'NE': 10, 'ne': 10, 'Na': 11, 'NA': 11, 'na': 11, 'Mg': 12, 'MG': 12, 'mg': 12, 'Al': 13, 'AL': 13, 'al': 13, 'Si': 14, 'SI': 14, 'si': 14, 'P': 15, 'p': 15, 'S': 16, 's': 16, 'Cl': 17, 'CL': 17, 'cl': 17, 'Ar': 18, 'AR': 18, 'ar': 18, 'K': 19, 'k': 19, 'Ca': 20, 'CA': 20, 'ca': 20, 'Sc': 21, 'SC': 21, 'sc': 21, 'Ti': 22, 'TI': 22, 'ti': 22, 'V': 23, 'v': 23, 'Cr': 24, 'CR': 24, 'cr': 24, 'Mn': 25, 'MN': 25, 'mn': 25, 'Fe': 26, 'FE': 26, 'fe': 26, 'Co': 27, 'CO': 27, 'co': 27, 'Ni': 28, 'NI': 28, 'ni': 28, 'Cu': 29, 'CU': 29, 'cu': 29, 'Zn': 30, 'ZN': 30, 'zn': 30, 'Ga': 31, 'GA': 31, 'ga': 31, 'Ge': 32, 'GE': 32, 'ge': 32, 'As': 33, 'AS': 33, 'as': 33, 'Se': 34, 'SE': 34, 'se': 34, 'Br': 35, 'BR': 35, 'br': 35, 'Kr': 36, 'KR': 36, 'kr': 36, 'Rb': 37, 'RB': 37, 'rb': 37, 'Sr': 38, 'SR': 38, 'sr': 38, 'Y': 39, 'y': 39, 'Zr': 40, 'ZR': 40, 'zr': 40, 'Nb': 41, 'NB': 41, 'nb': 41, 'Mo': 42, 'MO': 42, 'mo': 42, 'Tc': 43, 'TC': 43, 'tc': 43, 'Ru': 44, 'RU': 44, 'ru': 44, 'Rh': 45, 'RH': 45, 'rh': 45, 'Pd': 46, 'PD': 46, 'pd': 46, 'Ag': 47, 'AG': 47, 'ag': 47, 'Cd': 48, 'CD': 48, 'cd': 48, 'In': 49, 'IN': 49, 'in': 49, 'Sn': 50, 'SN': 50, 'sn': 50, 'Sb': 51, 'SB': 51, 'sb': 51, 'Te': 52, 'TE': 52, 'te': 52, 'I': 53, 'i': 53, 'Xe': 54, 'XE': 54, 'xe': 54, 'Cs': 55, 'CS': 55, 'cs': 55, 'Ba': 56, 'BA': 56, 'ba': 56, 'La': 57, 'LA': 57, 'la': 57, 'Ce': 58, 'CE': 58, 'ce': 58, 'Pr': 59, 'PR': 59, 'pr': 59, 'Nd': 60, 'ND': 60, 'nd': 60, 'Pm': 61, 'PM': 61, 'pm': 61, 'Sm': 62, 'SM': 62, 'sm': 62, 'Eu': 63, 'EU': 63, 'eu': 63, 'Gd': 64, 'GD': 64, 'gd': 64, 'Tb': 65, 'TB': 65, 'tb': 65, 'Dy': 66, 'DY': 66, 'dy': 66, 'Ho': 67, 'HO': 67, 'ho': 67, 'Er': 68, 'ER': 68, 'er': 68, 'Tm': 69, 'TM': 69, 'tm': 69, 'Yb': 70, 'YB': 70, 'yb': 70, 'Lu': 71, 'LU': 71, 'lu': 71, 'Hf': 72, 'HF': 72, 'hf': 72, 'Ta': 73, 'TA': 73, 'ta': 73, 'W': 74, 'w': 74, 'Re': 75, 'RE': 75, 're': 75, 'Os': 76, 'OS': 76, 'os': 76, 'Ir': 77, 'IR': 77, 'ir': 77, 'Pt': 78, 'PT': 78, 'pt': 78, 'Au': 79, 'AU': 79, 'au': 79, 'Hg': 80, 'HG': 80, 'hg': 80, 'Tl': 81, 'TL': 81, 'tl': 81, 'Pb': 82, 'PB': 82, 'pb': 82, 'Bi': 83, 'BI': 83, 'bi': 83, 'Po': 84, 'PO': 84, 'po': 84, 'At': 85, 'AT': 85, 'at': 85, 'Rn': 86, 'RN': 86, 'rn': 86, 'Fr': 87, 'FR': 87, 'fr': 87, 'Ra': 88, 'RA': 88, 'ra': 88, 'Ac': 89, 'AC': 89, 'ac': 89, 'Th': 90, 'TH': 90, 'th': 90, 'Pa': 91, 'PA': 91, 'pa': 91, 'U': 92, 'u': 92, 'Np': 93, 'NP': 93, 'np': 93, 'Pu': 94, 'PU': 94, 'pu': 94, 'Am': 95, 'AM': 95, 'am': 95, 'Cm': 96, 'CM': 96, 'cm': 96, 'Bk': 97, 'BK': 97, 'bk': 97, 'Cf': 98, 'CF': 98, 'cf': 98, 'Es': 99, 'ES': 99, 'es': 99, 'Fm': 100, 'FM': 100, 'fm': 100, 'Md': 101, 'MD': 101, 'md': 101, 'No': 102, 'NO': 102, 'no': 102, 'Lr': 103, 'LR': 103, 'lr': 103, 'Rf': 104, 'RF': 104, 'rf': 104, 'Db': 105, 'DB': 105, 'db': 105, 'Sg': 106, 'SG': 106, 'sg': 106, 'Bh': 107, 'BH': 107, 'bh': 107, 'Hs': 108, 'HS': 108, 'hs': 108, 'Mt': 109, 'MT': 109, 'mt': 109 };
