app/static.py

CSS = """
/* HTML: <div class="loader"></div> */
.loader {
  width: 60px;
  aspect-ratio: 1.154;
  color: #25b09b;
  display: grid;
  animation: l38-0 6s infinite linear;
}
.loader:before,
.loader:after {
  content: "";
  grid-area: 1/1;
}
.loader:before {
  clip-path: polygon(25% 0,75% 0,100% 50%,75% 100%,25% 100%,0 50%);
  background: conic-gradient(from -30deg,#0000 60deg,currentColor 0);
}
.loader:after {
  background: conic-gradient(from -30deg,currentColor 60deg,#0000 0);
  animation: l38 0.5s infinite alternate;
}
@keyframes l38-0 {
  0%,16.66%     {transform: rotate(0deg)}
  16.67%,33.33% {transform: rotate(60deg)}
  33.34%,50%    {transform: rotate(120deg)}
  50.1%,66.66%  {transform: rotate(180deg)}
  66.67%,83.33% {transform: rotate(240deg)}
  83.34%,100%   {transform: rotate(300deg)}
}
@keyframes l38 {
  100%  {transform: translateY(-20px)}
}

.loader.first-frame {
  animation: none; /* Stop the main animation */
}

.loader.first-frame:before {
    transform: rotate(0deg); /* Explicitly set the rotation to the first frame */
}

.loader.first-frame:after {
    animation: none; /* Stop the after animation */
    transform: translateY(0px); /*reset the translate Y*/
}

.help-tip {
  position: absolute;
  display: inline-block;
  top: 16px;
  right: 0px;
  text-align: center;
  border-radius: 40%;
  /* border: 2px solid darkred; background-color: #8B0000;*/
  width: 24px;
  height: 24px;
  font-size: 16px;
  line-height: 26px;
  cursor: default;
  transition: all 0.5s cubic-bezier(0.55, 0, 0.1, 1);
  z-index: 100 !important;
}

.help-tip:hover {
  cursor: pointer;
  /*background-color: #ccc;*/
}

.help-tip:before {
  content: '?';
  font-weight: 700;
  color: #8B0000;
  z-index: 100 !important;
}

.help-tip p {
  visibility: hidden;
  opacity: 0;
  text-align: left;
  background-color: #EFDDE3;
  padding: 20px;
  width: 300px;
  position: absolute;
  border-radius: 4px;
  right: -4px;
  color: #494F5A;
  font-size: 13px;
  line-height: normal;
  transform: scale(0.7);
  transform-origin: 100% 0%;
  transition: all 0.5s cubic-bezier(0.55, 0, 0.1, 1);
  z-index: 100;
}

.help-tip:hover p {
  cursor: default;
  visibility: visible;
  opacity: 1;
  transform: scale(1.0);
}

.help-tip p:before {
  position: absolute;
  content: '';
  width: 0;
  height: 0;
  border: 6px solid transparent;
  border-bottom-color: #EFDDE3;
  right: 10px;
  top: -12px;
}

.help-tip p:after {
  width: 100%;
  height: 40px;
  content: '';
  position: absolute;
  top: -5px;
  left: 0;
  z-index: 101;
}

.upload_button {
  background-color: #008000;
}

.absolute {
  position: absolute;
}

.example {
  padding: 0;
  background: none;
  border: none;
  text-decoration: underline;
  box-shadow: none;
  text-align: left !important;
  display: block; 
}

footer {
  visibility: hidden
}

.html-container { 
  padding: 0px; 
}

.block .table-wrap {
  width: 100% !important;
  aspect-ratio: 1.618 / 1 !important;
  height: auto !important;
}

.mol-container {
    width: 100%;
    aspect-ratio: 1.618 / 1;
}

.mol-container > canvas {
    position: relative ! important;
}

.gr-btn-grp {
    display: flex;
    flex-wrap: wrap;
    gap: var(--layout-gap);
    width: var(--size-full);
    position: relative
    border-radius: 0
    border-radius: var(--container-radius);
    background: var(--background-fill-secondary);
    padding: var(--size-2)
    align-items: stretch
}

