diff --git a/src/apps/structure-info/index.ts b/src/apps/structure-info/index.ts
index 6f606817361e4b7afd05269a9d2335d0cb7c7289..c98178e02529df6c4982212619c75a59b999089c 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 } 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);
@@ -37,24 +38,34 @@ 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)} -- ${atomLabel(model, neighbor[bI])}`)
- // }
- // }
+function printBonds(structure: Structure) {
+
+ const { units, elements } = structure;
+ const unitIds = ElementSet.unitIndices(elements);
+
+ for (let i = 0, _i = OrderedSet.size(unitIds); i < _i; i++) {
+ const unit = units[OrderedSet.getAt(unitIds, i)];
+ const group = ElementSet.groupFromUnitIndex(elements, OrderedSet.getAt(unitIds, i));
+
+ const { count, offset, neighbor } = Unit.getGroupBonds(unit, group);
+ const { model } = unit;
+
+ for (let j = 0; j < count; ++j) {
+ const start = offset[j];
+ const end = offset[j + 1];
+ for (let bI = start; bI < end; bI++) {
+ console.log(`${atomLabel(model, j)} -- ${atomLabel(model, neighbor[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-math/geometry/lookup3d/grid.ts b/src/mol-math/geometry/lookup3d/grid.ts
index 7abb47781969df8deb176c5e1f9918f3cf2b532d..69d65672ea3a03c5a188ebdcaf91e6c70833de10 100644
--- a/src/mol-math/geometry/lookup3d/grid.ts
+++ b/src/mol-math/geometry/lookup3d/grid.ts
@@ -256,7 +256,7 @@ function query(ctx: QueryContext): boolean {
if (distSq <= rSq) {
if (maxRadius > 0 && Math.sqrt(distSq) - radius![idx] > inputRadius) continue;
if (isCheck) return true;
- Result.add(result, bucketArray[i], distSq);
+ Result.add(result, idx, distSq);
}
}
}
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/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/structure/element/group.ts b/src/mol-model/structure/structure/element/group.ts
index 0dcb551536ab54acacbecdccf9f2fbaed3d5ee26..e89b3d37e87b6611a0630fe4978fe1218ceaa76b 100644
--- a/src/mol-model/structure/structure/element/group.ts
+++ b/src/mol-model/structure/structure/element/group.ts
@@ -7,13 +7,15 @@
import { OrderedSet } from 'mol-data/int'
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 {
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..7e58040f13444d26e3078682619944767c9061df
--- /dev/null
+++ b/src/mol-model/structure/structure/element/properties/bonds/group-compute.ts
@@ -0,0 +1,256 @@
+/**
+ * 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 { residueKey } = unit.model.hierarchy;
+ 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 = 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.find(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
+ };
+}
+
+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/unit.ts b/src/mol-model/structure/structure/unit.ts
index 4489f88a8b8043848a6ec74c4bb8dac7dca51c10..0084b15e6b1bdce018db1016e16f7ccc539294a7 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -8,6 +8,7 @@ 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'.
@@ -95,6 +96,16 @@ namespace Unit {
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