+
+const __ElementBondThresholds: { [e: number]: number | undefined } = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 1.9, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
+
+const __ElementPairThresholds: { [e: number]: number | undefined } = { 0: 0.8, 20: 1.31, 27: 1.3, 35: 1.3, 44: 1.05, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.55, 113: 1.59, 114: 1.36, 129: 1.45, 144: 1.6, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
+
+const __DefaultBondingRadius = 2.001;
+
+const MetalsSet = (function () {
+ const metals = ['LI', 'NA', 'K', 'RB', 'CS', 'FR', 'BE', 'MG', 'CA', 'SR', 'BA', 'RA', 'AL', 'GA', 'IN', 'SN', 'TL', 'PB', 'BI', 'SC', 'TI', 'V', 'CR', 'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', 'Y', 'ZR', 'NB', 'MO', 'TC', 'RU', 'RH', 'PD', 'AG', 'CD', 'LA', 'HF', 'TA', 'W', 'RE', 'OS', 'IR', 'PT', 'AU', 'HG', 'AC', 'RF', 'DB', 'SG', 'BH', 'HS', 'MT', 'CE', 'PR', 'ND', 'PM', 'SM', 'EU', 'GD', 'TB', 'DY', 'HO', 'ER', 'TM', 'YB', 'LU', 'TH', 'PA', 'U', 'NP', 'PU', 'AM', 'CM', 'BK', 'CF', 'ES', 'FM', 'MD', 'NO', 'LR'];
+ const set = new Set<number>();
+ for (const m of metals) {
+ set.add(__ElementIndex[m]!);
+ }
+ return set;
+})();
+
+function pair(a: number, b: number) {
+ if (a < b) return (a + b) * (a + b + 1) / 2 + b;
+ else return (a + b) * (a + b + 1) / 2 + a;
+}
+
+function idx(e: ElementSymbol) {
+ const i = __ElementIndex[e as any as string];
+ if (i === void 0) return -1;
+ return i;
+}
+
+function pairThreshold(i: number, j: number) {
+ if (i < 0 || j < 0) return -1;
+ const r = __ElementPairThresholds[pair(i, j)];
+ if (r === void 0) return -1;
+ return r;
+}
+
+function threshold(i: number) {
+ if (i < 0) return __DefaultBondingRadius;
+ const r = __ElementBondThresholds[i];
+ if (r === void 0) return __DefaultBondingRadius;
+ return r;
+}
+
+const H_ID = __ElementIndex['H']!;
+function isHydrogen(i: number) {
+ return i === H_ID;
+}
+
+function computePerAtomBonds(atomA: number[], atomB: number[], _order: number[], _flags: number[], atomCount: number) {
+ const bucketSizes = new Int32Array(atomCount);
+ const bucketOffsets = new Int32Array(atomCount + 1) as any as number[];
+ const bucketFill = new Int32Array(atomCount);
+
+ for (const i of atomA) bucketSizes[i]++;
+ for (const i of atomB) bucketSizes[i]++;
+
+ let offset = 0;
+ for (let i = 0; i < atomCount; i++) {
+ bucketOffsets[i] = offset;
+ offset += bucketSizes[i];
+ }
+ bucketOffsets[atomCount] = offset;
+
+ const neighbor = new Int32Array(offset) as any as number[];
+ const flags = new Uint16Array(offset) as any as number[];
+ const order = new Int8Array(offset) as any as number[];
+
+ for (let i = 0, _i = atomA.length; i < _i; i++) {
+ const a = atomA[i], b = atomB[i], f = _flags[i], o = _order[i];
+
+ const oa = bucketOffsets[a] + bucketFill[a];
+ const ob = bucketOffsets[b] + bucketFill[b];
+
+ neighbor[oa] = b;
+ flags[oa] = f;
