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parseDatabases.js
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import fetch from "node-fetch"
import { parse } from 'node-html-parser'
import puppeteer from "puppeteer-extra"
import AdblockerPlugin from 'puppeteer-extra-plugin-adblocker'
import StealthPlugin from 'puppeteer-extra-plugin-stealth'
import flat from 'flat'
import fs from "fs"
import requestretry from 'requestretry'
// parse from bioentity
function copyToClipboard(text) { if (window.clipboardData && window.clipboardData.setData) return window.clipboardData.setData("Text", text);
else if (document.queryCommandSupported && document.queryCommandSupported("copy")) { var textarea = document.createElement("textarea");
textarea.textContent = text;
textarea.style.position = "fixed";
document.body.appendChild(textarea);
textarea.select(); try { return document.execCommand("copy") } catch (ex) { console.warn("Copy to clipboard failed.", ex); return prompt("Copy to clipboard: Ctrl+C, Enter", text) } finally { document.body.removeChild(textarea) } } };
function copyDrugBankDrug() {
let answer = "";
let drugs = [];
let actions = [];
let title = document.querySelectorAll('.card-content > dl > dd')[0]?.textContent;
let id = window.location.href.split('/').slice(-1)[0];
const rows = document.querySelectorAll('#target-relations > tbody > tr');
console.log(rows.length);
rows.forEach(row => { col = row.querySelectorAll('td');
drugs.push(col[0]?.textContent);
actions.push(col[4]?.textContent) });
answer = title + '\t' + id + '\t' + drugs.join('\;') + '\t' + actions.join(';');
copyToClipboard(answer);
}
const fetchAsync = async(url) => (
await requestretry({
url: url,
fullResponse: false,
maxAttempts: 10, // (default) try 5 times
retryDelay: 500, // (default) wait for 5s before trying again
retrySrategy: requestretry.RetryStrategies.HTTPOrNetworkError // (default) retry on 5xx or network errors
}).then(async (res) => {
// console.log(url)
// await new Promise(resolve => setTimeout(resolve, 200))
return res
}).catch((error) => {
console.log({error})
return 'error'
})
)
const getBioEnity = async(id) => {
const res = await fetchAsync(`https://go.drugbank.com/bio_entities/${id}`)
const document = parse(res)
const name = document.querySelectorAll('.card-content dt#name + dd')[0]?.textContent || ""
const kind = document.querySelectorAll('.card-content dt#kind + dd')[0]?.textContent || ""
const organism = document.querySelectorAll('.card-content dt#organism + dd')[0]?.textContent || ""
const proteins = document.querySelectorAll('#details-header + dl > dd:last-child tbody tr').map(row => (
!row ? {} : {
name: row.querySelector('td:nth-of-type(1)')?.textContent || "",
uniprotId: row.querySelector('td:nth-of-type(2)')?.textContent || "",
id: row.querySelector('td:nth-of-type(3) a')?.getAttribute('href').split('/')[2] || ""
}
))
const drugs = document.querySelectorAll('#target-relations > tbody > tr').map(row => (
!row ? {} : {
id: row.querySelector('td:nth-of-type(1)')?.textContent || "",
name: row.querySelector('td:nth-of-type(2)')?.textContent || "",
group: row.querySelector('td:nth-of-type(3)')?.textContent || "",
pharmAction: row.querySelector('td:nth-of-type(4)')?.textContent || "",
action: row.querySelector('td:nth-of-type(5)')?.textContent || ""
}
))
console.log(id, name)
return {
id,
name,
kind,
organism,
proteins,
drugs
}
}
const getDrug = async(id) => {
console.log(id)
if (!id.length) { return undefined }
let res = await fetchAsync(`https://go.drugbank.com/drugs/${id}`)
if (!res) res = await fetchAsync(`https://go.drugbank.com/drugs/${id}`)
const document = parse(res)
const drugBankId = document.querySelector('#identification-header + dl #drugbank-accession-number + dd')?.textContent || ''
const summary = document.querySelector('#identification-header + dl #summary + dd')?.textContent || ''
const brandNames = document.querySelector('#identification-header + dl #brand-names + dd')?.textContent || ''
