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|
<!doctype html>
<html lang="en">
<head>
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="Author" content="greg Landrum">
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css"
integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
<style>
h1,
h2,
h3,
h4 {
color: #044484;
}
</style>
</head>
<script src="./RDKit_minimal.js"></script>
<script>
onRuntimeInitialized: initRDKitModule().then(function (instance) {
RDKitModule = instance;
console.log('version: ' + RDKitModule.version());
});
</script>
<body>
<div class="container-fluid col-md-12">
<h1>Getting started with RDKit-JS</h1>
<h2>Drawing molecules</h2>
<p>First we'll work with an SVG drawing:
<div class="row">
<div class="col-sm-6">
<textarea id="example-1" cols="40" rows="5" wrap="off">
var smiles = "CC(=O)Oc1ccccc1C(=O)O";
var mol = RDKitModule.get_mol(smiles);
var dest = document.getElementById("example-1-output");
var svg = mol.get_svg();
dest.outerHTML = "<div id='drawing'>" + svg + "</div>";
</textarea>
<br /><input value="run" onclick="eval(document.getElementById('example-1').value)" type="button" />
</div>
<div id="example-1-output" class="col-sm-6">
</div>
</div>
</p>
<p>As of v2020.09 of the RDKit we can do the same thing using the HTML5 canvas:
<div class="row">
<div class="col-sm-6">
<textarea id="example-2" cols="40" rows="5" wrap="off">
var smiles = "CC(=O)Oc1ccccc1C(=O)O";
var mol = RDKitModule.get_mol(smiles);
var canvas = document.getElementById("canvas-2");
mol.draw_to_canvas(canvas, -1, -1);
</textarea>
<br /><input value="run" onclick="eval(document.getElementById('example-2').value)" type="button" />
</div>
<div id="example-2-output" class="col-sm-6">
<canvas id="canvas-2" width="250" height="200" >
</canvas>
</div>
</div>
</p>
<p>We can do substructure searches and highlight the results:
<div class="row">
<div class="col-sm-6">
<textarea id="example-3" cols="40" rows="5" wrap="off">
var smiles = "CC(=O)Oc1ccccc1C(=O)O";
var mol = RDKitModule.get_mol(smiles);
var smarts = "Oc1[c,n]cccc1";
var qmol = RDKitModule.get_qmol(smarts)
var mdetails = mol.get_substruct_match(qmol)
var canvas = document.getElementById("canvas-3");
mol.draw_to_canvas_with_highlights(canvas, mdetails);
</textarea>
<br /><input value="run" onclick="eval(document.getElementById('example-3').value)" type="button" />
</div>
<div id="example-3-output" class="col-sm-6">
<canvas id="canvas-3" width="250" height="200">
</canvas>
</div>
</div>
</p>
You can also change drawing options and do highlighting with the SVG renderer,
but we don't show it here. You just need to replace
<pre>
mol.draw_to_canvas_with_highlights(canvas, mdetails);
</pre>
with
<pre>
var svg = mol.get_svg_with_highlights(mdetails);
</pre>
<p>The same call can be used to control drawing options or to manually
set the atoms/bonds which should be highlighted:
<div class="row">
<div class="col-sm-6">
<textarea id="example-4" cols="40" rows="5" wrap="off">
var smiles = "CC(=O)Oc1ccccc1C(=O)O";
var mol = RDKitModule.get_mol(smiles);
var mdetails = {};
mdetails['atoms']=[0,1,10];
mdetails['explicitMethyl'] = true;
mdetails['addAtomIndices'] = true;
mdetails['legend']='aspirin';
var canvas = document.getElementById("canvas-4");
mol.draw_to_canvas_with_highlights(canvas, JSON.stringify(mdetails));
</textarea>
<br /><input value="run" onclick="eval(document.getElementById('example-4').value)" type="button" />
</div>
<div id="example-4-output" class="col-sm-6">
<canvas id="canvas-4" width="250" height="200">
</canvas>
</div>
</div>
</p>
<p>and of course we can combine the two:
<div class="row">
<div class="col-sm-6">
<textarea id="example-5" cols="40" rows="5" wrap="off">
var smiles = "CC(=O)Oc1ccccc1C(=O)O";
var mol = RDKitModule.get_mol(smiles);
var smarts = "O=C";
var qmol = RDKitModule.get_qmol(smarts)
var mdetails = JSON.parse(mol.get_substruct_match(qmol));
mdetails['highlightColour'] = [1,0,1];
mdetails['legend']='aspirin';
var canvas = document.getElementById("canvas-5");
mol.draw_to_canvas_with_highlights(canvas, JSON.stringify(mdetails));
</textarea>
<br /><input value="run" onclick="eval(document.getElementById('example-5').value)" type="button" />
</div>
<div id="example-5-output" class="col-sm-6">
<canvas id="canvas-5" width="250" height="200">
</canvas>
</div>
</div>
</p>
The currently supported options are:
<ol>
<li><tt>atoms</tt>,<tt>bonds</tt>: lists to specify which atoms/bonds are highlighted</li>
<li><tt>width</tt>,<tt>height</tt><tt>offsetx</tt>,<tt>offsety</tt>: used to
draw in a subregion of a canvas. Only supported by the HTML5 canvas
drawer.</li>
<li><tt>legend</tt>: the legend drawn under the molecule</li>
<li>These <tt>MolDrawOptions</tt> values: <tt>
atomLabelDeuteriumTritium,
dummiesAreAttachments,
circleAtoms,
splitBonds,
continuousHighlight,
fillHighlights,
highlightRadius,
flagCloseContactsDist,
includeAtomTags,
clearBackground,
legendFontSize,
maxFontSize,
minFontSize,
annotationFontScale,
fontFile,
multipleBondOffset,
padding,
additionalAtomLabelPadding,
noAtomLabels,
bondLineWidth,
scaleBondWidth,
scaleHighlightBondWidth,
highlightBondWidthMultiplier,
prepareMolsBeforeDrawing,
fixedScale,
fixedBondLength,
rotate,
addAtomIndices,
addBondIndices,
isotopeLabels,
dummyIsotopeLabels,
addStereoAnnotation,
atomHighlightsAreCircles,
centreMoleculesBeforeDrawing,
explicitMethyl,
includeMetadata,
includeRadicals,
comicMode,
variableBondWidthMultiplier,
variableAtomRadius,
includeChiralFlagLabel,
simplifiedStereoGroupLabel,
singleColourWedgeBonds
</tt></li>
</ol>
<p>It's often useful to generate molecule renderings where the coordinates of a core are constrained.