.gr-btn-grp > button {
    flex: 1 1 0;
    display: inline-flex;
    justify-content: center;
    align-items: center;
    transition: var(--button-transition);
    padding: var(--size-0-5) var(--size-2);
    text-align: center;
    border: var(--button-border-width) solid var(--button-secondary-border-color);
    background: var(--button-secondary-background-fill);
    color: var(--button-secondary-text-color);
    box-shadow: var(--button-secondary-shadow)
    border-radius: var(--button-large-radius);
    padding: calc(var(--button-large-padding) - 1px);
    font-family: monospace;
    font-weight: var(--button-large-text-weight);
    font-size: calc(var(--button-large-text-size) - 1px);
}
"""

IFRAME_TEMPLATE = """
<iframe style="width: 100%; aspect-ratio: {aspect_ratio}; overflow: visible; border: none;" scrolling="no"
frameborder="0" allow="display-capture; encrypted-media;" 
sandbox="allow-modals allow-forms allow-scripts allow-same-origin allow-popups 
allow-top-navigation-by-user-activation allow-downloads" srcdoc='{srcdoc}'></iframe>
"""

SETUP_JS = """
() => {
    const scripts = [
        "https://code.jquery.com/jquery-3.7.1.min.js",
        "https://3dmol.org/build/3Dmol.js"
    ];
    scripts.forEach((script) => {
        const scriptElement = document.createElement("script");
        scriptElement.src = script;
        scriptElement.async = true;
        document.head.appendChild(scriptElement);
    });

    viewerConfig = { backgroundColor: "white" };
    ligandStyle = { stick: { colorscheme: "greenCarbon" } };
    proteinStyle = { cartoon: { colorscheme: "Jmol" } };
    pocketStyle = { clicksphere: { radius: 1.5 } };
    pocketSurfaceStyle = { opacity: 0.854, color: "aquamarine" };

    selectedElements = {
        "atoms": [],
        "ligand": {name: null, resn: null, chain: null, resi: null},
        "pocket": {name: null, id: null}
    }
}
"""

# function handleMessage(event) {
# if (event.data.name == "atom_selection") {
#     console.log("New message: ", event.data)
# let atom = event.data.data["atom"];
# let add = event.data.data["add"];
# console.log("add: ", add, " atom: ", atom);
# window.selected_elements["atom_selection"][atom] = add;
# }
# if (event.data.name == "ligand_selection") {
# console.log("New message: ", event.data)
# let residue_info = event.data.data["residue"];
# let add = event.data.data["add"];
# residue = residue_info.resi + ":" + residue_info.resn + ":" + residue_info.chain;
# console.log("add: ", add, " residue: ", residue);
# window.selected_elements["ligand_selection"][residue] = add;
# }
# if (event.data.name == "pocket_selection") {
# let pocket = event.data.data["pocket"];
# console.log("add: ", add, " pocket: ", pocket);
# window.selected_elements["pocket_selection"][pocket] = add;
# }
# }
#
# window.addEventListener("message", handleMessage);
# console.log("Listener Added");
# console.log(window.selected_elements);

RETURN_LIGAND_SELECTION_JS = """
(prot_file, selected_ligand) => {
    const selectedElements = window.selected_elements || {}; // Handle potential undefined

    if ("ligand_selection" in selectedElements) {
        ligandElements = selectedElements["ligand_selection"];
        for (const [residue, add] of Object.entries(ligandElements)) {
            if (add) {
                selectedLigand = residue
                console.log("Selecting ligand ", selectedLigand);
            }
        }
    }
    console.log("Finished parsing selection.");
    window.selected_elements["ligand_selection"] = {}
    return [prot_file, selectedLigand];
}
"""

