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Demo of using icn3d #12

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1 change: 1 addition & 0 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
"@mui/icons-material": "^5.15.10",
"clustal-js": "^2.0.1",
"g2p_mapper": "^1.0.3",
"load-script": "^2.0.0",
"molstar": "^4.0.0",
"pako": "^2.1.0"
},
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115 changes: 115 additions & 0 deletions src/ProteinView/components/Icn3dProteinView.tsx
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@@ -0,0 +1,115 @@
import React, { useEffect, useState } from 'react'
import { observer } from 'mobx-react'
import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
import { PluginContext } from 'molstar/lib/mol-plugin/context'
import domLoadScript from 'load-script'

// locals
import { JBrowsePluginProteinViewModel } from '../model'
import Header from './Header'

// hooks
import useProteinView from '../useProteinView'
import useProteinViewClickBehavior from '../useProteinViewClickBehavior'
import useProteinViewHoverBehavior from '../useProteinViewHoverBehavior'

// utils
import selectResidue from '../selectResidue'
import highlightResidue from '../highlightResidue'
import clearSelection from '../clearSelection'
import ProteinViewer from '../..'

function injectStylesheet(param: string) {
if (document?.head) {
const link = document.createElement('link')
link.type = 'text/css'
link.rel = 'stylesheet'

//link.href = 'http://fonts.googleapis.com/css?family=Oswald&effect=neon';
document.head.appendChild(link)

link.href = param
}
}

injectStylesheet(
'https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery-ui.min.css',
)

injectStylesheet('https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css')

function promisifiedLoadScript(src: string) {
return new Promise((resolve, reject) => {
domLoadScript(src, (err, script) => {
if (err) {
reject(err)
} else {
resolve(script.src)
}
})
})
}

function Icn3dProteinPanel({ model }: { model: ProteinViewer }) {
const { url } = model
const [error, setError] = useState<unknown>()
useEffect(() => {
// eslint-disable-next-line @typescript-eslint/no-floating-promises
;(async () => {
try {
const icn3dui = new icn3d.iCn3DUI({
divid: 'viewer',
mobilemenu: true,
url: 'mmcif|' + url,
})
await icn3dui.show3DStructure()
} catch (e) {
console.error(e)
setError(e)
}
})()
}, [url])
return error ? <ErrorMessage error={error} /> : <div id="viewer" />
}

const Icn3dProteinView = observer(function ({
model,
}: {
model: JBrowsePluginProteinViewModel
}) {
const [error, setError] = useState<unknown>()
const [completed, setCompleted] = useState(false)
useEffect(() => {
// eslint-disable-next-line @typescript-eslint/no-floating-promises
;(async () => {
try {
await promisifiedLoadScript(
'https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery.min.js',
)
await promisifiedLoadScript(
'https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery-ui.min.js',
)
await promisifiedLoadScript(
'https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/threeClass.min.js',
)
await promisifiedLoadScript(
'https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.min.js',
)
setCompleted(true)
} catch (e) {
console.error(e)
setError(e)
}
})()
}, [])

return error ? (
<ErrorMessage error={error} />
) : completed ? (
<Icn3dProteinPanel model={model} />
) : (
<LoadingEllipses />
)
})

export default Icn3dProteinView
14 changes: 8 additions & 6 deletions src/ProteinView/components/ProteinView.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ import clearSelection from '../clearSelection'

// css
import css from '../css/molstar'
import Icn3dViewer from './Icn3dProteinView'

if (document?.head) {
const style = document.createElement('style')
Expand All @@ -40,12 +41,13 @@ const ProteinView = observer(function ({
return error ? (
<ErrorMessage error={error} />
) : (
<ProteinViewContainer
model={model}
plugin={plugin}
seq={seq}
parentRef={parentRef}
/>
// <ProteinViewContainer
// model={model}
// plugin={plugin}
// seq={seq}
// parentRef={parentRef}
// />
<Icn3dViewer model={model} />
)
})

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9 changes: 9 additions & 0 deletions src/ProteinView/components/dependencies.js
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@@ -0,0 +1,9 @@
import * as THREE from 'icn3d/three'
import $ from 'jquery'
import 'jquery-ui-bundle'

import 'jquery-ui-bundle/jquery-ui.min.css'

global.THREE = THREE
global.$ = $
global.jQuery = $
79 changes: 42 additions & 37 deletions yarn.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -494,7 +494,7 @@
dependencies:
eslint-visitor-keys "^3.3.0"