const genericName = document.querySelector('#identification-header + dl #generic-name + dd')?.textContent || ''
const type = document.querySelector('#identification-header + dl #type + dd')?.textContent || ''
const groups = document.querySelector('#identification-header + dl #groups + dd')?.textContent || ''
const molecularWeight = document.querySelector('#identification-header + dl #weight + dd')?.textContent.match(/Average: ([0-9]*\.[0-9]*)/)?.at(1) || ''
const chemicalFormula = document.querySelector('#identification-header + dl #chemical-formula + dd')?.textContent || ''
const volumeOfDistribution = document.querySelector('#pharmacology-header + dl #volume-of-distribution + dd')?.textContent || ''
const halfLife = document.querySelector('#pharmacology-header + dl #half-life + dd')?.textContent || ''
const clearance = document.querySelector('#pharmacology-header + dl #clearance + dd')?.textContent.replace('\n','').trim() || ''
const toxicity = document.querySelector('#pharmacology-header + dl #toxicity + dd')?.textContent || ''
const pathways = Array.from(document.querySelectorAll('#pharmacology-header + dl #pathways + dd tbody tr')).map(pathway => (
!pathway ? {} : {
link: pathway.querySelector('td:nth-of-type(1) a')?.getAttribute('href') || '',
name: pathway.querySelector('td:nth-of-type(1) a')?.textContent || '',
category: pathway.querySelector('td:nth-of-type(2)')?.textContent || ''
}))
const smiles = document.querySelector('#chemical-identifiers-header + dl #smiles + dd')?.textContent || ''
const inChI = document.querySelector('#chemical-identifiers-header + dl #inchi + dd')?.textContent || ''
const inChIKey = document.querySelector('#chemical-identifiers-header + dl #inchi-key + dd')?.textContent || ''
const externalLinks = {}
let tempAttrs = document.querySelectorAll('#references-header + dl #external-links + dd dt')
let tempValues = document.querySelectorAll('#references-header + dl #external-links + dd dd')
tempAttrs.forEach((el, index) => {
if (el) {
Object.defineProperty(externalLinks, el.textContent, {
value: tempValues[index]?.textContent,
enumerable: true
})
}
})
const state = document.querySelector('#properties-header + dl #state + dd')?.textContent || ''
let propertiesExperimental = {}
Array.from(document.querySelectorAll('#properties-header + dl #experimental-properties + dd tbody tr')).forEach(row => {
if (row) {
Object.defineProperty(propertiesExperimental, row.querySelector('td:nth-of-type(1)')?.textContent || '', {
value: row.querySelector('td:nth-of-type(2)')?.textContent || '',
enumerable: true,
configurable: true
})
}
})
let propertiesPredicted = {}
Array.from(document.querySelectorAll('#properties-header + dl #predicted-properties + dd tbody tr')).forEach(row => {
if (row) {
Object.defineProperty(propertiesPredicted, row.querySelector('td:nth-of-type(1)')?.textContent || '', {
value: row.querySelector('td:nth-of-type(2)')?.textContent || '',
enumerable: true,
configurable: true
})
}
})
let propertiesAdmet = {}
Array.from(document.querySelectorAll('#properties-header + dl #predicted-admet-features + dd tbody tr')).forEach(row => {
if (row) {
Object.defineProperty(propertiesAdmet, row.querySelector('td:nth-of-type(1)')?.textContent || '', {
value: row.querySelector('td:nth-of-type(2)')?.textContent || '',
enumerable: true,
configurable: true
})
}
})
const phases = Array.from(document.querySelectorAll('#clinical-trials-header + dl tbody tr'))?.map(row=> {
if (!row) return ''
const result = row.querySelector('td:nth-of-type(2)')?.textContent || ''
const phases = row.querySelector('td:nth-of-type(1)')?.textContent || ''
if (result === 'Completed') return Math.max(...phases.match(/\d+/g)?.map(ii => parseInt(ii)) || []) || ''
return ''
}) || []
const maxPhase = phases.length ? Math.max(...phases) : ''
const targets = Array.from(document.querySelectorAll('#targets .bond.card')).map(target => (
!target ? {} : {
name: target.querySelector('.card-header')?.textContent.replace('\n\n\n Details','') || '',