RETURN_SELECTION = """
(selected_ligand, selected_pocket) => {
    selectedAtoms = selectedElements.atoms;
    selectedLigand = selectedElements.ligand.name;
    console.log("Selected Ligand:", selectedLigand);
    selectedPocket = selectedElements.pocket.name;
    console.log("Selected Pocket:", selectedPocket);
    return [selectedLigand, selectedPocket];
}
"""


RETURN_POCKET_SELECTION_JS = """
(prot_file, selected_pocket) => {
    const selectedElements = window.selected_elements || {}; // Handle potential undefined

    if ("pocket_selection" in selectedElements) {
        pocketElements = selectedElements["pocket_selection"];
        for (const [pocket, add] of Object.entries(pocketElements)) {
            if (add) {
                console.log("Selecting pocket ", pocket);
                selected_pocket = pocket;
            }
        }
    }
    console.log("Finished parsing selection.");
    window.selected_elements["pocket_selection"] = {}
    return [prot_file, selected_pocket];
}
"""

RETURN_ATOM_SELECTION_JS = """
(input_file, selected_atoms) => {
    let selectedAtoms = [];
    if ("atom_selection" in selectedElements) {
        atomElements = selectedElements["atom_selection"];
        for (const [atom, add] of Object.entries(atomElements)) {
            if (add) {
                console.log("Adding atom ", atom);
                selectedAtoms.push(String(atom));
            }
        }
    }
    const selectedAtomsString = selectedAtoms.join(",");
    console.log("Finished parsing selection.");
    window.selected_elements["atom_selection"] = {}
    return [input_file, selectedAtomsString];
}
"""

CREATE_INPUT_MOL_VIEW = """
(mol_file, view_html) => {
    try {
        let viewer;
        // Get element id of the view_html string with error handling
        const idMatch = view_html.match(/id="(\w+)"/);
        if (!idMatch || !idMatch[1]) {
            console.error("Invalid view_html: No ID found.");
            return; // Exit the function if no ID is found
        }
        const element_id = idMatch[1];
        const element = document.getElementById(element_id);

        if (!element.querySelector('canvas')) {
            viewer = $3Dmol.createViewer(element, viewerConfig);
        } else {
            viewer = element.querySelector('canvas')._3dmol_viewer;
            viewer.clear();
            selectedElements = {
                "atoms": [],
                "ligand": {name: null, resn: null, chain: null, resi: null},
                "pocket": {name: null, id: null}
            }
        }

        if (mol_file == null) {
          return;
        }

        $.get(mol_file.url, function(molContent) {
            fmt = mol_file.path.split('.').pop();
            model = viewer.addModel(molContent, fmt);
            model.setStyle({ hetflag: false }, proteinStyle);
            model.setStyle({ hetflag: true }, ligandStyle);
            selectedLigand = selectedElements.ligand.name;
            model.setClickable(
                { hetflag: true, byres: true },
                true,
                function (_atom, _viewer, _event, _container) {
                    let selectedLigand = selectedElements.ligand;
                    let currentLigand = { resn: _atom.resn, chain: _atom.chain, resi: _atom.resi };
                    currentLigand.name = currentLigand.resi + ":" + currentLigand.resn + ":" + currentLigand.chain;
                    if (selectedLigand.name == currentLigand.name) {
                        // Deselect ligand
                        _viewer.setStyle(
                            { resn: currentLigand.resn, chain: currentLigand.chain, resi: currentLigand.resi }, 
                            ligandStyle
                        );
                        console.log("Deselected Ligand:", currentLigand);
                        selectedElements.ligand = {name: null, resn: null, chain: null, resi: null};
                    } else {
                        // Select ligand and deselect previous
                        if (selectedLigand.name) {
                            _viewer.setStyle(
                                { resn: selectedLigand.resn, chain: selectedLigand.chain, resi: selectedLigand.resi }, 
                                ligandStyle
                            );
                        }
                        selectedElements.ligand = currentLigand;
                        _viewer.setStyle(
                            { resn: currentLigand.resn, chain: currentLigand.chain, resi: currentLigand.resi },
                            { stick: { color: "red", radius: "0.4"} }
                        );
                        console.log("Selected Ligand:", currentLigand);
                    }
                    _viewer.render();
                }
            );
            viewer.zoomTo();
            viewer.render();
        }).fail(function(error) {
            console.error("Error loading molecule:", error);
        });
    } catch (error) {
        console.error("An error occurred:", error);
    }
}
"""

