1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
|
<!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="Greg Landrum">
<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>
onRuntimeInitialized: initRDKitModule().then(function(instance) {
RDKitModule = instance;
console.log('version: ' + RDKitModule.version());
var m1 = RDKitModule.get_mol("c1ccccc1O");
console.log('smiles: ' + m1.get_smiles());
m1.delete();
callback("CC(=O)Oc1ccccc1C(=O)O");
rxn_callback("[C:1](=[O:2])-O.[N:3]>>[O:2]=[C:1]-[N:3]");
});
function form_to_details(details) {
var controls = ["addAtomIndices", "addBondIndices", "explicitMethyl", "addStereoAnnotation"];
for (i in controls) {
var control = controls[i];
details[control] = document.getElementById(control).checked
}
var texts = ["legend", "bondLineWidth", "legendFontSize"];
for (i in texts) {
var control = texts[i];
details[control] = document.getElementById(control).value
}
}
function draw_with_highlights(mol, details) {
form_to_details(details);
var tdetails = JSON.stringify(details)
var svg = mol.get_svg_with_highlights(tdetails);
if (svg == "") return;
var ob = document.getElementById("drawing");
ob.outerHTML = "<div id='drawing'>" + svg + "</div>";
var canvas = document.getElementById("rdkit-canvas");
mol.draw_to_canvas_with_highlights(canvas, tdetails);
}
function draw(mol) {
var details = {};
draw_with_highlights(mol, details);
return;
var svg = mol.get_svg();
if (svg == "") return;
var ob = document.getElementById("drawing");
ob.outerHTML = "<div id='drawing'>" + svg + "</div>";
var canvas = document.getElementById("rdkit-canvas");
mol.draw_to_canvas(canvas, -1, -1);
}
function callback(text, update_descrs) {
var mol = RDKitModule.get_mol(text);
if (mol.is_valid()) {
draw(mol);
var ob = document.getElementById("can_smiles");
ob.outerHTML = "<div id='can_smiles'>" + mol.get_smiles() + "</div>";
if (update_descrs) {
var descrs = JSON.parse(mol.get_descriptors());
var db = document.getElementById("descrs");
db.outerHTML = "<div id='descrs'>" +
"<b>AMW:</b> " + descrs.amw +
"<br /><b>MolLogP:</b> " + descrs.CrippenClogP +
"<br /><b>MFP2:</b> " + mol.get_morgan_fp(JSON.stringify({ radius: 2, nBits: 128 })) +
"</div>";
}
}
mol.delete();
}
function sma_callback(text) {
var qmol = RDKitModule.get_qmol(text);
var mol = RDKitModule.get_mol(document.getElementById("smiles_input").value);
if (mol.is_valid() && qmol.is_valid()) {
var mdetails = mol.get_substruct_match(qmol);
var match = JSON.parse(mdetails);
if (match.atoms && match.atoms.length) draw_with_highlights(mol, match);
}
mol.delete();
qmol.delete();
}
function template_callback(text) {
if(text==""){
text = document.getElementById("template_input").value;
}
var qmol = RDKitModule.get_mol(text);
var mol = RDKitModule.get_mol(document.getElementById("smiles_input").value);
if (mol.is_valid() && qmol.is_valid()) {
var mdetails = mol.get_substruct_match(qmol);
var match = JSON.parse(mdetails);
var useCoordgen = document.getElementById("useCoordgen").checked;
mol.generate_aligned_coords(qmol,useCoordgen);
if (match.atoms && match.atoms.length) draw_with_highlights(mol, match);
}
mol.delete();
qmol.delete();
}
function rxn_callback(text, details) {
details = details || {};
var rxn = RDKitModule.get_rxn(text, JSON.stringify(details));
var svg = "";
try {
svg = rxn.get_svg(798, 198);
} catch (e) {}
if (svg == "") {
return;
}
var ob = document.getElementById("drawing_reaction");
ob.innerHTML = svg;
var canvas = document.getElementById("rdkit-rxn-canvas");
rxn.draw_to_canvas(canvas, -1, -1);
}
function option_changed(cb) {
