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<script>
import { createEventDispatcher, afterUpdate } from "svelte";
const dispatch = createEventDispatcher();
import * as mol from "3dmol/build/3Dmol.js";
let Dmol = mol;
console.log(Dmol);
// export let whichCovMod = 0;
let viewer = null;
let attachmentIndex = null;
let deleteIndexes = [];
let mode = "attach";
function updateReps(viewer) {
viewer.setStyle({ stick: {} });
if (showCovMod > -1) {
if (attachmentIndex !== null) {
viewer.addStyle(
{ index: attachmentIndex },
{ sphere: { color: "blue", scale: 0.5 } }
);
}
viewer.addStyle(
{ index: deleteIndexes },
{ sphere: { color: "red", scale: 0.5 } }
);
dispatch("updateMol", {
attachmentIndex: attachmentIndex,
deleteIndexes: deleteIndexes,
index: showCovMod,
mol: viewer.exportJSON(),
});
}
}
function initializeMoleculeViewer(molecule, container) {
let viewer = Dmol.createViewer(container, {});
viewer.addModel(molecule, "sdf");
updateReps(viewer);
viewer.setBackgroundColor("white");
viewer.zoomTo();
viewer
.getModel(0)
.setClickable({}, true, function (atom, viewer, event, container) {
if (showCovMod > -1) {
if (mode === "attach") {
attachmentIndex = atom.serial;
} else {
if (deleteIndexes.includes(atom.serial)) {
deleteIndexes = deleteIndexes.filter(
(index) => index !== atom.serial
);
} else {
deleteIndexes.push(atom.serial);
}
deleteIndexes = deleteIndexes;
updateReps(viewer);
}
}
});
viewer.render();
return viewer;
}
export let molvalue = "";
export let showCovMod = -1;
let molcontainer = null;
afterUpdate(() => {
viewer = initializeMoleculeViewer(molvalue, molcontainer);
});
</script>
<div class="mol-wrapper">
<div class="relative">
<div class="mol-canvas" bind:this={molcontainer}></div>
</div>
<div class="flex flex-col justify-center">
{#if showCovMod > -1}
<div class="w-full text-center text-lg mb-2">Covalent Modification</div>
<div class="flex items-center space-x-2 justify-center mb-2 text-xs">
<svg
data-slot="icon"
fill="none"
stroke-width="1.5"
class="w-4 h-4"
stroke="currentColor"
viewBox="0 0 24 24"
xmlns="http://www.w3.org/2000/svg"
aria-hidden="true"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
d="M15.042 21.672 13.684 16.6m0 0-2.51 2.225.569-9.47 5.227 7.917-3.286-.672Zm-7.518-.267A8.25 8.25 0 1 1 20.25 10.5M8.288 14.212A5.25 5.25 0 1 1 17.25 10.5"
></path>
</svg> <span class="px-2">click on atoms in viewer to select them</span>
</div>
<div
class="flex rounded-full border-2 border-gray-200 bg-gray-200 text-sm leading-none text-gray-500"
>
<button
class="w-1/2 flex items-center rounded-l-full px-4 py-2 transition-colors duration-300 ease-in hover:text-orange-600 focus:text-orange-600 focus:outline-none"
id="attach"
class:active={mode === "attach"}
on:click={() => (mode = "attach")}
>
<svg
xmlns="http://www.w3.org/2000/svg"
fill="none"
viewBox="0 0 24 24"
stroke-width="1.5"
stroke="currentColor"