UPDATE_MOL_VIEW = """
(mol_files, view_html) => {
    try {
        let viewer;
        // Get element id of the view_html string with error handling
        const idMatch = view_html.match(/id="(\w+)"/);
        if (!idMatch || !idMatch[1]) {
            console.error("Invalid view_html: No ID found.");
            return; // Exit the function if no ID is found
        }
        const element_id = idMatch[1];
        const element = document.getElementById(element_id);
        if (element.querySelector('canvas')) {
            viewer = element.querySelector('canvas')._3dmol_viewer;
            for (let i = 1; i < viewer.models.length; i++) {
                viewer.removeModel(i);
            }
            viewer.removeAllSurfaces();
        } else {
            console.error("Invalid view_html: No canvas found.");
            return;
        }
        for (var mol_file of mol_files) {
            // Get the file format
            const fmt = mol_file.orig_name.split('.').pop();
            const filename = mol_file.orig_name;
            console.log("File:", mol_file.orig_name, "Format:", fmt); // Check values
            $.get(mol_file.url, function(molContent) {
                model = viewer.addModel(molContent, fmt);
                if (fmt == "pqr") {
                    model.setStyle(pocketStyle);
                    surface = viewer.addSurface('VDW', pocketSurfaceStyle, {model: model}, {model: model});
                    const surface_id = surface.surfid;
                    const pocket_name = filename.replace("_vert.pqr", "");
                    model.setClickable(
                        { byres: true },
                        true,
                        function (_atom, _viewer, _event, _container) {
                            let selectedPocket = selectedElements.pocket;
                            let currentPocket = { name: pocket_name, id: _atom.model, surface: surface_id };
                            if (currentPocket.name == selectedPocket.name) {
                                // Deselect pocket
                                // _viewer.setStyle({model: currentPocket.id}, pocketStyle);
                                _viewer.setSurfaceMaterialStyle(currentPocket.surface, pocketSurfaceStyle);
                                
                                console.log("Deselected Pocket:", currentPocket);
                                selectedElements.pocket = {name: null, id: null};
                            } else {
                                // Select pocket and deselect previous
                                if (selectedPocket.name) {
                                    console.log("Deselected Pocket:", selectedPocket);
                                    //_viewer.setStyle({model: selectedPocket.id}, pocketStyle);
                                    _viewer.setSurfaceMaterialStyle(selectedPocket.surface, pocketSurfaceStyle);
                                }
                                selectedElements.pocket = currentPocket;
                                //_viewer.setStyle({model: currentPocket.id}, {sphere: {color: "red", opacity: 0.944} });
                                _viewer.setSurfaceMaterialStyle(currentPocket.surface, { opacity: 0.944, color: "red" });
                                
                                console.log("Selected Pocket:", currentPocket);
                            }
                            _viewer.render();
                        }
                    );

                } else {
                    model.setStyle({ hetflag: false }, proteinStyle);
                    model.setStyle({ hetflag: true }, ligandStyle);
                }
                viewer.render();
            }).fail(function(error) {
                console.error("Error loading molecule:", error);
            })
        }
        console.log("Rendering protein view.");
        viewer.zoomTo();
        viewer.render();
        selectedElements = {
            "atoms": [],
            "ligand": {name: null, resn: null, chain: null, resi: null},
            "pocket": {name: null, id: null}
        }
    } catch (error) {
        console.error("An error occurred:", error);
    }
}
"""

