MolView/index.html at main · atomicarchitects/MolView · GitHub

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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>MolView</title>
<script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
<script src="https://chemapps.stolaf.edu/jmol/jsmol/JSmol.min.js"></script>
<style>
    body {
        margin: 0;
        padding: 0;
        font-family: Roboto, sans-serif;
    }

    .container {
        display: flex;
        height: 100vh;
        width: 100vw;
    }

    #appdiv {
        flex: 1;
        background: #ffffff;
        display: flex;
        align-items: left;
        justify-content: left;
        min-width: 0;
    }

    .controls {
        width: min(400px, 30vw);
        max-width: 500px;
        min-width: 300px;
        padding: 20px;
        background: white;
        border-left: 1px solid #ddd;
        overflow-y: auto;
    }

    .control-group {
        margin-bottom: 20px;
        padding: 15px;
        background: #f9f9f9;
        border-radius: 5px;
        display: flex;
        align-items: center;
        gap: 10px;
        flex-wrap: wrap;
    }

    .load-group {
        display: block;
    }

    .control-group h3 {
        margin: 0;
        color: #333;
        font-size: clamp(12px, 1.5vw, 14px);
        font-weight: bold;
        white-space: nowrap;
    }

    .load-group h3 {
        margin-bottom: 5px;
    }

    button, input[type="radio"] {
        margin: 5px 0;
        cursor: pointer;
    }

    input[type="file"], input[type="text"] {
        width: 100%;
        max-width: 100%;
        padding: 8px;
        border: 1px solid #ddd;
        border-radius: 4px;
        font-size: clamp(12px, 1.5vw, 14px);
        box-sizing: border-box;
    }

    button, input[type="button"] {
        padding: 8px 12px;
        background: #e1e3e1;
        color: rgb(11, 3, 3);
        border: none;
        border-radius: 4px;
        font-size: clamp(13px, 1.5vw, 15px);
        margin: 3px;
    }

    button:hover, input[type="button"]:hover {
        background: #589f5b;
    }

    label {
        margin-left: 5px;
        font-size: clamp(11px, 1.5vw, 13px);
    }

    /* Mobile responsiveness */
    @media (max-width: 768px) {
        .container {
            flex-direction: column;
        }

        .controls {
            width: 100vw;
            max-width: 100vw;
            min-width: unset;
            border-left: none;
            border-top: 1px solid #ddd;
            max-height: 50vh;
        }

        #appdiv {
            height: 50vh;
        }
    }
</style>
</head>
<body>
    <script>
        var MP_PROXY_SERVER = "https://mp-proxy-1067494591843.us-central1.run.app/";  // Change this if you host your own proxy server
        var defaultZoomLevel = 70;
        var myJmol = 'myJmol';
        var Info = {
            width: $(window).width() * 0.8,
            height: $(window).height() * 1.0 - 6,
            use: "HTML5",
            j2sPath: "https://chemapps.stolaf.edu/jmol/jsmol/j2s",
            serverURL: "https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
            script: `set antialiasDisplay;`,

            readyFunction: function(applet) {
                console.log("JSmol ready!");
            }
        };


        function default_render() {
            // Set default display parameters
            return `
            // Reset view and clear previous selections
            reset;

            // Set default zoom level
            zoom ${defaultZoomLevel};

            // Enable anti-aliasing for smoother rendering
            set antialiasDisplay true;

            spacefill off;
            wireframe off;
            cartoons off;

            // Select all protein chains
            select protein;

            // Render proteins in cartoon representation
            cartoon only;
            color structure;

            select not protein;
            // Render non-protein molecules (ligands, ions, etc.) in ball-and-stick
            spacefill 23%;
            wireframe 0.15;
            color cpk;
            `;
        }


        $(document).ready(function() {
            $("#appdiv").html(Jmol.getAppletHtml(myJmol, Info));
            Jmol.script(myJmol, `load examples/theobromine.sdf; ${default_render()}; set picking ATOM; select none; set display selected; set selecthalo true;`);  // Load a default structure
        });
    </script>

    <div class="container">
        <div id="appdiv">Loading...</div>

        <div class="controls">
            <h2 style="margin-top: 0;">Controls</h2>

            <div class="control-group load-group">
                <h3>Upload File</h3>
                <input type="file" id="file-input" accept=".xyz,.pdb,.mol,.sdf,.cif" style="display: none;" onchange="handleFileUpload(event)">
                <input type="text" id="file-name-display" placeholder=".xyz,.pdb,.mol,.sdf,.cif" readonly style="width: 50%; margin-right: 5px;">
                <script type="text/javascript">
                    function handleFileUpload(event) {
                        const file = event.target.files[0];
                        if (!file) return;

                        document.getElementById('file-name-display').value = file.name;