+ order[oa] = o;
+ bucketFill[a]++;
+
+ neighbor[ob] = a;
+ flags[ob] = f;
+ order[ob] = o;
+ bucketFill[b]++;
+ }
+
+ return {
+ offsets: bucketOffsets,
+ neighbor,
+ flags,
+ order
+ };
+}
+
+function _computeBonds(unit: Unit.Atomic, atoms: ElementGroup, params: BondComputationParameters): GroupBonds {
+ const MAX_RADIUS = 3;
+
+ const { x, y, z } = unit.model.conformation;
+ const atomCount = ElementGroup.size(atoms);
+ const { residueIndex } = unit;
+ const { type_symbol, label_atom_id, label_alt_id } = unit.model.hierarchy.atoms;
+ const { label_comp_id } = unit.model.hierarchy.residues;
+ const query3d = Unit.getLookup3d(unit, atoms);
+
+ const structConn = unit.model.sourceData.kind === 'mmCIF' ? StructConn.create(unit.model) : void 0
+ const component = unit.model.sourceData.kind === 'mmCIF' ? ComponentBondInfo.create(unit.model) : void 0
+
+ const atomA: number[] = [];
+ const atomB: number[] = [];
+ const flags: number[] = [];
+ const order: number[] = [];
+
+ let lastResidue = -1;
+ let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
+
+ for (let _aI = 0; _aI < atomCount; _aI++) {
+ const aI = ElementGroup.getAt(atoms, _aI);
+ const raI = residueIndex[aI];
+
+ if (!params.forceCompute && raI !== lastResidue) {
+ const resn = label_comp_id.value(raI)!;
+ if (!!component && component.entries.has(resn)) {
+ componentMap = component.entries.get(resn)!.map;
+ } else {
+ componentMap = void 0;
+ }
+ }
+ lastResidue = raI;
+
+ const componentPairs = componentMap ? componentMap.get(label_atom_id.value(aI)) : void 0;
+
+ const aeI = idx(type_symbol.value(aI)!);
+
+ const { indices, count, squaredDistances } = query3d.find(x[aI], y[aI], z[aI], MAX_RADIUS);
+ const isHa = isHydrogen(aeI);
+ const thresholdA = threshold(aeI);
+ const altA = label_alt_id.value(aI);
+ const metalA = MetalsSet.has(aeI);
+ const structConnEntries = params.forceCompute ? void 0 : structConn && structConn.getAtomEntries(aI);
+
+ for (let ni = 0; ni < count; ni++) {
+ const _bI = indices[ni];
+ const bI = ElementGroup.getAt(atoms, _bI);
+ if (bI <= aI) continue;
+
+ const altB = label_alt_id.value(bI);
+ if (altA && altB && altA !== altB) continue;
+
+ const beI = idx(type_symbol.value(bI)!);
+ const isMetal = metalA || MetalsSet.has(beI);
+
+ const rbI = residueIndex[bI];
+ // handle "component dictionary" bonds.
+ if (raI === rbI && componentPairs) {
+ const e = componentPairs.get(label_atom_id.value(bI)!);
+ if (e) {
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ order[order.length] = e.order;
+ let flag = e.flags;
+ if (isMetal) {
+ if (flag | BondType.Flag.Covalent) flag ^= BondType.Flag.Covalent;
+ flag |= BondType.Flag.MetallicCoordination;
+ }
+ flags[flags.length] = flag;
+ }
+ continue;
+ }
+
+ const isHb = isHydrogen(beI);
+ if (isHa && isHb) continue;
+
+ const dist = Math.sqrt(squaredDistances[ni]);
+ if (dist === 0) continue;
+
+ // handle "struct conn" bonds.
