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<!--
Visualize R group decomposition results similarly to
https://greglandrum.github.io/rdkit-blog/posts/2021-08-07-rgd-and-highlighting.html
Use
rgd_demo.html?output=svg
to switch from canvas to SVG output
-->
<!doctype html>
<html>
<head>
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="Author" content="Paolo Tosco">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css">
<style>
h1,
h2,
h3,
h4 {
color: #044484;
}
</style>
</head>
<script src="./RDKit_minimal.js"></script>
<script>
const urlParams = new URLSearchParams(document.location.search);
const useSvg = (urlParams.get('output') || '').toLowerCase() === 'svg';
const NAME = '_Name';
const useCoordGen = true;
const generateStructureDiv = (row, core, {
width,
height,
labels
}) => {
const RGROUP_TARGET_ATOMS = '_rgroupTargetAtoms';
const RGROUP_TARGET_BONDS = '_rgroupTargetBonds';
const HIGHLIGHT_RADIUS = 0.4;
const HIGHLIGHT_LINEWIDTH_MULTIPLIER = 2;
// Okabe_Ito colormap from https://jfly.uni-koeln.de/color/
const COLORS = [[230, 159, 0], [86, 180, 233], [0, 158, 115], [240, 228, 66], [0, 114, 178], [213, 94, 0], [204, 121, 167]].map(
((t) => t.map((v) => v / 255))
);
const div = document.createElement('div');
const mol = row['Mol'];
if (!mol) {
return div;
}
const highlightAtomMultipleColors = {};
const highlightBondMultipleColors = {};
const highlightAtomRadii = {};
const highlightLineWidthMultipliers = {};
labels.every((label, i) => {
const rgroup = row[label];
if (!rgroup) {
return true;
}
const targetAtoms = rgroup.has_prop(RGROUP_TARGET_ATOMS)
? JSON.parse(rgroup.get_prop(RGROUP_TARGET_ATOMS)) : [];
const targetBonds = rgroup.has_prop(RGROUP_TARGET_BONDS)
? JSON.parse(rgroup.get_prop(RGROUP_TARGET_BONDS)) : [];
const color = COLORS[i % COLORS.length];
targetAtoms.forEach((idx) => {
if (!highlightAtomMultipleColors[idx]) {
highlightAtomMultipleColors[idx] = [];
}
highlightAtomMultipleColors[idx].push(color);
highlightAtomRadii[idx] = HIGHLIGHT_RADIUS;
});
targetBonds.forEach((idx) => {
if (!highlightBondMultipleColors[idx]) {
highlightBondMultipleColors[idx] = [];
}
highlightBondMultipleColors[idx].push(color);
highlightLineWidthMultipliers[idx] = HIGHLIGHT_LINEWIDTH_MULTIPLIER;
});
return true;
});
mol.generate_aligned_coords(core, JSON.stringify({
useCoordGen,
allowRGroups: true,
}));
const details = {
width,
height,
highlightAtomMultipleColors,
highlightBondMultipleColors,
highlightAtomRadii,
highlightLineWidthMultipliers,
};
if (useSvg) {
const svg = mol.get_svg_with_highlights(JSON.stringify(details));
div.innerHTML = svg;
} else {
const canvas = document.createElement('canvas');
canvas.width = width;
canvas.height = height;
mol.draw_to_canvas_with_highlights(canvas, JSON.stringify(details));
div.appendChild(canvas);
}
const legendtext = mol.has_prop(NAME) ? mol.get_prop(NAME) : '';
const legend = document.createTextNode(legendtext);
div.appendChild(legend);