class="mx-1 h-4 w-4"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
d="m18.375 12.739-7.693 7.693a4.5 4.5 0 0 1-6.364-6.364l10.94-10.94A3 3 0 1 1 19.5 7.372L8.552 18.32m.009-.01-.01.01m5.699-9.941-7.81 7.81a1.5 1.5 0 0 0 2.112 2.13"
/>
</svg>
<span>Attachment atom</span>
</button>
<button
class="w-1/2 flex items-center rounded-r-full px-4 py-2 transition-colors duration-300 ease-in hover:text-orange-600 focus:text-orange-600 focus:outline-none"
id="delete"
class:active={mode === "delete"}
on:click={() => (mode = "delete")}
>
<svg
xmlns="http://www.w3.org/2000/svg"
fill="none"
viewBox="0 0 24 24"
stroke-width="1.5"
stroke="currentColor"
class="mx-1 h-4 w-4"
>
<path
stroke-linecap="round"
stroke-linejoin="round"
d="m14.74 9-.346 9m-4.788 0L9.26 9m9.968-3.21c.342.052.682.107 1.022.166m-1.022-.165L18.16 19.673a2.25 2.25 0 0 1-2.244 2.077H8.084a2.25 2.25 0 0 1-2.244-2.077L4.772 5.79m14.456 0a48.108 48.108 0 0 0-3.478-.397m-12 .562c.34-.059.68-.114 1.022-.165m0 0a48.11 48.11 0 0 1 3.478-.397m7.5 0v-.916c0-1.18-.91-2.164-2.09-2.201a51.964 51.964 0 0 0-3.32 0c-1.18.037-2.09 1.022-2.09 2.201v.916m7.5 0a48.667 48.667 0 0 0-7.5 0"
/>
</svg>
<span>Atoms to delete</span>
</button>
</div>
<div class="relative overflow-x-auto mt-3">
<table
class="w-full text-sm text-left rtl:text-right text-gray-500 dark:text-gray-400"
>
<thead
class="text-xs text-gray-700 uppercase bg-gray-50 dark:bg-gray-700 dark:text-gray-400"
>
<tr>
<th scope="col" class="px-6 py-3"> </th>
<th scope="col" class="px-6 py-3"> index </th>
</tr>
</thead>
<tbody>
<tr class="bg-white border-b dark:bg-gray-800 dark:border-gray-700">
<th
scope="row"
class="px-6 py-4 font-medium text-gray-900 whitespace-nowrap dark:text-white text-right"
>
Attachment atom
</th>
<td class="px-6 py-4 font-mono">
{#if attachmentIndex !== null}
{attachmentIndex}
{:else}
not selected
{/if}
</td>
</tr>
<tr class="bg-white dark:bg-gray-800">
<th
scope="row"
class="px-6 py-4 font-medium text-gray-900 whitespace-nowrap dark:text-white text-right"
>
Deleted atoms
</th>
<td class="px-6 py-4 font-mono">
{#if deleteIndexes.length > 0}
{deleteIndexes.join(", ")}
{:else}
no atoms are deleted
{/if}
</td>
</tr>
</tbody>
</table>
</div>
{/if}
</div>
</div>
<style>
.active {
background: white;
border-radius: 9999px;
color: rgb(234, 88, 12);
}
.mol-canvas {
width: 200px;
height: 200px;
margin: 0 auto;
}
.mol-wrapper {
width: 100%;
display: flex;
justify-content: center;
}
/*
! tailwindcss v3.4.3 | MIT License | https://tailwindcss.com
*/
/*
1. Prevent padding and border from affecting element width. (https://github.com/mozdevs/cssremedy/issues/4)
2. Allow adding a border to an element by just adding a border-width. (https://github.com/tailwindcss/tailwindcss/pull/116)
*/
*,
::before,
::after {
box-sizing: border-box;
/* 1 */
border-width: 0;
/* 2 */
border-style: solid;
/* 2 */
border-color: #e5e7eb;
/* 2 */
}
::before,
::after {
--tw-content: "";