var smi = document.getElementById('smiles_input').value;
var sma = document.getElementById('smarts_input').value;
if (sma) {
sma_callback(sma);
} else {
callback(smi, false);
}
}
function abbreviation_option_changed(cb) {
var smi = document.getElementById('smiles_input').value;
var mol = RDKitModule.get_mol(smi);
if(document.getElementById('useAbbreviations').checked){
var useLinkers = document.getElementById('useLinkers').checked;
var maxCoverage = +(document.getElementById('maxCoverage').value);
mol.condense_abbreviations(maxCoverage,useLinkers);
}
draw(mol);
}
</script>
<body>
<div class="container-fluid col-md-8">
<h1>RDKit-JS demo</h1>
<div id="molecule">
<div id="drawing"></div>
<div id="can_smiles"></div>
</div>
<br>
SMILES: <input id="smiles_input" type="text" value="CC(=O)Oc1ccccc1C(=O)O" onkeyup="callback(this.value,true)">
SMARTS: <input id="smarts_input" type="text" value="" onkeyup="sma_callback(this.value)">
<br>
<h2>Computed values</h2>
<div id="descrs"></div>
<div id="canvas-div">
<h1>HTML5 canvas</h1>
<canvas id="rdkit-canvas" width="400" height="300" style="border:1px solid #000000;">
</canvas>
<br />
<input type="checkbox" id="addAtomIndices" name="atomIndices" onclick="option_changed(this);">
<label for="addAtomIndices">atomIndices</label>
<input type="checkbox" id="addBondIndices" name="bondIndices" onclick="option_changed(this);">
<label for="addBondIndices">bondIndices</label>
<input type="checkbox" id="addStereoAnnotation" name="addStereoAnnotation" onclick="option_changed(this);">
<label for="addStereoAnnotation">addStereoAnnotation</label>
<br />
<input type="checkbox" id="explicitMethyl" name="explicitMethyl" onclick="option_changed(this);" />
<label for="explicitMethyl">explicitMethyl</label>
<br />
<input type="text" id="legend" onkeyup="option_changed(this);"><label for="legend">legend</label>
<input type="text" id="legendFontSize" onkeyup="option_changed(this);"><label
for="legendFontSize">legendFontSize</label>
<br />
<input type="number" id="bondLineWidth" onkeyup="option_changed(this);"><label
for="bondLineWidth">bondLineWidth</label>
</div>
<div id="abbrev-div">
<h1>Abbreviations</h1>
<input type="checkbox" id="useAbbreviations" name="useAbbreviations" onclick="abbreviation_option_changed(this);" />
<label for="useAbbreviations">Use Abbreviations</label>
<input type="checkbox" id="useLinkers" name="useLinkers" onclick="abbreviation_option_changed(this);" />
<label for="useLinkers">Use Linkers</label>
<input type="text" id="maxCoverage" value="0.4" name="maxCoverage" onclick="abbreviation_option_changed(this);" />
<label for="maxCoverage">Max Coverage</label>
</div>
<div id="template-div">
<h1>Template Mol Block</h1>
<input type="checkbox" id="useCoordgen" name="use_coordgen" onclick="template_callback('');">
<label for="useCoordgen">useCoordgen</label>
<br>
<textarea id="template_input" cols="80" rows="20" value="" onkeyup="template_callback(this.value)"></textarea>
</div>
<h1>Reactions</h1>
SMARTS: <input id="reaction_smarts_input" type="text" value="[C:1](=[O:2])-O.[N:3]>>[O:2]=[C:1]-[N:3]" onkeyup="rxn_callback(this.value)">
SMILES: <input id="reaction_smiles_input" type="text" value="[CH:1](=[O:2])-[OH].[NH3:3]>>[O:2]=[CH:1]-[NH2:3]" onkeyup="rxn_callback(this.value, { useSmiles: true })">
<br>
<h3>SVG render</h3>
<div id="drawing_reaction" style="width:800px; height:200px; border:1px solid #000000;"></div>
<br>
<h3>Canvas render</h3>
<canvas id="rdkit-rxn-canvas" width="800" height="200" style="border:1px solid #000000;">
</canvas>
</div>
</body>
</html>
|