BEId: target.getAttribute('id') || '',
PId: target.querySelector('.card-header strong a')?.getAttribute('href')?.split('/').splice(-1)[0] || '',
actions: target.querySelector('#actions + dd')?.textContent || '',
gene: target.querySelector('#gene-name + dd')?.textContent || '',
}))
const enzymes = Array.from(document.querySelectorAll('#enzymes .bond.card')).map(enzyme => (
!enzyme ? {} : {
name: enzyme.querySelector('.card-header')?.textContent.replace('\n\n\n Details','') || '',
BEId: enzyme.getAttribute('id') || '',
PId: enzyme.querySelector('.card-header strong a')?.getAttribute('href')?.split('/').splice(-1)[0] || '',
actions: enzyme.querySelector('#actions + dd')?.textContent || '',
gene: enzyme.querySelector('#gene-name + dd')?.textContent || '',
}))
const back = {
general: {
id:drugBankId,
genericName,
summary,
brandNames,
type,
groups,
inChI,
inChIKey,
toxicity,
maxPhase,
},
biochemical: {
volumeOfDistribution,
halfLife,
clearance,
state,
smiles,
molecularWeight,
chemicalFormula,
},
pathways,
externalLinks,
propertiesExperimental,
propertiesPredicted,
propertiesAdmet,
targets,
enzymes
}
return back
}
const getPharmaco = async(document) => {
// change="increased" / "decreased"
// what="proteomics" / "transcriptomics"
// {gene="", change="", what="transcriptomics"}
// const res = await fetchAsync(`https://go.drugbank.com/pharmaco/${what}?q%5Bg%5B0%5D%5D%5Bm%5D=or&q%5Bg%5B0%5D%5D%5Bdrug_approved_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_nutraceutical_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_illicit_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_investigational_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_withdrawn_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_experimental_true%5D=all&q%5Bg%5B1%5D%5D%5Bm%5D=or&q%5Bg%5B1%5D%5D%5Bdrug_available_in_us_true%5D=all&q%5Bg%5B1%5D%5D%5Bdrug_available_in_ca_true%5D=all&q%5Bg%5B1%5D%5D%5Bdrug_available_in_eu_true%5D=all&commit=Apply+Filter&q%5Bdrug_precise_names_name_cont%5D=&q%5Bgene_symbol_eq%5D=${gene}&q%5Bgene_id_eq%5D=&q%5Bchange_eq%5D=${change}&q%5Binteraction_cont%5D=&q%5Bchromosome_location_cont%5D=`)
// const document = parse(res)
const drugs = Array.from(document.querySelectorAll(
'.table-gene-regulations tbody tr, .table-protein-regulations tbody tr'
))?.map(row => (
!row ? {} : {
name: row.querySelector('td:nth-of-type(1)')?.textContent || "",
id: row.querySelector('td:nth-of-type(1) a')?.getAttribute('href').split('/')[2] || "",
groups: Array.from(row.querySelectorAll('td:nth-of-type(2) span')).map(i => i?.textContent || ""),
gene: row.querySelector('td:nth-of-type(3)')?.textContent || "",
geneId: row.querySelector('td:nth-of-type(4)')?.textContent || "",
change: row.querySelector('td:nth-of-type(5)')?.textContent.replace('\n', '').trim() || "",
interaction: row.querySelector('td:nth-of-type(6)')?.textContent || "",
chromosome: row.querySelector('td:nth-of-type(7)')?.textContent || "",
references: Array.from(row.querySelectorAll('td:nth-of-type(8) li')).map(article => article?.textContent || "")
}
)) || []
return drugs || []
}
const getArticle = async(id) => {
// TODO: release
const res = await fetchAsync(`https://go.drugbank.com/articles/${id}`)
const document = parse(res)
const authors = document.querySelector('#article-details-header + dl #citation + dd > p:nth-of-type(1)')?.textContent || ""
const title = document.querySelector('#article-details-header + dl #citation + dd > p:nth-of-type(2)')?.textContent || ""
const journal = document.querySelector('#article-details-header + dl #citation + dd > p:nth-of-type(3)')?.textContent || ""
const pubMedId = document.querySelector('#article-details-header + dl #pubmed-id + dd a')?.getAttribute('href')?.split('/').slice(-1)[0] || ""
const abstract = document.querySelector('#article-details-header + dl #abstract + dd > p')?.textContent || ""
return {
id,
authors,
title,
journal,
pubMedId,
abstract
}
}
const getIndication = async(id) => {