}
/*
1. Use a consistent sensible line-height in all browsers.
2. Prevent adjustments of font size after orientation changes in iOS.
3. Use a more readable tab size.
4. Use the user's configured `sans` font-family by default.
5. Use the user's configured `sans` font-feature-settings by default.
6. Use the user's configured `sans` font-variation-settings by default.
7. Disable tap highlights on iOS
*/
html,
:host {
line-height: 1.5;
/* 1 */
-webkit-text-size-adjust: 100%;
/* 2 */
-moz-tab-size: 4;
/* 3 */
tab-size: 4;
/* 3 */
font-family: ui-sans-serif, system-ui, sans-serif, "Apple Color Emoji",
"Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji";
/* 4 */
font-feature-settings: normal;
/* 5 */
font-variation-settings: normal;
/* 6 */
-webkit-tap-highlight-color: transparent;
/* 7 */
}
/*
1. Remove the margin in all browsers.
2. Inherit line-height from `html` so users can set them as a class directly on the `html` element.
*/
body {
margin: 0;
/* 1 */
line-height: inherit;
/* 2 */
}
/*
1. Add the correct height in Firefox.
2. Correct the inheritance of border color in Firefox. (https://bugzilla.mozilla.org/show_bug.cgi?id=190655)
3. Ensure horizontal rules are visible by default.
*/
hr {
height: 0;
/* 1 */
color: inherit;
/* 2 */
border-top-width: 1px;
/* 3 */
}
/*
Add the correct text decoration in Chrome, Edge, and Safari.
*/
abbr:where([title]) {
text-decoration: underline dotted;
}
/*
Remove the default font size and weight for headings.
*/
h1,
h2,
h3,
h4,
h5,
h6 {
font-size: inherit;
font-weight: inherit;
}
/*
Reset links to optimize for opt-in styling instead of opt-out.
*/
a {
color: inherit;
text-decoration: inherit;
}
/*
Add the correct font weight in Edge and Safari.
*/
b,
strong {
font-weight: bolder;
}
/*
1. Use the user's configured `mono` font-family by default.
2. Use the user's configured `mono` font-feature-settings by default.
3. Use the user's configured `mono` font-variation-settings by default.
4. Correct the odd `em` font sizing in all browsers.
*/
code,
kbd,
samp,
pre {
font-family: ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas,
"Liberation Mono", "Courier New", monospace;
/* 1 */
font-feature-settings: normal;
/* 2 */
font-variation-settings: normal;
/* 3 */
font-size: 1em;
/* 4 */
}
/*
Add the correct font size in all browsers.
*/
small {
font-size: 80%;
}
/*
Prevent `sub` and `sup` elements from affecting the line height in all browsers.
*/
sub,
sup {
font-size: 75%;
line-height: 0;
position: relative;
vertical-align: baseline;
}
sub {
bottom: -0.25em;
}
sup {
top: -0.5em;
}
/*
1. Remove text indentation from table contents in Chrome and Safari. (https://bugs.chromium.org/p/chromium/issues/detail?id=999088, https://bugs.webkit.org/show_bug.cgi?id=201297)
2. Correct table border color inheritance in all Chrome and Safari. (https://bugs.chromium.org/p/chromium/issues/detail?id=935729, https://bugs.webkit.org/show_bug.cgi?id=195016)
3. Remove gaps between table borders by default.
*/
table {
text-indent: 0;
/* 1 */
border-color: inherit;
/* 2 */
border-collapse: collapse;
/* 3 */
}
/*
1. Change the font styles in all browsers.
2. Remove the margin in Firefox and Safari.
3. Remove default padding in all browsers.
*/
button,
input,
optgroup,
select,
textarea {
font-family: inherit;
/* 1 */
font-feature-settings: inherit;
/* 1 */
font-variation-settings: inherit;
/* 1 */
font-size: 100%;
/* 1 */
font-weight: inherit;
/* 1 */
line-height: inherit;
/* 1 */
letter-spacing: inherit;
/* 1 */
color: inherit;
/* 1 */
margin: 0;
/* 2 */
padding: 0;
/* 3 */
}
/*
Remove the inheritance of text transform in Edge and Firefox.
*/
button,
select {
text-transform: none;
}
/*
1. Correct the inability to style clickable types in iOS and Safari.
2. Remove default button styles.
*/
button,
input:where([type="button"]),
input:where([type="reset"]),
input:where([type="submit"]) {
-webkit-appearance: button;
/* 1 */
background-color: transparent;
/* 2 */
background-image: none;
/* 2 */
}
/*
Use the modern Firefox focus style for all focusable elements.
