@iktos-oss/molecule-representation
Version:
exports interactif molecule represnetations as react components
198 lines (194 loc) • 10.2 kB
JavaScript
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
return new (P || (P = Promise))(function (resolve, reject) {
function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
step((generator = generator.apply(thisArg, _arguments || [])).next());
});
};
/*
MIT License
Copyright (c) 2023 Iktos
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
import { getSvg, getMoleculeDetails, getCanonicalFormForStructure, getMatchingSubstructure, getSvgFromSmarts, convertMolNotation, } from '@iktos-oss/rdkit-provider';
import { HIGHLIGHT_RDKIT_COLORS, TRANSPARANT_RDKIT_COLOR } from '../constants';
import { appendEllipsesToSvg } from './svg-computation';
const DEFAULT_DRAWING_DETAILS = {
bondLineWidth: 1,
backgroundColour: [1, 1, 1, 0],
highlightColour: HIGHLIGHT_RDKIT_COLORS[0],
highlightRadius: 0.3,
fixedBondLength: 50,
};
export const get_svg = (props, worker) => __awaiter(void 0, void 0, void 0, function* () {
var _a;
const { smiles: initialSmiles, width, height, details = {}, atomsToHighlight = [], bondsToHighlight = [], isClickable, clickableAtoms, alignmentDetails, heatmapAtomsWeights = {}, highlightColor, canonicalize, generateClickableHotspots = false, } = props;
if (!initialSmiles)
return null;
let smiles = initialSmiles;
if (canonicalize) {
const { canonicalForm } = yield getCanonicalFormForStructure(worker, { structure: initialSmiles });
if (!canonicalForm)
return null;
smiles = canonicalForm;
}
let clickableSvg;
if (isClickable && !generateClickableHotspots) {
clickableSvg = yield get_svg(Object.assign(Object.assign({}, props), { smiles, generateClickableHotspots: true }), worker);
}
const moleculeDetails = yield getMoleculeDetails(worker, { smiles, returnFullDetails: true });
if (!moleculeDetails)
return null;
const baseAtomColors = getHighlightColors(atomsToHighlight, highlightColor);
const baseBondColors = getHighlightColors(bondsToHighlight, highlightColor);
const { highlightAtomRadii, heatmapHighlightColors } = computeHeatmapOptions(heatmapAtomsWeights, highlightColor);
const { atomHighlights: alignmentAtomColors, bondHighlights: alignmentBondColors } = alignmentDetails
? yield computeAlignmentHighlights(worker, smiles, alignmentDetails)
: { atomHighlights: {}, bondHighlights: {} };
const clickableAtomBgColors = computeClickableAtomHighlights(moleculeDetails, clickableAtoms, generateClickableHotspots);
const highlightAtomColors = Object.assign(Object.assign(Object.assign(Object.assign({}, clickableAtomBgColors), heatmapHighlightColors), alignmentAtomColors), baseAtomColors);
const highlightBondColors = Object.assign(Object.assign({}, alignmentBondColors), baseBondColors);
const atomsToDraw = generateClickableHotspots
? Object.keys(highlightAtomColors).map(Number)
: [
...atomsToHighlight.flat(),
...((_a = clickableAtoms === null || clickableAtoms === void 0 ? void 0 : clickableAtoms.clickableAtomsIds) !== null && _a !== void 0 ? _a : []),
...Object.keys(heatmapAtomsWeights)
.map((n) => { var _a; return (_a = parseInt(n)) !== null && _a !== void 0 ? _a : null; })
.filter((n) => n !== null),
];
const bondsToDraw = Object.keys(highlightBondColors).map(Number);
const rdkitDrawingOptions = Object.assign(Object.assign(Object.assign({}, DEFAULT_DRAWING_DETAILS), { width,
height, atoms: atomsToDraw, bonds: bondsToDraw, highlightAtomColors,
highlightBondColors,
highlightAtomRadii }), details);
try {
let { svg } = yield getSvg(worker, {
smiles,
drawingDetails: rdkitDrawingOptions,
alignmentDetails,
});
if (svg && clickableSvg) {
svg = appendEllipsesToSvg(svg, clickableSvg);
}
if (!svg && alignmentDetails) {
console.error('@iktos-oss/molecule-representation: Failed to draw with alignment, falling back to no alignment.');
const { svg: svgRetry } = yield getSvg(worker, { smiles, drawingDetails: rdkitDrawingOptions });
return svgRetry;
}
return svg;
}
catch (error) {