// TODO: release
const res = await fetchAsync(`https://go.drugbank.com/indications/${id}`)
const document = parse(res)
const back = {}
return back
}
const getProtein = async(id) => {
const res = await fetchAsync(`https://go.drugbank.com/polypeptides/${id}`)
const document = parse(res)
const name = document.querySelector('.card-content dt#name + dd')?.textContent || ""
const synonyms = document.querySelectorAll('.card-content dt#synonyms + dd li').map(i => i?.textContent || "") || []
const gene = document.querySelector('.card-content dt#gene-name + dd')?.textContent || ""
const acSeq = document.querySelector('.card-content dt#amino-acid-sequence + dd')?.textContent || ""
const residues = document.querySelector('.card-content dt#number-of-residues + dd')?.textContent || ""
const weight = document.querySelector('.card-content dt#molecular-weight + dd')?.textContent || ""
const pi = document.querySelector('.card-content dt#theoretical-pi + dd')?.textContent || ""
const GOFunctions = document.querySelectorAll('.card-content dt#go-classification + dd > .card > .card-body:nth-of-type(2) .separated-list-item').map(i => i?.textContent || "") || []
const GOProcesses = document.querySelectorAll('.card-content dt#go-classification + dd > .card > .card-body:nth-of-type(4) .separated-list-item').map(i => i?.textContent || "") || []
const GOComponents = document.querySelectorAll('.card-content dt#go-classification + dd > .card > .card-body:nth-of-type(6) .separated-list-item').map(i => i?.textContent || "") || []
const generalFunction = document.querySelector('.card-content dt#general-function + dd')?.textContent || ""
const specificFunction = document.querySelector('.card-content dt#specific-function + dd')?.textContent || ""
const pfamDomainFunction = document.querySelectorAll('.card-content dt#pfam-domain-function + dd li').map(row => (
!row ? {} : {
title: row.textContent || "",
id: row.querySelector('a')?.textContent || ""
}
))
const transmembraneRegions = document.querySelector('.card-content dt#transmembrane-regions + dd')?.textContent || ""
const cellularLocation = document.querySelector('.card-content dt#cellular-location + dd')?.textContent || ""
const chromosomeLocation = document.querySelector('.card-content dt#chromosome-location + dd')?.textContent || ""
const locus = document.querySelector('.card-content dt#locus + dd')?.textContent || ""
const externalIdentifiers = {}
document.querySelectorAll('.card-content dt#external-identifiers + dd tbody tr').forEach(i => {
const props = i?.querySelectorAll('td').map(ii => ii?.textContent || "") || []
Object.defineProperty(externalIdentifiers, props[0], {
value: props[1],
enumerable: true,
configurable: true
})
})
const articles = document.querySelectorAll('.card-content dt#general-references + dd li').map(row => (
!row ? {} : {
title: row.textContent || "",
id: row.querySelector('a')?.getAttribute('href').split('/')[2] || ""
}
))
const drugs = document.querySelectorAll('#target-relations > tbody > tr').map(row => (
!row ? {} : {
id: row.querySelector('td:nth-of-type(1)')?.textContent || "",
name: row.querySelector('td:nth-of-type(2)')?.textContent || "",
group: row.querySelector('td:nth-of-type(3)')?.textContent || "",
pharmAction: row.querySelector('td:nth-of-type(4)')?.textContent || "",
action: row.querySelector('td:nth-of-type(5)')?.textContent || ""
}
))
const back = {
id,
name,
synonyms,
gene,
acSeq,
residues,
weight,
pi,
GO: {
GOFunctions,
GOProcesses,
GOComponents
},
generalFunction,
specificFunction,
pfamDomainFunction,
transmembraneRegions,
cellularLocation,
chromosomeLocation,
locus,
externalIdentifiers,
articles,
drugs
}
// console.log(back)
return back
}
const getMolsFromPubChem = async (document) => {
const cid = document.querySelector('.summary tbody tr:nth-of-type(1) td')?.textContent || ''
const synonyms = Array.from(document.querySelectorAll('.summary tbody tr:nth-of-type(4) td p')).map(i => i?.textContent || '').join(';!')