*/
:-moz-focusring {
outline: auto;
}
/*
Remove the additional `:invalid` styles in Firefox. (https://github.com/mozilla/gecko-dev/blob/2f9eacd9d3d995c937b4251a5557d95d494c9be1/layout/style/res/forms.css#L728-L737)
*/
:-moz-ui-invalid {
box-shadow: none;
}
/*
Add the correct vertical alignment in Chrome and Firefox.
*/
progress {
vertical-align: baseline;
}
/*
Correct the cursor style of increment and decrement buttons in Safari.
*/
::-webkit-inner-spin-button,
::-webkit-outer-spin-button {
height: auto;
}
/*
1. Correct the odd appearance in Chrome and Safari.
2. Correct the outline style in Safari.
*/
[type="search"] {
-webkit-appearance: textfield;
/* 1 */
outline-offset: -2px;
/* 2 */
}
/*
Remove the inner padding in Chrome and Safari on macOS.
*/
::-webkit-search-decoration {
-webkit-appearance: none;
}
/*
1. Correct the inability to style clickable types in iOS and Safari.
2. Change font properties to `inherit` in Safari.
*/
::-webkit-file-upload-button {
-webkit-appearance: button;
/* 1 */
font: inherit;
/* 2 */
}
/*
Add the correct display in Chrome and Safari.
*/
summary {
display: list-item;
}
/*
Removes the default spacing and border for appropriate elements.
*/
blockquote,
dl,
dd,
h1,
h2,
h3,
h4,
h5,
h6,
hr,
figure,
p,
pre {
margin: 0;
}
fieldset {
margin: 0;
padding: 0;
}
legend {
padding: 0;
}
ol,
ul,
menu {
list-style: none;
margin: 0;
padding: 0;
}
/*
Reset default styling for dialogs.
*/
dialog {
padding: 0;
}
/*
Prevent resizing textareas horizontally by default.
*/
textarea {
resize: vertical;
}
/*
1. Reset the default placeholder opacity in Firefox. (https://github.com/tailwindlabs/tailwindcss/issues/3300)
2. Set the default placeholder color to the user's configured gray 400 color.
*/
input::placeholder,
textarea::placeholder {
opacity: 1;
/* 1 */
color: #9ca3af;
/* 2 */
}
/*
Set the default cursor for buttons.
*/
button,
[role="button"] {
cursor: pointer;
}
/*
Make sure disabled buttons don't get the pointer cursor.
*/
:disabled {
cursor: default;
}
/*
1. Make replaced elements `display: block` by default. (https://github.com/mozdevs/cssremedy/issues/14)
2. Add `vertical-align: middle` to align replaced elements more sensibly by default. (https://github.com/jensimmons/cssremedy/issues/14#issuecomment-634934210)
This can trigger a poorly considered lint error in some tools but is included by design.