"@eslint-community/regexpp@^4.10.0", "@eslint-community/regexpp@^4.6.1":
"@eslint-community/regexpp@^4.10.0", "@eslint-community/regexpp@^4.11.0":
version "4.11.0"
resolved "https://registry.yarnpkg.com/@eslint-community/regexpp/-/regexpp-4.11.0.tgz#b0ffd0312b4a3fd2d6f77237e7248a5ad3a680ae"
integrity sha512-G/M/tIiMrTAxEWRfLfQJMmGNX28IxBg4PBz8XqQhqUHLFI6TL2htpIB1iQCj144V5ee/JaKyT9/WZ0MGZWfA7A==
Expand Down Expand Up @@ -528,10 +528,10 @@
minimatch "^3.1.2"
strip-json-comments "^3.1.1"

"@eslint/js@9.6.0":
version "9.6.0"
resolved "https://registry.yarnpkg.com/@eslint/js/-/js-9.6.0.tgz#5b0cb058cc13d9c92d4e561d3538807fa5127c95"
integrity sha512-D9B0/3vNg44ZeWbYMpBoXqNP4j6eQD5vNwIlGAuFRRzK/WtT/jvDQW3Bi9kkf3PMDMlM7Yi+73VLUsn5bJcl8A==
"@eslint/js@9.7.0":
version "9.7.0"
resolved "https://registry.yarnpkg.com/@eslint/js/-/js-9.7.0.tgz#b712d802582f02b11cfdf83a85040a296afec3f0"
integrity sha512-ChuWDQenef8OSFnvuxv0TCVxEwmu3+hPNKvM9B34qpM0rDRbjL8t5QkQeHHeAfsKQjuH9wS82WeCi1J/owatng==

"@eslint/object-schema@^2.1.4":
version "2.1.4"
Expand Down Expand Up @@ -1897,9 +1897,9 @@ camelcase@^6.2.0:
integrity sha512-Gmy6FhYlCY7uOElZUSbxo2UCDH8owEk996gkbrpsgGtrJLM3J7jGxl9Ic7Qwwj4ivOE5AWZWRMecDdF7hqGjFA==

caniuse-lite@^1.0.30001640:
version "1.0.30001641"
resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001641.tgz#3572862cd18befae3f637f2a1101cc033c6782ac"
integrity sha512-Phv5thgl67bHYo1TtMY/MurjkHhV4EDaCosezRXgZ8jzA/Ub+wjxAvbGvjoFENStinwi5kCyOYV3mi5tOGykwA==
version "1.0.30001642"
resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001642.tgz#6aa6610eb24067c246d30c57f055a9d0a7f8d05f"
integrity sha512-3XQ0DoRgLijXJErLSl+bLnJ+Et4KqV1PY6JJBGAFlsNsz31zeAIncyeZfLCabHK/jtSh+671RM9YMldxjUPZtA==

canvas-sequencer@^3.1.0:
version "3.1.0"
Expand Down Expand Up @@ -2249,7 +2249,7 @@ define-data-property@^1.0.1, define-data-property@^1.1.4:
es-errors "^1.3.0"
gopd "^1.0.1"

define-properties@^1.2.0, define-properties@^1.2.1:
define-properties@^1.1.3, define-properties@^1.2.0, define-properties@^1.2.1:
version "1.2.1"
resolved "https://registry.yarnpkg.com/define-properties/-/define-properties-1.2.1.tgz#10781cc616eb951a80a034bafcaa7377f6af2b6c"
integrity sha512-8QmQKqEASLd5nx0U1B1okLElbUuuttJ/AnYmRXbbbGDWh6uS208EjD4Xqq/I9wK7u0v6O08XhTWnt5XtEbR6Dg==
Expand Down Expand Up @@ -2381,7 +2381,7 @@ error-ex@^1.3.1:
dependencies:
is-arrayish "^0.2.1"

es-abstract@^1.22.1, es-abstract@^1.22.3, es-abstract@^1.23.0, es-abstract@^1.23.1, es-abstract@^1.23.2, es-abstract@^1.23.3:
es-abstract@^1.17.5, es-abstract@^1.22.1, es-abstract@^1.22.3, es-abstract@^1.23.0, es-abstract@^1.23.1, es-abstract@^1.23.2, es-abstract@^1.23.3:
version "1.23.3"
resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.23.3.tgz#8f0c5a35cd215312573c5a27c87dfd6c881a0aa0"
integrity sha512-e+HfNH61Bj1X9/jLc5v1owaLYuHdeHHSQlkhCBiTK8rBvKaULl/beGMxwrMXjpYrv4pz22BlY570vVePA2ho4A==
Expand Down Expand Up @@ -2591,9 +2591,9 @@ eslint-plugin-react-refresh@^0.4.3:
integrity sha512-MIKAclwaDFIiYtVBLzDdm16E+Ty4GwhB6wZlCAG1R3Ur+F9Qbo6PRxpA5DK7XtDgm+WlCoAY2WxAwqhmIDHg6Q==