+ if (structConnEntries && structConnEntries.length) {
+ let added = false;
+ for (const se of structConnEntries) {
+ for (const p of se.partners) {
+ if (p.atomIndex === bI) {
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ flags[flags.length] = se.flags;
+ order[order.length] = se.order;
+ added = true;
+ break;
+ }
+ }
+ if (added) break;
+ }
+ if (added) continue;
+ }
+
+ if (isHa || isHb) {
+ if (dist < params.maxHbondLength) {
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ order[order.length] = 1;
+ flags[flags.length] = BondType.Flag.Covalent | BondType.Flag.Computed; // TODO: check if correct
+ }
+ continue;
+ }
+
+ const thresholdAB = pairThreshold(aeI, beI);
+ const pairingThreshold = thresholdAB > 0
+ ? thresholdAB
+ : beI < 0 ? thresholdA : Math.max(thresholdA, threshold(beI));
+
+
+ if (dist <= pairingThreshold) {
+ atomA[atomA.length] = _aI;
+ atomB[atomB.length] = _bI;
+ order[order.length] = 1;
+ flags[flags.length] = (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed;
+ }
+ }
+ }
+
+ const bonds = computePerAtomBonds(atomA, atomB, order, flags, atomCount);
+
+ return {
+ offset: bonds.offsets,
+ neighbor: bonds.neighbor,
+ flags: bonds.flags,
+ order: bonds.order,
+ count: atomA.length
+ };
+}
+
+function computeUnitBonds(unit: Unit.Atomic, atoms: ElementGroup, params?: Partial<BondComputationParameters>) {
+ return _computeBonds(unit, atoms, {
+ maxHbondLength: (params && params.maxHbondLength) || 1.15,
+ forceCompute: !!(params && params.forceCompute),
+ });
+}
+
+export { computeUnitBonds }
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/bonds.ts b/src/mol-model/structure/structure/element/properties/bonds/group-data.ts
similarity index 88%
rename from src/mol-model/structure/model/properties/bonds.ts
rename to src/mol-model/structure/structure/element/properties/bonds/group-data.ts
index 706202d4d4693a3df4d235969a5e8f7a8fafeaae..0406f05d326db903c081be750001b069b4a89578 100644
--- a/src/mol-model/structure/model/properties/bonds.ts
+++ b/src/mol-model/structure/structure/element/properties/bonds/group-data.ts
@@ -5,9 +5,9 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { BondType } from '../types'
+import { BondType } from '../../../../model/types'
-interface Bonds {
+interface GroupBonds {
/**
* Where bonds for atom A start and end.
* Start offset at idx, end at idx + 1
@@ -21,8 +21,8 @@ interface Bonds {
count: number
}
-namespace Bonds {
- export function createEmpty(): Bonds {
+namespace GroupBonds {
+ export function createEmpty(): GroupBonds {
return { offset: [], neighbor: [], order: [], flags: [], count: 0 }
}
export function isCovalent(flags: number) {
@@ -46,6 +46,4 @@ namespace Bonds {
}
}
-
-
-export default Bonds
\ No newline at end of file
+export { GroupBonds }
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/element/set.ts b/src/mol-model/structure/structure/element/set.ts
index 0ecb481cd92560f156c9155ff75768de1403aabc..dddebe8bfd28b73505e0c93d18840a68087d83d4 100644
--- a/src/mol-model/structure/structure/element/set.ts
+++ b/src/mol-model/structure/structure/element/set.ts
@@ -9,26 +9,32 @@ import Element from '../element'
import ElementGroup from './group'
import * as Impl from './impl/set'
import * as Builders from './impl/set-builder'
+import { ElementSetLookup3D } from '../util/lookup3d';
+import Structure from '../structure';
-/** A map-like representation of grouped atom set */
+/**
+ * A map-like representation of grouped atom set
+ *
+ * Essentially corresponds to the type { [unitId: number]: ElementGroup }.
+ */
namespace ElementSet {
export const Empty: ElementSet = Impl.Empty as any;
export const ofAtoms: (elements: ArrayLike<Element>, template: ElementSet) => ElementSet = Impl.ofElements as any;
export const singleton: (element: Element, template: ElementSet) => ElementSet = Impl.singleton as any;
- export const unitCount: (set: ElementSet) => number = Impl.keyCount as any;
- export const unitIds: (set: ElementSet) => SortedArray = Impl.getKeys as any;
- export const unitHas: (set: ElementSet, id: number) => boolean = Impl.hasKey as any;
- export const unitGetId: (set: ElementSet, i: number) => number = Impl.getKey as any;
+ export const unitIndices: (set: ElementSet) => SortedArray = Impl.getKeys as any;
+ export const unitHas: (set: ElementSet, index: number) => boolean = Impl.hasKey as any;
- export const unitGetById: (set: ElementSet, key: number) => ElementGroup = Impl.getByKey as any;
- export const unitGetByIndex: (set: ElementSet, i: number) => ElementGroup = Impl.getByIndex as any;
+ export const groupCount: (set: ElementSet) => number = Impl.keyCount as any;
+ export const groupUnitIndex: (set: ElementSet, index: number) => number = Impl.getKey as any;
+ export const groupFromUnitIndex: (set: ElementSet, unitId: number) => ElementGroup = Impl.getByKey as any;
+ export const groupAt: (set: ElementSet, index: number) => ElementGroup = Impl.getByIndex as any;
export const elementCount: (set: ElementSet) => number = Impl.size as any;
export const elementHas: (set: ElementSet, x: Element) => boolean = Impl.hasAtom as any;
export const elementIndexOf: (set: ElementSet, x: Element) => number = Impl.indexOf as any;
- export const elementGetAt: (set: ElementSet, i: number) => Element = Impl.getAt as any;
+ export const elementAt: (set: ElementSet, i: number) => Element = Impl.getAt as any;
export const elements: (set: ElementSet) => Iterator<Element> = Impl.values as any;
export const hashCode: (set: ElementSet) => number = Impl.hashCode as any;
@@ -49,12 +55,13 @@ namespace ElementSet {
export interface TemplateGenerator { add(unit: number, set: OrderedSet): void, getSet(): ElementSet }
export const TemplateGenerator: (template: ElementSet) => TemplateGenerator = Impl.TemplateGenerator as any
- // TODO: bounding sphere
+ export const getLookup3d: (s: Structure) => ElementSetLookup3D = Impl.getLookup3d;
+
// TODO: distance, areWithIn?