                        const reader = new FileReader();
                        reader.onload = function(e) {
                            const fileContent = e.target.result;
                            const fileName = file.name;

                            // Load the file content into JSmol
                            Jmol.script(myJmol, `load DATA "${fileName}"\n${fileContent}\nEND "${fileName}"; ${default_render()}`);

                            console.log("Loaded file:", fileName);
                        };
                        reader.readAsText(file);
                    }

                    function openFileDialog() {
                        document.getElementById('file-input').click();
                    }

                    Jmol.jmolButton(myJmol, "javascript openFileDialog()", "Choose File");
                </script>
            </div>

            <div class="control-group load-group">
                <h3>Load Structure</h3>
                <div style="margin-bottom: 10px;">
                    <label><input type="radio" name="load-source" value="pdb" checked onchange="updatePlaceholder()"> Protein Data Bank</label>
                    <label><input type="radio" name="load-source" value="mp" onchange="updatePlaceholder()"> Materials Project</label>
                    <label><input type="radio" name="load-source" value="pubchem" onchange="updatePlaceholder()"> PubChem</label>
                </div>
                <input type="text" id="structure-id" placeholder="Enter PDB code (e.g., 1crn)" style="width: 62%; margin-right: 5px;">
                <script type="text/javascript">
                    function updatePlaceholder() {
                        var source = document.querySelector('input[name="load-source"]:checked').value;
                        var input = document.getElementById('structure-id');

                        if (source === 'pdb') {
                            input.placeholder = "Enter PDB code (e.g., 1crn)";
                        } else if (source === 'mp') {
                            input.placeholder = "Enter MP ID (e.g., mp-149)";
                        } else if (source === 'pubchem') {
                            input.placeholder = "Enter name or CID (e.g., aspirin)";
                        }
                    }

                    async function loadStructure() {
                        var structureId = document.getElementById('structure-id').value.trim();
                        if (!structureId) return;

                        var source = document.querySelector('input[name="load-source"]:checked').value;

                        if (source === 'pdb') {
                            Jmol.script(myJmol, `load =${structureId}; ${default_render()}`);
                        } else if (source === 'mp') {
                            try {
                                const response = await fetch(`${MP_PROXY_SERVER}/mp/${structureId}`);
                                const cifContent = await response.text();

                                if (cifContent && !cifContent.includes('error')) {
                                    Jmol.script(myJmol, `load DATA "${structureId}.cif"\n${cifContent}\nEND "${structureId}.cif"; ${default_render()}`);
                                    console.log("Loaded from Materials Project:", structureId);
                                } else {
                                    alert("Structure not found: " + structureId);
                                }
                            } catch (error) {
                                console.error("Error:", error);
                                alert("Error loading structure. Check console for details.");
                            }
                        } else if (source === 'pubchem') {
                            Jmol.script(myJmol, `load :${structureId}; ${default_render()}`);  // PubChem supports name and CID directly
                        }
                    }

                    Jmol.jmolButton(myJmol, "javascript loadStructure()", "Load");
                </script>
            </div>

            <div class="load-group control-group">
                <h3>Load Trajectory</h3>
                <div style="margin-bottom: 10px;">
                    <label style="display: block; margin-bottom: 5px;">Topology (.xyz,.pdb,.mol,.sdf,.cif):</label>
                    <input type="file" id="topology-input" accept=".xyz,.pdb,.mol,.sdf,.cif" style="display: none;">
                    <input type="text" id="topology-name-display" placeholder=".xyz, .pdb, .mol, .sdf, .cif" readonly style="width: 50%; margin-right: 5px;">
                    <script type="text/javascript">
                        function openTopologyDialog() {
                            document.getElementById('topology-input').click();
                        }
                        Jmol.jmolButton(myJmol, "javascript openTopologyDialog()", "Choose File");
                    </script>
                </div>
                <div style="margin-bottom: 10px;">
                    <label style="display: block; margin-bottom: 5px;">Trajectory (.dcd, .xtc, .trr):</label>
                    <input type="file" id="trajectory-input" accept=".dcd,.xtc,.trr,.xyz" style="display: none;">
                    <input type="text" id="trajectory-name-display" placeholder=".dcd, .xtc, .trr, .xyz" readonly style="width: 50%; margin-right: 5px;">
                    <script type="text/javascript">
                        function openTrajectoryDialog() {
                            document.getElementById('trajectory-input').click();
                        }
                        Jmol.jmolButton(myJmol, "javascript openTrajectoryDialog()", "Choose File");
                    </script>
                </div>
                <script type="text/javascript">
                    let topologyData = null;
                    let topologyFileName = null;

                    document.getElementById('topology-input').addEventListener('change', function(e) {
                        const file = e.target.files[0];
                        if (!file) return;