CREATE_OUTPUT_MOL_VIEW = """
(mol_file, view_html) => {
    try {
        let viewer;
        const idMatch = view_html.match(/id="(\w+)"/);
        if (!idMatch || !idMatch[1]) {
            console.error("Invalid view_html: No ID found.");
            return;
        }
        const element_id = idMatch[1];
        const element = document.getElementById(element_id);

        fmt = mol_file.path.split('.').pop();
        $.get(mol_file.url, function(molContent) {
            if (!element.querySelector('canvas')) {
                viewer = $3Dmol.createViewer(element, viewerConfig);
            } else {
                viewer = element.querySelector('canvas')._3dmol_viewer;
                viewer.clear();
            }
            model = viewer.addModel(molContent, fmt);
            model.setStyle({ hetflag: false }, proteinStyle);
            model.setStyle({ hetflag: true }, ligandStyle);
            viewer.zoomTo();
            viewer.render();

            let container = element.parentElement.querySelector(".gr-btn-grp");
            if (!container) {
                container = document.createElement("div");
                container.classList.add("gr-btn-grp");
                element.parentElement.appendChild(container);
            }

            // Molecule Button
            let toggleMoleculeButton = container.querySelector("#toggleMoleculeButton");
            if (!toggleMoleculeButton) {
                toggleMoleculeButton = document.createElement("button");
                toggleMoleculeButton.id = "toggleMoleculeButton"; // Add an ID
                toggleMoleculeButton.textContent = "Hide Generated Molecule";
                let moleculeIsHidden = false;
                toggleMoleculeButton.onclick = function() {
                    if (viewer.models.length === 2) {
                        moleculeIsHidden = !moleculeIsHidden;
                        viewer.addStyle({model: 1}, {stick: {hidden: moleculeIsHidden} });
                        toggleMoleculeButton.textContent = moleculeIsHidden ? "Show Generated Molecule" : "Hide Generated Molecule";
                        viewer.render();
                    }
                };
                container.appendChild(toggleMoleculeButton);
            }

            // Ligand Button
            const ligandButtonId = "toggleLigandButton";
            let toggleLigandButton = container.querySelector("#" + ligandButtonId);

            // Check for ligands and existing button
            const hasLigands = viewer.getAtomsFromSel({model: 0, hetflag : true}).length > 0;
            if (hasLigands && !toggleLigandButton) {
                // Create button if ligands exist and it doesn't exist yet
                toggleLigandButton = document.createElement("button");
                toggleLigandButton.id = ligandButtonId;
                toggleLigandButton.textContent = "Hide Co-Crystallized Ligand";
                let ligandIsHidden = false;
                toggleLigandButton.onclick = function() {
                    ligandIsHidden = !ligandIsHidden;
                    viewer.addStyle({model: 0, hetflag: true}, {stick: {hidden: ligandIsHidden} });
                    toggleLigandButton.textContent = ligandIsHidden ? "Show Co-Crystallized Ligand" : "Hide Co-Crystallized Ligand";
                    viewer.render();
                };
                container.appendChild(toggleLigandButton);
            } else if (!hasLigands && toggleLigandButton) {
                // Remove button if no ligands exist and it already exists
                container.removeChild(toggleLigandButton);
            }

            // Protein Button
            let toggleProteinButton = container.querySelector("#toggleProteinButton");
            if (!toggleProteinButton) {
                toggleProteinButton = document.createElement("button");
                toggleProteinButton.id = "toggleProteinButton";
                toggleProteinButton.textContent = "Hide Target Protein";
                let proteinIsHidden = false;
                toggleProteinButton.onclick = function() {
                    proteinIsHidden = !proteinIsHidden;
                    viewer.addStyle({model: 0, hetflag: false}, {cartoon: {hidden: proteinIsHidden} });
                    toggleProteinButton.textContent = proteinIsHidden ? "Show Target Protein" : "Hide Target Protein";
                    viewer.render();
                };
                container.appendChild(toggleProteinButton);
            }

        }).fail(function(error) {
            console.error("Error loading molecule:", error);
        });
    } catch (error) {
        console.error("An error occurred:", error);
    }
}
"""