<div class="row">
<div class="col-sm-6">
<textarea id="example-6" cols="40" rows="5" wrap="off">
var smiles = "c1cnc(C)nc1C(=O)O";
var mol = RDKitModule.get_mol(smiles);
var template = `
Mrv2014 10192005332D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 6 6 0 0 0
M V30 BEGIN ATOM
M V30 1 C -5.7917 2.5817 0 0
M V30 2 N -7.1253 1.8117 0 0
M V30 3 C -7.1253 0.2716 0 0
M V30 4 C -5.7917 -0.4984 0 0
M V30 5 C -4.458 0.2716 0 0
M V30 6 N -4.458 1.8117 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 END BOND
M V30 END CTAB
M END
`;
var qmol = RDKitModule.get_mol(template);
mol.generate_aligned_coords(qmol,true);
var tdetails = mol.get_substruct_match(qmol);
var canvas = document.getElementById("canvas-6");
mol.draw_to_canvas_with_highlights(canvas,tdetails);
</textarea>
<br /><input value="run" onclick="eval(document.getElementById('example-6').value)" type="button" />
</div>
<div id="example-6-output" class="col-sm-6">
<canvas id="canvas-6" width="250" height="200">
</canvas>
</div>
</div>
</p>
<p><tt>get_mol</tt> can be passed a JSON dictionary of boolean options. Currently supported options are:
<tt>
sanitize,
kekulize,
removeHs,
mergeQueryHs
</tt>
<div class="row">
<div class="col-sm-6">
<textarea id="example-7" cols="40" rows="5" wrap="off">
var smiles = "[*:1]ccc[*:2]";
var mol = RDKitModule.get_mol(smiles, JSON.stringify({ kekulize: false }));
var canvas = document.getElementById("canvas-7");
mol.draw_to_canvas(canvas, -1, -1);
</textarea>
<br /><input value="run" onclick="eval(document.getElementById('example-7').value)" type="button" />
</div>
<div id="example-7-output" class="col-sm-6">
<canvas id="canvas-7" width="250" height="200">
</canvas>
</div>
</div>
</p>
<p>The <tt>SubstructLibrary</tt> functionality is exposed to enable running fast substructure searches
taking advantage of pre-filtering through pattern fingerprints:
<div class="row">
<div class="col-sm-6">
<textarea id="example-8" cols="40" rows="5" wrap="off">
var sslib = new RDKitModule.SubstructLibrary();
var mol0 = RDKitModule.get_mol("Cc1cc(F)ccc1");
var mol1 = RDKitModule.get_mol("Clc1ccccn1");
sslib.add_trusted_smiles(mol0.get_smiles());
sslib.add_trusted_smiles(mol1.get_smiles());
var query = RDKitModule.get_mol(`
MJ201100 2D
6 6 0 0 0 0 0 0 0 0999 V2000
-1.0491 0.7134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 0.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7635 -0.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0491 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 -0.5241 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3346 0.3009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
5 6 2 0 0 0 0
1 2 2 0 0 0 0
6 1 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
M END`);
matches = JSON.parse(sslib.get_matches(query));
var canvas_query = document.getElementById("canvas-8-query");
query.draw_to_canvas_with_highlights(canvas_query, JSON.stringify({ legend: 'query' }));
var canvas_mol0 = document.getElementById("canvas-8-mol0");
mol0.draw_to_canvas_with_highlights(canvas_mol0, JSON.stringify({ legend: `mol0 matches: ${matches.includes(0)}` }));
var canvas_mol1 = document.getElementById("canvas-8-mol1");
mol1.draw_to_canvas_with_highlights(canvas_mol1, JSON.stringify({ legend: `mol1 matches: ${matches.includes(1)}` }));
</textarea>
<br /><input value="run" onclick="eval(document.getElementById('example-8').value)" type="button" />
</div>
<div id="example-8-output" class="col-sm-6">
<canvas id="canvas-8-query" width="150" height="150">
</canvas>
<canvas id="canvas-8-mol0" width="150" height="150">
</canvas>
<canvas id="canvas-8-mol1" width="150" height="150">
</canvas>
</div>
</div>
</p>
</div>
</body>
</html>
|