                        document.getElementById('topology-name-display').value = file.name;

                        const reader = new FileReader();
                        reader.onload = function(event) {
                            topologyData = event.target.result;
                            topologyFileName = file.name;
                            console.log("Topology loaded:", topologyFileName);
                        };
                        reader.readAsText(file);
                    });

                    document.getElementById('trajectory-input').addEventListener('change', function(e) {
                        const file = e.target.files[0];
                        if (!file) return;

                        if (!topologyData) {
                            alert("Please load topology file first!");
                            return;
                        }

                        document.getElementById('trajectory-name-display').value = file.name;

                        const reader = new FileReader();
                        reader.onload = function(event) {
                            const trajectoryData = event.target.result;
                            const trajectoryFileName = file.name;

                            // Then load trajectory coordinates
                            Jmol.script(myJmol, `load trajectory DATA "${trajectoryFileName}"\n${trajectoryData}\nEND "${trajectoryFileName}" coord "${topologyFileName}"; ${default_render()}`);

                            // Alternative way to get frame count
                            const frameCount = Jmol.evaluate(myJmol, '{*}.length');
                            console.log(`Loaded trajectory with ${frameCount} frames`);

                            // Show trajectory controls
                            document.getElementById('trajectory-controls').style.display = 'block';

                            // Update slider
                            const slider = document.getElementById('frame-slider');
                            slider.max = frameCount;
                            slider.value = 1;
                            document.getElementById('frame-display').textContent = `Frame: 1 / ${frameCount}`;

                        };

                        // Read as binary for .dcd, .xtc, .trr
                        if (file.name.endsWith('.dcd') || file.name.endsWith('.xtc') || file.name.endsWith('.trr')) {
                            reader.readAsArrayBuffer(file);
                        } else {
                            reader.readAsText(file);
                        }
                    });
                </script>
            </div>

            <div id="trajectory-controls" style="display: none;">
            <div class="control-group">
                <h3>Frame Navigation</h3>
                <div style="display: flex; align-items: center; gap: 10px; width: 100%;">
                    <input type="range" id="frame-slider" min="1" max="100" value="1"
                        style="flex: 1;" oninput="updateFrame(this.value)">
                    <span id="frame-display" style="min-width: 100px; font-size: 12px;">Frame: 1 / 100</span>
                </div>
                <script type="text/javascript">
                function updateFrame(frameNum) {
                    Jmol.script(myJmol, `frame ${frameNum}`);
                    const maxFrames = document.getElementById('frame-slider').max;
                    document.getElementById('frame-display').textContent = `Frame: ${frameNum} / ${maxFrames}`;
                }

                Jmol.jmolButton(myJmol, "javascript updateSliderToFirst()", "First");
                Jmol.jmolButton(myJmol, "javascript decrementFrame()", "◀");
                Jmol.jmolButton(myJmol, "javascript incrementFrame()", "▶");
                Jmol.jmolButton(myJmol, "javascript updateSliderToLast()", "Last");

                function updateSliderToFirst() {
                    document.getElementById('frame-slider').value = 1;
                    updateFrame(1);
                }

                function incrementFrame() {
                    let currentFrame = parseInt(document.getElementById('frame-slider').value);
                    const maxFrames = document.getElementById('frame-slider').max;
                    if (currentFrame < maxFrames) {
                        currentFrame += 1;
                        document.getElementById('frame-slider').value = currentFrame;
                        updateFrame(currentFrame);
                    }
                }

                function decrementFrame() {
                    let currentFrame = parseInt(document.getElementById('frame-slider').value);
                    if (currentFrame > 1) {
                        currentFrame -= 1;
                        document.getElementById('frame-slider').value = currentFrame;
                        updateFrame(currentFrame);
                    }
                }

                function updateSliderToLast() {
                    const maxFrames = document.getElementById('frame-slider').max;
                    document.getElementById('frame-slider').value = maxFrames;
                    updateFrame(maxFrames);
                }
                </script>
            </div>

            <div class="control-group">
                <h3>Animation</h3>
                <script type="text/javascript">
                Jmol.jmolButton(myJmol, "animation on", "Play");
                Jmol.jmolButton(myJmol, "animation off", "Pause");
                Jmol.jmolButton(myJmol, "animation mode loop", "Loop");
                Jmol.jmolButton(myJmol, "animation mode palindrome", "Palindrome");
                </script>
            </div>

            <div class="control-group">
                <h3>Animation Speed</h3>
                <script type="text/javascript">
                Jmol.jmolButton(myJmol, "animation fps 5", "Slow (5 fps)");
                Jmol.jmolButton(myJmol, "animation fps 10", "Medium (10 fps)");
                Jmol.jmolButton(myJmol, "animation fps 20", "Fast (20 fps)");
                </script>
            </div>
            </div>