// TODO: check connected
// TODO: add "parent" property? how to avoid using too much memory? Transitive parents? Parent unlinking?
}
-interface ElementSet { '@type': 'element-set' | Element['@type'] }
+interface ElementSet { '@type': 'element-set' }
export default ElementSet
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 5dbcd62ec20c11c7be36c782638bb13a5d70d544..710926b6138c69d9e2b85a8b3823fd32cee9e348 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -12,15 +12,12 @@ import Unit from './unit'
import ElementSet from './element/set'
import ElementGroup from './element/group'
import Element from './element'
-import { StructureLookup3D } from './util/lookup3d';
// A structure is a pair of "units" and an element set.
// Each unit contains the data and transformation of its corresponding elements.
interface Structure {
readonly units: ReadonlyArray<Unit>,
- readonly elements: ElementSet,
-
- __lookup3d__?: StructureLookup3D
+ readonly elements: ElementSet
}
namespace Structure {
@@ -77,7 +74,7 @@ namespace Structure {
export function getModels(s: Structure) {
const { units, elements } = s;
const arr = UniqueArray.create<Model['id'], Model>();
- const ids = ElementSet.unitIds(elements);
+ const ids = ElementSet.unitIndices(elements);
for (let i = 0; i < ids.length; i++) {
const u = units[ids[i]];
UniqueArray.add(arr, u.model.id, u.model);
@@ -86,9 +83,7 @@ namespace Structure {
}
export function getLookup3d(s: Structure) {
- if (s.__lookup3d__) return s.__lookup3d__;
- s.__lookup3d__ = StructureLookup3D.create(s);
- return s.__lookup3d__;
+ return ElementSet.getLookup3d(s);
}
export function getBoundary(s: Structure) {
diff --git a/src/mol-model/structure/structure/symmetry.ts b/src/mol-model/structure/structure/symmetry.ts
index 179a058aca6aaeea502a28bc7749d5f55a458555..7fe2fb2bb874e1402537df5ec312c3df5677e5ed 100644
--- a/src/mol-model/structure/structure/symmetry.ts
+++ b/src/mol-model/structure/structure/symmetry.ts
@@ -9,36 +9,39 @@ import ElementSet from './element/set'
import Unit from './unit'
import { Selection } from '../query'
import { ModelSymmetry } from '../model'
+import { Task } from 'mol-task';
namespace Symmetry {
- export const buildAssembly = buildAssemblyImpl;
+ export const buildAssembly = buildAssemblyImpl;
}
export default Symmetry;
function buildAssemblyImpl(structure: Structure, name: string) {
- const models = Structure.getModels(structure);
- if (models.length !== 1) throw new Error('Can only build assemblies from structures based on 1 model.');
+ return Task.create('Build Symmetry', async ctx => {
+ const models = Structure.getModels(structure);
+ if (models.length !== 1) throw new Error('Can only build assemblies from structures based on 1 model.');
- const assembly = ModelSymmetry.findAssembly(models[0], name);
- if (!assembly) throw new Error(`Assembly '${name}' is not defined.`);
+ const assembly = ModelSymmetry.findAssembly(models[0], name);
+ if (!assembly) throw new Error(`Assembly '${name}' is not defined.`);
- const assembler = Structure.Builder();
+ const assembler = Structure.Builder();
- for (const g of assembly.operatorGroups) {
- const selection = g.selector(structure);
- if (Selection.structureCount(selection) === 0) continue;
- const { units, elements } = Selection.unionStructure(selection);
+ for (const g of assembly.operatorGroups) {
+ const selection = await ctx.runChild(g.selector(structure));
+ if (Selection.structureCount(selection) === 0) continue;
+ const { units, elements } = Selection.unionStructure(selection);
- const unitIds = ElementSet.unitIds(elements);
+ const unitIds = ElementSet.unitIndices(elements);
- for (const oper of g.operators) {
- for (let uI = 0, _uI = unitIds.length; uI < _uI; uI++) {
- const unit = units[unitIds[uI]];
- assembler.add(Unit.withOperator(unit, oper), ElementSet.unitGetByIndex(elements, uI));
+ for (const oper of g.operators) {
+ for (let uI = 0, _uI = unitIds.length; uI < _uI; uI++) {
+ const unit = units[unitIds[uI]];
+ assembler.add(Unit.withOperator(unit, oper), ElementSet.groupAt(elements, uI));
+ }
}
}
- }
- return assembler.getStructure();
+ return assembler.getStructure();
+ });
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index 76accfeaf0fd69c0f787362deb99388daf9c1d4d..2109cc10b299b6932a99f05acf410f86abdb45f9 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -7,6 +7,8 @@
import { SymmetryOperator } from 'mol-math/geometry/symmetry-operator'
import ElementGroup from './element/group'
import { Model } from '../model'
+import { GridLookup3D } from 'mol-math/geometry'
+import { computeUnitBonds } from './element/properties/bonds/group-compute';
// A building block of a structure that corresponds to an atomic or a coarse grained representation
// 'conveniently grouped together'.