return div;
};
const generateTable = (rows, core, {
nPerRow, ...opts
}) => {
const table = document.createElement('table');
const tbody = document.createElement('tbody');
table.appendChild(tbody);
let tr;
rows.forEach((row, i) => {
if (!(i % nPerRow)) {
tr = document.createElement('tr');
tbody.appendChild(tr);
}
const td = document.createElement('td');
td.style = 'text-align: center;';
tr.appendChild(td);
const div = generateStructureDiv(row, core, opts);
td.appendChild(div);
});
return table;
}
const displayRgdTable = (RDKitModule) => {
console.log('version: ' + RDKitModule.version());
const smiArray = [
['Cc1ccc2c(c3ccnc(Nc4cccc(c4)C(F)(F)F)n3)c(nn2n1)c5ccc(F)cc5', 'CHEMBL182493'],
['Cc1ccc2c(c3ccnc(Nc4ccc(F)c(F)c4)n3)c(nn2n1)c5ccc(F)cc5', 'CHEMBL182326'],
['Cc1ccc2c(c3ccnc(Nc4ccc5OCCOc5c4)n3)c(nn2n1)c6ccc(F)cc6', 'CHEMBL183064'],
['Cc1ccc2c(c3ccnc(Nc4ccc(Cl)c(c4)C(F)(F)F)n3)c(nn2n1)c5ccc(F)cc5', 'CHEMBL361038'],
['C1CC1c2nn3ncccc3c2c4ccnc(Nc5ccccc5)n4', 'CHEMBL362296'],
['Fc1ccc(Nc2nccc(n2)c3c(nn4ncccc34)C5CC5)cc1F', 'CHEMBL185516'],
['C1CCC(CC1)c2nn3ncccc3c2c4ccnc(Nc5ccccc5)n4', 'CHEMBL273870'],
['Fc1ccc(Nc2nccc(n2)c3c(nn4ncccc34)C5CCCCC5)cc1F', 'CHEMBL185044'],
['COCCOc1cnn2ncc(c3ccnc(Nc4cccc(OC)c4)n3)c2c1', 'CHEMBL180593'],
['Cc1ccc2c(c3ccnc(Nc4ccc(F)c(F)c4)n3)c(nn2n1)c5ccccc5', 'CHEMBL364197'],
['Cc1ccc2c(c3ccnc(Nc4ccc(Cl)c(c4)C(F)(F)F)n3)c(nn2n1)c5ccccc5', 'CHEMBL186010'],
['Cc1ccc2c(c3ccnc(Nc4ccc5OCCOc5c4)n3)c(nn2n1)c6ccccc6', 'CHEMBL361723'],
['Cc1ccc2c(c3ccnc(Nc4ccccc4)n3)c(nn2n1)c5cccc(c5)C(F)(F)F', 'CHEMBL364539'],
['Cc1ccc2c(c3ccnc(Nc4ccc(F)c(F)c4)n3)c(nn2n1)c5cccc(c5)C(F)(F)F', 'CHEMBL186195'],
['Cc1ccc2c(c3ccnc(Nc4ccc(Cl)c(c4)C(F)(F)F)n3)c(nn2n1)c5cccc(c5)C(F)(F)F', 'CHEMBL184657'],
['Cc1ccc2c(c3ccnc(Nc4ccc5OCCOc5c4)n3)c(nn2n1)c6cccc(c6)C(F)(F)F', 'CHEMBL189617'],
];
const LABELS = ['R1', 'R2', 'R3', 'R4'];
let core;
let mols;
let rgd;
try {
core = RDKitModule.get_mol(
'c1cc(-c2c([*:1])nn3nc([*:2])ccc23)nc(N(c2ccc([*:4])c([*:3])c2))n1',
JSON.stringify({
makeDummiesQueries: true,
mappedDummiesAreRGroups: true,
})
);
core.set_new_coords(useCoordGen);
mols = smiArray.map(([smi, chemblId]) => {
const mol = RDKitModule.get_mol(smi);
mol.set_prop(NAME, chemblId);
return mol;
});
rgd = RDKitModule.get_rgd(core, JSON.stringify({
includeTargetMolInResults: true,
}));
mols.forEach((mol) => rgd.add(mol));
rgd.process();
const rows = rgd.get_rgroups_as_rows();
const table = generateTable(rows, core, {
labels: LABELS,
nPerRow: 4,
width: 250,
height: 200,
});
const tableDiv = document.getElementById('tableDiv');
if (tableDiv) {
tableDiv.appendChild(table);
}
} finally {
if (core) {
core.delete();
}
mols.forEach((mol) => {
if (mol) {
mol.delete();
}
});
if (rgd) {
rgd.delete();
}
}
};
initRDKitModule().then(displayRgdTable);
</script>
<body>
<div class="container-fluid col-md-8">
<h1>RDKit-JS R Group Decomposition demo</h1>
<div id="tableDiv"></div>
</body>
</html>
|