eslint-plugin-react@^7.20.3:
version "7.34.3"
resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.34.3.tgz#9965f27bd1250a787b5d4cfcc765e5a5d58dcb7b"
integrity sha512-aoW4MV891jkUulwDApQbPYTVZmeuSyFrudpbTAQuj5Fv8VL+o6df2xIGpw8B0hPjAaih1/Fb0om9grCdyFYemA==
version "7.34.4"
resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.34.4.tgz#1f0dc313a0937db7ce15fd1f6c3d77e70f3e02fb"
integrity sha512-Np+jo9bUwJNxCsT12pXtrGhJgT3T44T1sHhn1Ssr42XFn8TES0267wPGo5nNrMHi8qkyimDAX2BUmkf9pSaVzA==
dependencies:
array-includes "^3.1.8"
array.prototype.findlast "^1.2.5"
Expand All @@ -2603,16 +2603,17 @@ eslint-plugin-react@^7.20.3:
doctrine "^2.1.0"
es-iterator-helpers "^1.0.19"
estraverse "^5.3.0"
hasown "^2.0.2"
jsx-ast-utils "^2.4.1 || ^3.0.0"
minimatch "^3.1.2"
object.entries "^1.1.8"
object.fromentries "^2.0.8"
object.hasown "^1.1.4"
object.values "^1.2.0"
prop-types "^15.8.1"
resolve "^2.0.0-next.5"
semver "^6.3.1"
string.prototype.matchall "^4.0.11"
string.prototype.repeat "^1.0.0"

eslint-plugin-unicorn@^54.0.0:
version "54.0.0"
Expand All @@ -2636,10 +2637,10 @@ eslint-plugin-unicorn@^54.0.0:
semver "^7.6.1"
strip-indent "^3.0.0"

eslint-scope@^8.0.1:
version "8.0.1"
resolved "https://registry.yarnpkg.com/eslint-scope/-/eslint-scope-8.0.1.tgz#a9601e4b81a0b9171657c343fb13111688963cfc"
integrity sha512-pL8XjgP4ZOmmwfFE8mEhSxA7ZY4C+LWyqjQ3o4yWkkmD0qcMT9kkW3zWHOczhWcjTSgqycYAgwSlXvZltv65og==
eslint-scope@^8.0.2:
version "8.0.2"
resolved "https://registry.yarnpkg.com/eslint-scope/-/eslint-scope-8.0.2.tgz#5cbb33d4384c9136083a71190d548158fe128f94"
integrity sha512-6E4xmrTw5wtxnLA5wYL3WDfhZ/1bUBGOXV0zQvVRDOtrR8D0p6W7fs3JweNYhwRYeGvd/1CKX2se0/2s7Q/nJA==
dependencies:
esrecurse "^4.3.0"
estraverse "^5.2.0"
Expand All @@ -2655,15 +2656,15 @@ eslint-visitor-keys@^4.0.0:
integrity sha512-OtIRv/2GyiF6o/d8K7MYKKbXrOUBIK6SfkIRM4Z0dY3w+LiQ0vy3F57m0Z71bjbyeiWFiHJ8brqnmE6H6/jEuw==

eslint@^9.0.0:
version "9.6.0"
resolved "https://registry.yarnpkg.com/eslint/-/eslint-9.6.0.tgz#9f54373afa15e1ba356656a8d96233182027fb49"
integrity sha512-ElQkdLMEEqQNM9Njff+2Y4q2afHk7JpkPvrd7Xh7xefwgQynqPxwf55J7di9+MEibWUGdNjFF9ITG9Pck5M84w==
version "9.7.0"
resolved "https://registry.yarnpkg.com/eslint/-/eslint-9.7.0.tgz#bedb48e1cdc2362a0caaa106a4c6ed943e8b09e4"
integrity sha512-FzJ9D/0nGiCGBf8UXO/IGLTgLVzIxze1zpfA8Ton2mjLovXdAPlYDv+MQDcqj3TmrhAGYfOpz9RfR+ent0AgAw==
dependencies:
"@eslint-community/eslint-utils" "^4.2.0"
"@eslint-community/regexpp" "^4.6.1"
"@eslint-community/regexpp" "^4.11.0"
"@eslint/config-array" "^0.17.0"
"@eslint/eslintrc" "^3.1.0"
"@eslint/js" "9.6.0"
"@eslint/js" "9.7.0"
"@humanwhocodes/module-importer" "^1.0.1"
"@humanwhocodes/retry" "^0.3.0"
"@nodelib/fs.walk" "^1.2.8"
Expand All @@ -2672,7 +2673,7 @@ eslint@^9.0.0:
cross-spawn "^7.0.2"
debug "^4.3.2"
escape-string-regexp "^4.0.0"
eslint-scope "^8.0.1"
eslint-scope "^8.0.2"
eslint-visitor-keys "^4.0.0"
espree "^10.1.0"
esquery "^1.5.0"
Expand Down Expand Up @@ -4561,11 +4562,16 @@ micromatch@^4.0.4:
braces "^3.0.3"
picomatch "^2.3.1"