@@ -83,6 +85,27 @@ namespace Unit {
case Kind.Coarse: return createCoarse(unit.model, SymmetryOperator.compose(unit.operator, operator), unit.fullGroup);
}
}
+
+ export function getLookup3d(unit: Unit, group: ElementGroup) {
+ if (group.__lookup3d__) return group.__lookup3d__;
+ if (Unit.isAtomic(unit)) {
+ const { x, y, z } = unit.model.conformation;
+ group.__lookup3d__ = GridLookup3D({ x, y, z, indices: group.elements });
+ return group.__lookup3d__;
+ }
+
+ throw 'not implemented';
+ }
+
+ export function getGroupBonds(unit: Unit, group: ElementGroup) {
+ if (group.__bonds__) return group.__bonds__;
+ if (Unit.isAtomic(unit)) {
+ group.__bonds__ = computeUnitBonds(unit, group);
+ return group.__bonds__;
+ }
+
+ throw 'not implemented';
+ }
}
export default Unit;
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/util/boundary.ts b/src/mol-model/structure/structure/util/boundary.ts
index 83655a247c9ee8a2289b29d942bf68b7f7c2cf7b..547d3828eb2f892bcdb9b8b620cebe36fc0a0610 100644
--- a/src/mol-model/structure/structure/util/boundary.ts
+++ b/src/mol-model/structure/structure/util/boundary.ts
@@ -20,9 +20,9 @@ function computeStructureBoundary(s: Structure): { box: Box3D, sphere: Sphere3D
let radiusSq = 0;
let size = 0;
- for (let i = 0, _i = ElementSet.unitCount(elements); i < _i; i++) {
- const group = ElementSet.unitGetByIndex(elements, i);
- const { x, y, z } = units[ElementSet.unitGetId(elements, i)];
+ for (let i = 0, _i = ElementSet.groupCount(elements); i < _i; i++) {
+ const group = ElementSet.groupAt(elements, i);
+ const { x, y, z } = units[ElementSet.groupUnitIndex(elements, i)];
size += ElementGroup.size(group);
for (let j = 0, _j = ElementGroup.size(group); j < _j; j++) {
@@ -48,9 +48,9 @@ function computeStructureBoundary(s: Structure): { box: Box3D, sphere: Sphere3D
cz /= size;
}
- for (let i = 0, _i = ElementSet.unitCount(elements); i < _i; i++) {
- const group = ElementSet.unitGetByIndex(elements, i);
- const { x, y, z } = units[ElementSet.unitGetId(elements, i)];
+ for (let i = 0, _i = ElementSet.groupCount(elements); i < _i; i++) {
+ const group = ElementSet.groupAt(elements, i);
+ const { x, y, z } = units[ElementSet.groupUnitIndex(elements, i)];
size += ElementGroup.size(group);
for (let j = 0, _j = ElementGroup.size(group); j < _j; j++) {
diff --git a/src/mol-model/structure/structure/util/lookup3d.ts b/src/mol-model/structure/structure/util/lookup3d.ts
index 7434852bcb15496839eb74017aa6212041dbd12d..bb7230600205a39c78beeff7ac044b2d99a95d8d 100644
--- a/src/mol-model/structure/structure/util/lookup3d.ts
+++ b/src/mol-model/structure/structure/util/lookup3d.ts
@@ -7,15 +7,15 @@
import Structure from '../structure'
import Element from '../element'
import { Lookup3D, GridLookup3D, Result, Box3D, Sphere3D } from 'mol-math/geometry';
-import { ElementGroup, ElementSet } from '../../structure';
+import { ElementSet, Unit } from '../../structure';
import { Vec3 } from 'mol-math/linear-algebra';
import { OrderedSet } from 'mol-data/int';
import { computeStructureBoundary } from './boundary';
-interface StructureLookup3D extends Lookup3D<Element> {}
+interface ElementSetLookup3D extends Lookup3D<Element> {}
-namespace StructureLookup3D {
- class Impl implements StructureLookup3D {
+namespace ElementSetLookup3D {
+ class Impl implements ElementSetLookup3D {
private unitLookup: Lookup3D;
private result = Result.create<Element>();
private pivot = Vec3.zero();
@@ -28,14 +28,14 @@ namespace StructureLookup3D {
for (let t = 0, _t = closeUnits.count; t < _t; t++) {
const i = closeUnits.indices[t];
- const unitId = ElementSet.unitGetId(elements, i);
- const group = ElementSet.unitGetByIndex(elements, i);
+ const unitId = ElementSet.groupUnitIndex(elements, i);
+ const group = ElementSet.groupAt(elements, i);
const unit = units[unitId];
Vec3.set(this.pivot, x, y, z);
if (!unit.operator.isIdentity) {
Vec3.transformMat4(this.pivot, this.pivot, unit.operator.inverse);
}
- const groupLookup = ElementGroup.getLookup3d(unit, group);