            <div class="control-group">
                <h3>Atom Selection & Deletion</h3>
                <script type="text/javascript">
                    Jmol.jmolButton(myJmol, "select none", "Clear Selection");
                    Jmol.jmolButton(myJmol, "select within(2.0, selected)", "Expand Selection (2Å)");
                    Jmol.jmolButton(myJmol, "save state _beforeDelete; delete selected", "Delete Selected");
                    Jmol.jmolButton(myJmol, "restore state _beforeDelete; set picking ATOM;", "Undo Deletion");
                </script>
            </div>

            <div class="control-group">
                <h3>Atom Labels</h3>
                <script type="text/javascript">
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; label %a; select @temp", "Show");
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; label off; select @temp", "Hide");
                </script>
            </div>


            <div class="control-group">
                <h3>Save Image & Structure</h3>
                <script type="text/javascript">
                    Jmol.jmolButton(myJmol, "write image PNG 'molecule.png'", ".png");
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; write xyz 'molecule.xyz'; select @temp", ".xyz");
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; write pdb 'molecule.pdb'; select @temp", ".pdb");
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; write mol 'molecule.mol'; select @temp", ".mol");
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; write sdf 'molecule.sdf'; select @temp", ".sdf");
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; write cif 'molecule.cif'; select @temp", ".cif");
                </script>
            </div>

            <div class="control-group">
                <h3>Display Type</h3>
                <script type="text/javascript">
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; spacefill 23%; wireframe 0.15; select @temp", "Ball & Stick");
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; wireframe -0.1; select @temp", "Wire");
                    Jmol.jmolButton(myJmol, "var temp = {selected}; select *; spacefill only; select @temp", "Spacefill");
                </script>
            </div>

            <div class="control-group">
                <h3>Isosurface</h3>
                <script type="text/javascript">
                Jmol.jmolButton(myJmol, "var temp = {selected}; select *; isosurface vdw; select @temp", "Show");
                Jmol.jmolButton(myJmol, "isosurface off", "Hide");
                </script>
            </div>

            <div class="control-group">
                <h3>Color Scheme</h3>
                <script type="text/javascript">
                Jmol.jmolButton(myJmol, "color cpk", "CPK (Default)");
                Jmol.jmolButton(myJmol, "color rasmol", "RasMol");
                Jmol.jmolButton(myJmol, "color chain", "By Chain");
                Jmol.jmolButton(myJmol, "color structure", "By Structure");
                Jmol.jmolButton(myJmol, "color group", "By Group");
                </script>
            </div>

            <div class="control-group">
                <h3>Display Mode</h3>
                <script type="text/javascript">
                Jmol.jmolButton(myJmol, "cartoon only", "Ribbon Only");
                Jmol.jmolButton(myJmol, "cartoon off; wireframe 0.15; spacefill 23%", "Atoms Only");
                Jmol.jmolButton(myJmol, "cartoon on; wireframe 0.15; spacefill 23%", "Both");
                </script>
            </div>

            <div class="control-group">
                <h3>Background Color</h3>
                <input type="color" id="bg-color-picker" style="margin-left: 10px;" value="#ffffff" onchange="var hex = this.value; var r = parseInt(hex.substr(1,2), 16); var g = parseInt(hex.substr(3,2), 16); var b = parseInt(hex.substr(5,2), 16); Jmol.script(myJmol, 'background [' + r + ',' + g + ',' + b + ']')">
            </div>

            <div class="control-group">
                <h3>Rendering Quality</h3>
                <script type="text/javascript">
                Jmol.jmolButton(myJmol, "set antialiasDisplay true", "High");
                Jmol.jmolButton(myJmol, "set antialiasDisplay false", "Low");
                </script>
            </div>

            <div class="control-group">
                <h3>View Controls</h3>
                <script type="text/javascript">
                Jmol.jmolButton(myJmol, `reset; zoom ${defaultZoomLevel}`, "Reset View");
                </script>
            </div>

            <div class="control-group">
                <h3>Spin Controls</h3>
                <script type="text/javascript">
                Jmol.jmolButton(myJmol, "spin on", "Start Spinning");
                Jmol.jmolButton(myJmol, "spin off", "Stop Spinning");
                </script>
            </div>

            <div class="control-group">
                <h3>Zoom Controls</h3>
                <script type="text/javascript">
                    Jmol.jmolButton(myJmol, "zoom *1.5", "Zoom In");
                    Jmol.jmolButton(myJmol, "zoom /1.5", "Zoom Out");
                    Jmol.jmolButton(myJmol, `zoom ${defaultZoomLevel}`, "Reset Zoom");
                </script>
            </div>
        </div>
    </div>

</body>
</html>