*/
img,
svg,
video,
canvas,
audio,
iframe,
embed,
object {
display: block;
/* 1 */
vertical-align: middle;
/* 2 */
}
/*
Constrain images and videos to the parent width and preserve their intrinsic aspect ratio. (https://github.com/mozdevs/cssremedy/issues/14)
*/
img,
video {
max-width: 100%;
height: auto;
}
/* Make elements with the HTML hidden attribute stay hidden by default */
[hidden] {
display: none;
}
*,
::before,
::after {
--tw-border-spacing-x: 0;
--tw-border-spacing-y: 0;
--tw-translate-x: 0;
--tw-translate-y: 0;
--tw-rotate: 0;
--tw-skew-x: 0;
--tw-skew-y: 0;
--tw-scale-x: 1;
--tw-scale-y: 1;
--tw-pan-x: ;
--tw-pan-y: ;
--tw-pinch-zoom: ;
--tw-scroll-snap-strictness: proximity;
--tw-gradient-from-position: ;
--tw-gradient-via-position: ;
--tw-gradient-to-position: ;
--tw-ordinal: ;
--tw-slashed-zero: ;
--tw-numeric-figure: ;
--tw-numeric-spacing: ;
--tw-numeric-fraction: ;
--tw-ring-inset: ;
--tw-ring-offset-width: 0px;
--tw-ring-offset-color: #fff;
--tw-ring-color: rgb(59 130 246 / 0.5);
--tw-ring-offset-shadow: 0 0 #0000;
--tw-ring-shadow: 0 0 #0000;
--tw-shadow: 0 0 #0000;
--tw-shadow-colored: 0 0 #0000;
--tw-blur: ;
--tw-brightness: ;
--tw-contrast: ;
--tw-grayscale: ;
--tw-hue-rotate: ;
--tw-invert: ;
--tw-saturate: ;
--tw-sepia: ;
--tw-drop-shadow: ;
--tw-backdrop-blur: ;
--tw-backdrop-brightness: ;
--tw-backdrop-contrast: ;
--tw-backdrop-grayscale: ;
--tw-backdrop-hue-rotate: ;
--tw-backdrop-invert: ;
--tw-backdrop-opacity: ;
--tw-backdrop-saturate: ;
--tw-backdrop-sepia: ;
--tw-contain-size: ;
--tw-contain-layout: ;
--tw-contain-paint: ;
--tw-contain-style:
;
}
::backdrop {
--tw-border-spacing-x: 0;
--tw-border-spacing-y: 0;
--tw-translate-x: 0;
--tw-translate-y: 0;
--tw-rotate: 0;
--tw-skew-x: 0;
--tw-skew-y: 0;
--tw-scale-x: 1;
--tw-scale-y: 1;
--tw-pan-x: ;
--tw-pan-y: ;
--tw-pinch-zoom: ;
--tw-scroll-snap-strictness: proximity;
--tw-gradient-from-position: ;
--tw-gradient-via-position: ;
--tw-gradient-to-position: ;
--tw-ordinal: ;
--tw-slashed-zero: ;
--tw-numeric-figure: ;
--tw-numeric-spacing: ;
--tw-numeric-fraction: ;
--tw-ring-inset: ;
--tw-ring-offset-width: 0px;
--tw-ring-offset-color: #fff;
--tw-ring-color: rgb(59 130 246 / 0.5);
--tw-ring-offset-shadow: 0 0 #0000;
--tw-ring-shadow: 0 0 #0000;
--tw-shadow: 0 0 #0000;
--tw-shadow-colored: 0 0 #0000;
--tw-blur: ;
--tw-brightness: ;
--tw-contrast: ;
--tw-grayscale: ;
--tw-hue-rotate: ;
--tw-invert: ;
--tw-saturate: ;
--tw-sepia: ;
--tw-drop-shadow: ;
--tw-backdrop-blur: ;
--tw-backdrop-brightness: ;
--tw-backdrop-contrast: ;
--tw-backdrop-grayscale: ;
--tw-backdrop-hue-rotate: ;
--tw-backdrop-invert: ;
--tw-backdrop-opacity: ;
--tw-backdrop-saturate: ;
--tw-backdrop-sepia: ;
--tw-contain-size: ;
--tw-contain-layout: ;
--tw-contain-paint: ;
--tw-contain-style:
;
}
.relative {
position: relative;
}
.mx-1 {
margin-left: 0.25rem;
margin-right: 0.25rem;
}
.mb-2 {
margin-bottom: 0.5rem;
}
.mt-3 {
margin-top: 0.75rem;
}
.flex {
display: flex;
}
.table {
display: table;
}
.grid {
display: grid;
}
.h-4 {
height: 1rem;
}
.w-1\/2 {
width: 50%;
}
.w-4 {
width: 1rem;
}
.w-full {
width: 100%;
}
.flex-col {
flex-direction: column;
}
.items-center {
align-items: center;