+ const groupLookup = Unit.getLookup3d(unit, group);
const groupResult = groupLookup.find(this.pivot[0], this.pivot[1], this.pivot[2], radius);
for (let j = 0, _j = groupResult.count; j < _j; j++) {
Result.add(this.result, Element.create(unitId, groupResult.indices[j]), groupResult.squaredDistances[j]);
@@ -52,14 +52,14 @@ namespace StructureLookup3D {
for (let t = 0, _t = closeUnits.count; t < _t; t++) {
const i = closeUnits.indices[t];
- const unitId = ElementSet.unitGetId(elements, i);
- const group = ElementSet.unitGetByIndex(elements, i);
+ const unitId = ElementSet.groupUnitIndex(elements, i);
+ const group = ElementSet.groupAt(elements, i);
const unit = units[unitId];
Vec3.set(this.pivot, x, y, z);
if (!unit.operator.isIdentity) {
Vec3.transformMat4(this.pivot, this.pivot, unit.operator.inverse);
}
- const groupLookup = ElementGroup.getLookup3d(unit, group);
+ const groupLookup = Unit.getLookup3d(unit, group);
if (groupLookup.check(this.pivot[0], this.pivot[1], this.pivot[2], radius)) return true;
}
@@ -70,7 +70,7 @@ namespace StructureLookup3D {
constructor(private structure: Structure) {
const { units, elements } = structure;
- const unitCount = ElementSet.unitCount(elements);
+ const unitCount = ElementSet.groupCount(elements);
const xs = new Float32Array(unitCount);
const ys = new Float32Array(unitCount);
const zs = new Float32Array(unitCount);
@@ -78,9 +78,9 @@ namespace StructureLookup3D {
const center = Vec3.zero();
for (let i = 0; i < unitCount; i++) {
- const group = ElementSet.unitGetByIndex(elements, i);
- const unit = units[ElementSet.unitGetId(elements, i)];
- const lookup = ElementGroup.getLookup3d(unit, group);
+ const group = ElementSet.groupAt(elements, i);
+ const unit = units[ElementSet.groupUnitIndex(elements, i)];
+ const lookup = Unit.getLookup3d(unit, group);
const s = lookup.boundary.sphere;
Vec3.transformMat4(center, s.center, unit.operator.matrix);
@@ -96,9 +96,9 @@ namespace StructureLookup3D {
}
}
- export function create(s: Structure): StructureLookup3D {
+ export function create(s: Structure): ElementSetLookup3D {
return new Impl(s);
}
}
-export { StructureLookup3D }
\ No newline at end of file
+export { ElementSetLookup3D }
\ No newline at end of file
diff --git a/src/perf-tests/structure.ts b/src/perf-tests/structure.ts
index e27ae3f04b84dab91609b1a63219f888f7736d96..57a23cec6d93ba453392cf2c4bdb2fb1feb29f3c 100644
--- a/src/perf-tests/structure.ts
+++ b/src/perf-tests/structure.ts
@@ -11,7 +11,7 @@ import * as fs from 'fs'
import fetch from 'node-fetch'
import CIF from 'mol-io/reader/cif'
-import { Structure, Model, Queries as Q, Element, ElementGroup, ElementSet, Selection, Symmetry, Unit } from 'mol-model/structure'
+import { Structure, Model, Queries as Q, Element, ElementGroup, ElementSet, Selection, Symmetry, Unit, Query } from 'mol-model/structure'
import { Segmentation, OrderedSet } from 'mol-data/int'
import to_mmCIF from 'mol-model/structure/export/mmcif'
@@ -120,14 +120,14 @@ export namespace PropertyAccess {
function sumProperty(structure: Structure, p: Element.Property<number>) {
const { elements, units } = structure;
- const unitIds = ElementSet.unitIds(elements);
+ const unitIds = ElementSet.unitIndices(elements);
const l = Element.Location();
let s = 0;
for (let i = 0, _i = unitIds.length; i < _i; i++) {
l.unit = units[unitIds[i]];
- const set = ElementSet.unitGetByIndex(elements, i);
+ const set = ElementSet.groupAt(elements, i);
for (let j = 0, _j = ElementGroup.size(set); j < _j; j++) {
@@ -141,7 +141,7 @@ export namespace PropertyAccess {
function sumPropertySegmented(structure: Structure, p: Element.Property<number>) {
const { elements, units } = structure;
- const unitIds = ElementSet.unitIds(elements);
+ const unitIds = ElementSet.unitIndices(elements);
const l = Element.Location();
let s = 0;
@@ -150,7 +150,7 @@ export namespace PropertyAccess {
for (let i = 0, _i = unitIds.length; i < _i; i++) {
const unit = units[unitIds[i]];