console.error(error);
return null;
}
});
export const get_svg_from_smarts = (props, drawAsSmiles = false, worker) => __awaiter(void 0, void 0, void 0, function* () {
if (!worker || !props.smarts)
return null;
const { canonicalForm: canonicalSmarts } = yield getCanonicalFormForStructure(worker, {
structure: props.smarts,
useQMol: true,
});
if (!canonicalSmarts)
return null;
if (drawAsSmiles) {
const { svg } = yield getSvg(worker, Object.assign(Object.assign({}, props), { smiles: props.smarts }));
return svg;
}
const { svg } = yield getSvgFromSmarts(worker, Object.assign(Object.assign({}, props), { smarts: canonicalSmarts }));
return svg;
});
function getHighlightColors(items = [], highlightColor) {
// give each array of atoms a color, enabling multi-color highlights
const highlightColors = {};
const limit = HIGHLIGHT_RDKIT_COLORS.length;
items.forEach((item, i) => {
const color = highlightColor !== null && highlightColor !== void 0 ? highlightColor : HIGHLIGHT_RDKIT_COLORS[i % limit];
if (!item)
return;
for (const index of item) {
highlightColors[index] = color;
}
});
return highlightColors;
}
function computeHeatmapOptions(heatmapAtomsWeights = {}, highlightColor) {
const highlightAtomRadii = {};
const heatmapHighlightColors = {};
const weights = Object.values(heatmapAtomsWeights);
if (weights.length === 0)
return { highlightAtomRadii, heatmapHighlightColors };
const maxWeight = Math.max(...weights);
const minWeight = Math.min(...weights);
const weightRange = maxWeight - minWeight || 1;
const minRadius = 0.15;
const maxRadius = 0.5;
for (const [atomIdx, weight] of Object.entries(heatmapAtomsWeights)) {
const normalizedWeight = (weight - minWeight) / weightRange;
highlightAtomRadii[+atomIdx] = minRadius + normalizedWeight * (maxRadius - minRadius);
}
const atomIndices = [Object.keys(heatmapAtomsWeights).map(Number)];
Object.assign(heatmapHighlightColors, getHighlightColors(atomIndices, highlightColor));
return { highlightAtomRadii, heatmapHighlightColors };
}
function computeAlignmentHighlights(worker, smiles, alignmentDetails) {
var _a, _b;
return __awaiter(this, void 0, void 0, function* () {
const atomHighlights = {};
const bondHighlights = {};
if (!alignmentDetails.highlightColor || !alignmentDetails.molBlock) {
return { atomHighlights, bondHighlights };
}
const { structure: smarts } = yield convertMolNotation(worker, {
moleculeString: alignmentDetails.molBlock,
targetNotation: 'smarts',
sourceNotation: 'molblock',
});
if (!smarts)
return { atomHighlights, bondHighlights };
const match = yield getMatchingSubstructure(worker, { structure: smiles, substructure: smarts });
if (!match)
return { atomHighlights, bondHighlights };
const color = alignmentDetails.highlightColor;
(_a = match.matchingAtoms) === null || _a === void 0 ? void 0 : _a.forEach((idx) => (atomHighlights[idx] = color));
(_b = match.matchingBonds) === null || _b === void 0 ? void 0 : _b.forEach((idx) => (bondHighlights[idx] = color));
return { atomHighlights, bondHighlights };
});
}
function computeClickableAtomHighlights(moleculeDetails, clickableAtoms, isForClickableOverlay) {
var _a, _b;
if (!moleculeDetails)
return {};
const clickableAtomColors = {};
const backgroundColor = (_a = clickableAtoms === null || clickableAtoms === void 0 ? void 0 : clickableAtoms.clickableAtomsBackgroundColor) !== null && _a !== void 0 ? _a : TRANSPARANT_RDKIT_COLOR;
const clickableAtomIds = (_b = clickableAtoms === null || clickableAtoms === void 0 ? void 0 : clickableAtoms.clickableAtomsIds) !== null && _b !== void 0 ? _b : [...Array(moleculeDetails.NumHeavyAtoms).keys()];
for (const atomId of clickableAtomIds) {
clickableAtomColors[atomId] = isForClickableOverlay ? TRANSPARANT_RDKIT_COLOR : backgroundColor;
}
if (isForClickableOverlay) {
for (let i = 0; i < moleculeDetails.NumHeavyAtoms; i++) {
if (!clickableAtomIds.includes(i)) {
clickableAtomColors[i] = TRANSPARANT_RDKIT_COLOR;
}
}
}
return clickableAtomColors;
}
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