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https://github.com/obsidian-desci/Obsidian-Desci.git
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debug
This commit is contained in:
Taylor Hulsmans
parent
2033373495
commit
d79fc5317e
4 changed files with 89 additions and 47 deletions
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@ -1,7 +1,8 @@
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from plex import CoreTools, plex_init, plex_run
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from plex import CoreTools, plex_init, plex_run, plex_vectorize, plex_mint
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import sys
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import json
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import os
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import py3Dmol
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dir_path = sys.argv[1]
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protein_path = [f"{dir_path}/{sys.argv[2]}"]
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@ -17,3 +18,17 @@ initial_io_cid = plex_init(
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)
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completed_io_cid, io_local_filepath = plex_run(initial_io_cid, dir_path)
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print("after plex_run")
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print(completed_io_cid)
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results = plex_vectorize(completed_io_cid, CoreTools.EQUIBIND.value, output_dir=dir_path)
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print('after plex_vectorize')
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best_docked_small_molecule_path = results['best_docked_small_molecule']['filePaths'][0]
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best_docked_small_molecule_cid = results['best_docked_small_molecule']['cidPaths'][0]
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print(results)
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print("Docked Protein: ", best_docked_small_molecule_path.replace(dir_path, ""))
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print(best_docked_small_molecule_cid)
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os.environ["AUTOTASK_WEBHOOK"] = "https://api.defender.openzeppelin.com/autotasks/e15b3f39-28f8-4d30-9bf3-5d569bdf2e78/runs/webhook/8315d17c-c493-4d04-a257-79209f95bb64/2gmqi9SRRAQMoy1SRdktai"
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plex_mint(completed_io_cid)
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@ -48,18 +48,6 @@ export const getProtein = async function () {
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chat_role: 'assistant'
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}
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)
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const displayNode = createNode(canvas, created,
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{
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text: "test",
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size: { height: placeholderNoteHeight*3 }
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},
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{
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color: assistantColor,
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chat_role: 'assistant'
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}
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)
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displayNode.setText("")
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try {
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const res = await requestUrl({
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@ -79,24 +67,6 @@ export const getProtein = async function () {
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console.error('Error saving image:', error);
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} else {
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const file = this.app.vault.getAbstractFileByPath(`${filename}`)
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import("3dmol/build/3Dmol.js").then(async ($3Dmol) => {
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console.log('displayNode', displayNode)
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const el = displayNode.containerEl
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console.log($3Dmol);
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console.log('el', el)
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console.log('canvas', canvas)
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await sleep(200)
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let config = { backgroundColor: 'rgb(30,30,30)' };
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let viewer = $3Dmol.createViewer(el, config);
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let m = viewer.addModel()
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m.addMolData(fs.readFileSync(`${this.app.vault.adapter.basePath}/${filename}`, 'utf-8'), 'pdb')
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viewer.zoomTo();
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viewer.render();
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console.log('viewer', viewer)
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viewer.zoom(0.8, 2000);
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});
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const cidNode = createNode(canvas, created,
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{
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file,
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@ -83,9 +83,20 @@ export const runEquibind = async function () {
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equibind.stdout?.on('data', (data) => {
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console.log('stdout:data:', data)
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const outputDirRegex = /Created working directory: (.*)\n/;
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const outputFileRegex = /[^\/]+(?=\/$|$)/
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const outputDir = data.match(outputDirRegex)[1]
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const outputFileRegex = /[^\/]+(?=\/$|$)/
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const outputFile = outputDir.match(outputFileRegex)[0]
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const nftLinkRegex = / ProofOfScience NFT at (.*)\n/;
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const nftLink = data.match(nftLinkRegex)[0]
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const dockedProteinRegex = /Docked Protein: \/(.*)\n/;
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let dockedProteinPath = data.match(dockedProteinRegex)[1]
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console.log('dockedProteinPath', dockedProteinPath)
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dockedProteinPath = dockedProteinPath.replace(/DockedProtein: /, '')
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const dockedProteinFile = this.app.vault.getAbstractFileByPath(dockedProteinPath)
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console.log('dockedProteinPath', dockedProteinPath)
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console.log('dockerProteinFile', dockedProteinFile)
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console.log('nftLink', nftLink)
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console.log('outputfile', outputFile)
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const cidRegex = /Completed IO JSON CID: (.*)\n/;
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@ -111,7 +122,32 @@ export const runEquibind = async function () {
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chat_role: 'assistant'
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},
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{ x:-400, y:0}
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{ x:-650, y:0}
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)
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const dockedProteinNode = createNode(canvas, outputFileNode,
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{
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file: dockedProteinFile,
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size: { height: placeholderNoteHeight }
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},
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{
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color: assistantColor,
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chat_role: 'assistant'
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},
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)
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const nftNode = createNode(canvas, created,
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{
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text: `NFT: ${nftLink}`,
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size: {
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height: placeholderNoteHeight
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}
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},
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{
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color: assistantColor,
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chat_role: 'assistant'
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},
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{ x:650, y:0}
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)
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})
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@ -21,9 +21,10 @@ export const viewMolecule = async function () {
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return
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}
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const selection = canvas.selection
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if (selection?.size !== 1) return
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if (selection?.size > 2) return
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const values: CanvasNode[] = Array.from(selection.values())
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const node: CanvasNode = values[0]
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const node2: CanvasNode | null = values[1] ? values[1] : null
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if (node) {
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await canvas.requestSave()
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await sleep(200)
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@ -42,7 +43,8 @@ export const viewMolecule = async function () {
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text: "loading model",
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size: {
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width: 1000,
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height: 1000 }
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height: 1000
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}
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},
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{
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color: assistantColor,
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@ -73,26 +75,45 @@ export const viewMolecule = async function () {
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fs.readFileSync(`${this.app.vault.adapter.basePath}/${nodeData.file}`, 'utf-8'),
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fileType
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)
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if (fileType === 'pdb') {
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m.setStyle({ 'model': 0 }, { 'cartoon': { 'color': 'spectrum' } })
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} else {
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m.setStyle({ 'model': 1 }, { 'stick': {} })
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}
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if (node2) {
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const node2Data = node2.getData()
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console.log('node2Data', node2Data)
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const path2 = `${this.app.vault.adapter.basePath}/${node2Data.file}`
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console.log('path2', path2)
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const fileType2 = pdb.test(node2Data.file) ? 'pdb' : 'sdf'
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m.addMolData(
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fs.readFileSync(`${this.app.vault.adapter.basePath}/${node2Data.file}`, 'utf-8'),
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fileType2
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)
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console.log(viewer, 'viewer')
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console.log(m, 'm')
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m.setStyle({ 'model': 1 }, { 'stick': {} })
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}
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viewer.zoomTo();
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viewer.render();
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console.log('viewer', viewer)
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viewer.zoom(0.8, 2000);
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displayNode.setText("")
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});
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} catch (e) {
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const cideNodeError = createNode(canvas, node,
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{
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text: `error: ${e}`,
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size: { height: placeholderNoteHeight }
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},
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{
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color: assistantColor,
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chat_role: 'assistant'
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}
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)
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const cideNodeError = createNode(canvas, node,
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{
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text: `error: ${e}`,
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size: { height: placeholderNoteHeight }
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},
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{
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color: assistantColor,
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chat_role: 'assistant'
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}
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)
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}
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}
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}
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}
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