l.unit = unit;
- const set = ElementSet.unitGetByIndex(elements, i);
+ const set = ElementSet.groupAt(elements, i);
const chainsIt = Segmentation.transientSegments(unit.hierarchy.chainSegments, set.elements);
const residues = unit.hierarchy.residueSegments;
@@ -294,16 +294,16 @@ export namespace PropertyAccess {
console.log(to_mmCIF('test', s));
}
- export function testAssembly(id: string, s: Structure) {
+ export async function testAssembly(id: string, s: Structure) {
console.time('assembly')
- const a = Symmetry.buildAssembly(s, '1');
+ const a = await Run(Symmetry.buildAssembly(s, '1'));
console.timeEnd('assembly')
fs.writeFileSync(`${DATA_DIR}/${id}_assembly.bcif`, to_mmCIF(id, a, true));
console.log('exported');
}
- export function testGrouping(structure: Structure) {
- const { elements, units } = Symmetry.buildAssembly(structure, '1');
+ export async function testGrouping(structure: Structure) {
+ const { elements, units } = await Run(Symmetry.buildAssembly(structure, '1'));
console.log('grouping', units.length);
console.log('built asm');
@@ -312,15 +312,19 @@ export namespace PropertyAccess {
(a, b) => a.unit.model.id === b.unit.model.id && (a.group.key === b.group.key && OrderedSet.areEqual(a.group.elements, b.group.elements))
);
- for (let i = 0, _i = ElementSet.unitCount(elements); i < _i; i++) {
- const group = ElementSet.unitGetByIndex(elements, i);
- const unitId = ElementSet.unitGetId(elements, i);
+ for (let i = 0, _i = ElementSet.groupCount(elements); i < _i; i++) {
+ const group = ElementSet.groupAt(elements, i);
+ const unitId = ElementSet.groupUnitIndex(elements, i);
uniqueGroups.add(unitId, { unit: units[unitId], group });
}
console.log('group count', uniqueGroups.groups.length);
}
+ function query(q: Query, s: Structure) {
+ return Run((q(s)));
+ }
+
export async function run() {
//const { structures, models/*, mmcif*/ } = await getBcif('1cbs');
// const { structures, models } = await getBcif('3j3q');
@@ -375,26 +379,26 @@ export namespace PropertyAccess {
//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.atoms({ atomTest: Q.pred.eq(Q.props.residue.auth_comp_id, 'ALA') });
+ const q = Query(Q.generators.atoms({ atomTest: Q.pred.eq(Q.props.residue.auth_comp_id, 'ALA') }));
const P = Q.props
//const q0 = Q.generators.atoms({ atomTest: l => auth_comp_id(l) === 'ALA' });
- const q1 = Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' });
- const q2 = Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA', groupBy: Q.props.residue.key });
- const q3 = Q.generators.atoms({
+ const q1 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA' }));
+ const q2 = Query(Q.generators.atoms({ residueTest: l => auth_comp_id(l) === 'ALA', groupBy: Q.props.residue.key }));
+ const q3 = Query(Q.generators.atoms({
chainTest: Q.pred.inSet(P.chain.auth_asym_id, ['A', 'B', 'C', 'D']),
residueTest: Q.pred.eq(P.residue.auth_comp_id, 'ALA')
- });
- q(structures[0]);
+ }));
+ await query(q, structures[0]);
//console.log(to_mmCIF('test', Selection.union(q0r)));
console.time('q1')
- q1(structures[0]);
+ await query(q1, structures[0]);
console.timeEnd('q1')
console.time('q1')
- q1(structures[0]);
+ await query(q1, structures[0]);
console.timeEnd('q1')
console.time('q2')
- const q2r = q2(structures[0]);
+ const q2r = await query(q2, structures[0]);
console.timeEnd('q2')
console.log(Selection.structureCount(q2r));
//console.log(q1(structures[0]));
@@ -404,8 +408,8 @@ export namespace PropertyAccess {
suite
//.add('test q', () => q1(structures[0]))
//.add('test q', () => q(structures[0]))
- .add('test q1', () => q1(structures[0]))
- .add('test q3', () => q3(structures[0]))
+ .add('test q1', async () => await q1(structures[0]))
+ .add('test q3', async () => await q3(structures[0]))
//.add('test int', () => sumProperty(structures[0], l => col(l.element))
// .add('sum residue', () => sumPropertyResidue(structures[0], l => l.unit.hierarchy.residues.auth_seq_id.value(l.unit.residueIndex[l.atom])))