}
.justify-center {
justify-content: center;
}
.overflow-x-auto {
overflow-x: auto;
}
.whitespace-nowrap {
white-space: nowrap;
}
.rounded-full {
border-radius: 9999px;
}
.rounded-l-full {
border-top-left-radius: 9999px;
border-bottom-left-radius: 9999px;
}
.rounded-r-full {
border-top-right-radius: 9999px;
border-bottom-right-radius: 9999px;
}
.border-2 {
border-width: 2px;
}
.border-b {
border-bottom-width: 1px;
}
.border-gray-200 {
--tw-border-opacity: 1;
border-color: rgb(229 231 235 / var(--tw-border-opacity));
}
.bg-gray-200 {
--tw-bg-opacity: 1;
background-color: rgb(229 231 235 / var(--tw-bg-opacity));
}
.bg-gray-50 {
--tw-bg-opacity: 1;
background-color: rgb(249 250 251 / var(--tw-bg-opacity));
}
.bg-white {
--tw-bg-opacity: 1;
background-color: rgb(255 255 255 / var(--tw-bg-opacity));
}
.px-4 {
padding-left: 1rem;
padding-right: 1rem;
}
.px-6 {
padding-left: 1.5rem;
padding-right: 1.5rem;
}
.py-2 {
padding-top: 0.5rem;
padding-bottom: 0.5rem;
}
.py-3 {
padding-top: 0.75rem;
padding-bottom: 0.75rem;
}
.py-4 {
padding-top: 1rem;
padding-bottom: 1rem;
}
.text-left {
text-align: left;
}
.text-center {
text-align: center;
}
.text-right {
text-align: right;
}
.font-mono {
font-family: ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas,
"Liberation Mono", "Courier New", monospace;
}
.text-lg {
font-size: 1.125rem;
line-height: 1.75rem;
}
.text-sm {
font-size: 0.875rem;
line-height: 1.25rem;
}
.text-xs {
font-size: 0.75rem;
line-height: 1rem;
}
.font-medium {
font-weight: 500;
}
.uppercase {
text-transform: uppercase;
}
.leading-none {
line-height: 1;
}
.text-blue-400 {
--tw-text-opacity: 1;
color: rgb(96 165 250 / var(--tw-text-opacity));
}
.text-gray-500 {
--tw-text-opacity: 1;
color: rgb(107 114 128 / var(--tw-text-opacity));
}
.text-gray-700 {
--tw-text-opacity: 1;
color: rgb(55 65 81 / var(--tw-text-opacity));
}
.text-gray-900 {
--tw-text-opacity: 1;
color: rgb(17 24 39 / var(--tw-text-opacity));
}
.transition-colors {
transition-property: color, background-color, border-color,
text-decoration-color, fill, stroke;
transition-timing-function: cubic-bezier(0.4, 0, 0.2, 1);
transition-duration: 150ms;
}
.duration-300 {
transition-duration: 300ms;
}
.ease-in {
transition-timing-function: cubic-bezier(0.4, 0, 1, 1);
}
.hover\:text-orange-600:hover {
--tw-text-opacity: 1;
color: rgb(234 88 12 / var(--tw-text-opacity));
}
.focus\:text-orange-600:focus {
--tw-text-opacity: 1;
color: rgb(234 88 12 / var(--tw-text-opacity));
}
.focus\:outline-none:focus {
outline: 2px solid transparent;
outline-offset: 2px;
}
.rtl\:text-right:where([dir="rtl"], [dir="rtl"] *) {
text-align: right;
}
@media (prefers-color-scheme: dark) {
.dark\:border-gray-700 {
--tw-border-opacity: 1;
border-color: rgb(55 65 81 / var(--tw-border-opacity));
}
.dark\:bg-gray-700 {
--tw-bg-opacity: 1;
background-color: rgb(55 65 81 / var(--tw-bg-opacity));
}
.dark\:bg-gray-800 {
--tw-bg-opacity: 1;
background-color: rgb(31 41 55 / var(--tw-bg-opacity));
}
.dark\:text-gray-400 {
--tw-text-opacity: 1;
color: rgb(156 163 175 / var(--tw-text-opacity));
}
.dark\:text-white {
--tw-text-opacity: 1;
color: rgb(255 255 255 / var(--tw-text-opacity));
}
}
</style>