StructureContactViewer/index.html at master · sanshu/StructureContactViewer · GitHub

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
213
214
215
216
217
218
219
220
221
222
223
224
<!DOCTYPE html>
<html lang="en">

<head>
    <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.0/css/bootstrap.min.css"
        integrity="sha384-9aIt2nRpC12Uk9gS9baDl411NQApFmC26EwAOH8WgZl5MYYxFfc+NcPb1dKGj7Sk" crossorigin="anonymous">

    <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>

    <script src="https://d3js.org/d3.v5.js"></script>

    <script src='https://cdn.rawgit.com/nicgirault/circosJS/v2/dist/circos.js'></script>
    <script src="index.js"></script>
    <style>
        .highlighted {
            stroke: width 5px;
            stroke: red;
            fill: red;
            opacity: 1;
        }

        .range-wrap {
            position: relative;
            margin: 0 auto 3rem;
        }

        .range {
            width: 100%;
        }

        .bubble {
            background: lightgrey;
            color: black;
            padding: 4px 12px;
            position: absolute;
            border-radius: 4px;
            left: 50%;
            transform: translateX(-50%);
        }

        .bubble::after {
            content: "";
            position: absolute;
            width: 2px;
            height: 2px;
            background: lightgrey;
            top: -1px;
            left: 50%;
        }
    </style>
</head>

<body>
    <div class="container-fluid p-4">
        <div class="p-3 mb-2 bg-info text-white">
            <h3>Steps:</h3>
            <ol>
                <li>Enter PDB ID (no chain) and clicl PARSE button. This will parse out PDB file and init chain
                    selectors.</li>
                <li>Select <ul>
                        <li>same chain to show distances between single chain residues</li>
                        <li> different chains for
                            between-chain distances. </li>
                    </ul>
                </li>

                <li>Click DISPLAY to calculate distances and display chart. At this point program will show calculated
                    min and max distances.</li>
                <li>Adjust distance cutoffs and click DISPLAY again to refresh chart. Default cutoffs: single chain -
                    5A, two chains - 30A</li>
            </ol>
        </div>
        <h2 id="pdbtitle"></h2>
        <div>
            <div class="row">
                <div class="col-3">
                    <label for="pdbid">Enter PDB id</label>
                </div>
                <div class="col-4">
                    <input type="text" class="form-control" id="pdbid" value="6W9C">
                </div>
                <div class="col-4">
                    <button id="runBtn" type="submit" class="btn btn-primary mb-2">Parse</button>
                </div>
            </div>
            <div class="row small ml-3">
                Suggested PDBs (M.): <ul>
                    <li>1ake_A -It’s closed conformation of adenylate kinase. And has three subdomains</li>
                    <li>4ake_A is the open conformation.</li>
                    <li>7brrB and 3iwmB - 3C-like proteinase from SARS-CoV
                    </li>
                </ul>
            </div>

            <div id="controls" class="p-2 border border-secondary">
                <div class="row">
                    <div class="col col-6">
                        <form>
                            <div class="form-group">
                                <label for=" chain1">First chain:</label>
                                <select id="chain1" class="form-control-sm">
                                    <option></option>
                                </select>
                            </div>

                            <div class="form-group">
                                <label for="chain2">Second chain (same as first for single-chain view)</label>

                                <select id="chain2" class="form-control-sm ">
                                    <option value="none">none</option>
                                </select>
                            </div>
                        </form>
                    </div>
                    <div class="col col-6">
                        <label for="minDist">MIN distance cutoff:</label>
                        <div class="range-wrap">
                            <input id="minDist" type="range" class="range" value="1" step="0.1"/>
                            <output class="bubble mt-4"></output>
                        </div>
                        <br />
                        <label for="maxDist">MAX distance cutoff:</label>
                        <div class="range-wrap">
                            <input id="maxDist" type="range" class="range" value="5" step="0.1" />
                            <output class="bubble mt-4"></output>
                        </div>
                        <br />

                        <span id="minmax"></span>
                    </div>
                </div>
                <div class="row">
                    <div class="col">
                        <button type="button" class="btn btn-primary btn-block" id="showBtn"
                            type="submit">Display</button>
                    </div>
                </div>
            </div>
        </div>
    </div>
    <div id="chart" width="100%" align="center">
    </div>
</body>
<script>

    let chains; // chains for selected pdb
    let maxDist = $("#maxDist")
    let minDist = $("#minDist")
    let divId = "chart";
    let pdbID;

    $(document).ready(function () {

        $("#controls").hide()

        $("#runBtn").click(function () { runPDB() })
        $("#showBtn").click(function () { showPDB() })

        addBubbles()
        runPDB()

        $("#controls").show()

    });

    async function runPDB() {
        pdbID = $("#pdbid").val();

        $( "#"+ divId).empty();
        chains = await prepare(pdbID)
        if (chains)
            console.log(chains)
        else console.error("failed")
    }

    function showPDB() {
        let selChains = [];
        selChains[0] = $("#chain1").val();
        selChains[1] = $("#chain2").val();
        let mxdist = maxDist.val();
        let mndist = minDist.val();
        displayStructureContacts(pdbID, chains, divId, selChains, mxdist, mndist)
    }

    // const showSingle = function () {
    //     displayStructureContacts(pdbid, "chart", false)
    // }
    // const showMultiple = function () {
    //     displayStructureContacts(pdbid, "chart", true)
    // }
    // const showMultiple2 = function () {
    //     displayStructureContacts(pdbid, "chart", true, ["A", "C"])
    // }

    // let pdbid = '6W9C'
    // showSingle()

    function addBubbles() {
        const allRanges = document.querySelectorAll(".range-wrap");
        allRanges.forEach(wrap => {
            const range = wrap.querySelector(".range");
            const bubble = wrap.querySelector(".bubble");

            range.addEventListener("input", () => {
                setBubble(range, bubble);
            });
            setBubble(range, bubble);
        });

        function setBubble(range, bubble) {
            const val = range.value;
            const min = range.min ? range.min : 0;
            const max = range.max ? range.max : 100;
            const newVal = Number(((val - min) * 100) / (max - min));
            bubble.innerHTML = val;

            // Sorta magic numbers based on size of the native UI thumb
            bubble.style.left = `calc(${newVal}% + (${8 - newVal * 0.15}px))`;
        }

    }
</script>

</html>