[email protected], "mime-db@>= 1.43.0 < 2":
[email protected]:
version "1.52.0"
resolved "https://registry.yarnpkg.com/mime-db/-/mime-db-1.52.0.tgz#bbabcdc02859f4987301c856e3387ce5ec43bf70"
integrity sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg==

"mime-db@>= 1.43.0 < 2":
version "1.53.0"
resolved "https://registry.yarnpkg.com/mime-db/-/mime-db-1.53.0.tgz#3cb63cd820fc29896d9d4e8c32ab4fcd74ccb447"
integrity sha512-oHlN/w+3MQ3rba9rqFr6V/ypF10LSkdwUysQL7GkXoTgIWeV+tcXGA852TBxH+gsh8UWoyhR1hKcoMJTuWflpg==

mime-types@^2.1.12, mime-types@~2.1.24, mime-types@~2.1.34:
version "2.1.35"
resolved "https://registry.yarnpkg.com/mime-types/-/mime-types-2.1.35.tgz#381a871b62a734450660ae3deee44813f70d959a"
Expand Down Expand Up @@ -4808,15 +4814,6 @@ object.getownpropertydescriptors@^2.1.6:
gopd "^1.0.1"
safe-array-concat "^1.1.2"

object.hasown@^1.1.4:
version "1.1.4"
resolved "https://registry.yarnpkg.com/object.hasown/-/object.hasown-1.1.4.tgz#e270ae377e4c120cdcb7656ce66884a6218283dc"
integrity sha512-FZ9LZt9/RHzGySlBARE3VF+gE26TxR38SdmqOqliuTnl9wrKulaQs+4dee1V+Io8VfxqzAfHu6YuRgUy8OHoTg==
dependencies:
define-properties "^1.2.1"
es-abstract "^1.23.2"
es-object-atoms "^1.0.0"

object.values@^1.1.6, object.values@^1.2.0:
version "1.2.0"
resolved "https://registry.yarnpkg.com/object.values/-/object.values-1.2.0.tgz#65405a9d92cee68ac2d303002e0b8470a4d9ab1b"
Expand Down Expand Up @@ -5061,9 +5058,9 @@ prettier-linter-helpers@^1.0.0:
fast-diff "^1.1.2"

prettier@^3.2.5:
version "3.3.2"
resolved "https://registry.yarnpkg.com/prettier/-/prettier-3.3.2.tgz#03ff86dc7c835f2d2559ee76876a3914cec4a90a"
integrity sha512-rAVeHYMcv8ATV5d508CFdn+8/pHPpXeIid1DdrPwXnaAdH7cqjVbpJaT5eq4yRAFU/lsbwYwSF/n5iNrdJHPQA==
version "3.3.3"
resolved "https://registry.yarnpkg.com/prettier/-/prettier-3.3.3.tgz#30c54fe0be0d8d12e6ae61dbb10109ea00d53105"
integrity sha512-i2tDNA0O5IrMO757lfrdQZCc2jPNDVntV0m/+4whiDfWaTKfMNgR7Qz0NAeGz/nRqF4m5/6CLzbP4/liHt12Ew==

pretty-bytes@^6.1.1:
version "6.1.1"
Expand Down Expand Up @@ -5693,6 +5690,14 @@ string.prototype.padend@^3.0.0:
es-abstract "^1.23.2"
es-object-atoms "^1.0.0"

string.prototype.repeat@^1.0.0:
version "1.0.0"
resolved "https://registry.yarnpkg.com/string.prototype.repeat/-/string.prototype.repeat-1.0.0.tgz#e90872ee0308b29435aa26275f6e1b762daee01a"
integrity sha512-0u/TldDbKD8bFCQ/4f5+mNRrXwZ8hg2w7ZR8wa16e8z9XpePWl3eGEcUD0OXpEH/VJH/2G3gjUtR3ZOiBe2S/w==
dependencies:
define-properties "^1.1.3"
es-abstract "^1.17.5"

string.prototype.trim@^1.2.9:
version "1.2.9"
resolved "https://registry.yarnpkg.com/string.prototype.trim/-/string.prototype.trim-1.2.9.tgz#b6fa326d72d2c78b6df02f7759c73f8f6274faa4"
Expand Down