const inChIKey = document.querySelector('#Names-and-Identifiers #InChI-Key .section-content-item p')?.textContent || ''
const canonicalSmiles = document.querySelector('#Names-and-Identifiers #Canonical-SMILES .section-content-item p')?.textContent || ''
const molecularFormula = document.querySelector('#Names-and-Identifiers #Molecular-Formula .section-content-item p')?.textContent || ''
const phases = Array.from(document.querySelectorAll('#Drug-and-Medication-Information #ClinicalTrials-gov tbody tr'))?.map(row=> {
if (!row) return ''
const result = row.querySelector('td:nth-of-type(4)')?.textContent || ''
const phases = row.querySelector('td:nth-of-type(3)')?.textContent || ''
if (result === 'Completed') return Math.max(...phases.match(/\d+/g)?.map(ii => parseInt(ii)) || []) || ''
return ''
}) || []
const maxPhase = phases.length ? Math.max(...phases) : ''
let chemicalProperties = {}
Array.from(document.querySelectorAll('#Computed-Properties tbody tr')).forEach(row => {
if (row) {
Object.defineProperty(chemicalProperties, row.querySelector('td:nth-of-type(1)')?.textContent || '', {
value: row.querySelector('td:nth-of-type(2)')?.textContent || '',
enumerable: true,
configurable: true
})
}
})
return {
cid,
synonyms,
inChIKey,
canonicalSmiles,
molecularFormula,
chemicalProperties,
maxPhase
}
}
const runPubchemMol = async (cids) => {
puppeteer
.use(StealthPlugin())
.use(AdblockerPlugin({ blockTrackers: true }))
.launch({
headless: false,
args: ['--no-sandbox', '--disable-setuid-sandbox']
})
.then(async browser => {
const page = await browser.newPage()
page.setDefaultNavigationTimeout(0)
let infoList = []
let mols = []
for (let cid of cids) {
if (cid) {
await page.goto(`https://pubchem.ncbi.nlm.nih.gov/compound/${cid}#section=Clinical-Trials`)
await page.waitForSelector('#Names-and-Identifiers', {timeout:0})
await page.waitForTimeout(200)
const mol = await page.$eval('body', getMolsFromPubChem)
console.log(cid, mol)
if (mol) {
mols.push(mol)
} else {
mols.push({})
}
} else mols.push({})
}
await browser.close()
mols = mols.map(i => flat(i))
console.log(mols)
let headerSet = new Set()
mols.forEach(i => Object.keys(i).forEach(ii => headerSet.add(ii)))
headerSet = Array.from(headerSet).sort()
console.log(headerSet)
const header = headerSet.join('\t')
const rows = mols.map(i => headerSet.map(ii => {
console.log(i[ii], typeof i[ii], ii)
if (!i[ii]) return ''
if ((typeof i[ii] !== 'string') && (typeof i[ii] !== 'number')) return ''
return i[ii].toString().replace(/(?:\r\n|\r|\n)/g,'').trim()
}).join('\t'))
const toSave = [header].concat(rows).join('\n')
fs.writeFile('./data/molsInfo.tsv', toSave, (error) => {console.log(error)})
})
}
const saveToTSV = (dataObject, fileName) => {
const headings = Object.keys(dataObject[0]).join('\t');
const rows = dataObject.reduce((acc, c) => {
return acc.concat([Object.values(c).join('\t')]);
}, [])
// console.log({rows}, typeof rows)
// let data = [headings].concat(rows)
// console.log({data}, typeof data)
let data = rows.join('\n')
// data = data.join('\n')
// var logger = fs.createWriteStream('test.tsv', {
// flags: 'a' // 'a' means appending (old data will be preserved)
// })
// logger.write(data)
fs.writeFile(fileName, data, (erorr)=>{console.log(erorr)})
}
const saveToTSVWithFlat = (preData, fileName) => {
// console.log({preData})
let data = preData.map(i => flat(i))
// console.log({data})
let headerSet = new Set()
data.forEach(i => Object.keys(i).forEach(ii => headerSet.add(ii)))
headerSet = Array.from(headerSet).sort()
// console.log({headerSet})
const header = headerSet.join('\t')
const rows = data.map(i => headerSet.map(ii => {
// console.log(i[ii], typeof i[ii], ii)
if (!i[ii]) return ''
if ((typeof i[ii] !== 'string') && (typeof i[ii] !== 'number')) return ''
return i[ii].toString().replace(/(?:\r\n|\r|\n)/g,'').trim()
}).join('\t'))
const toSave = [header].concat(rows).join('\n')
// console.log({toSave})
fs.writeFile(fileName, toSave, (error) => {console.log(error)})
}
const runDrugBankPharmaco = (genes) => {
puppeteer
.use(StealthPlugin())
.use(AdblockerPlugin({ blockTrackers: true }))
.launch({
headless: false,
args: ['--no-sandbox', '--disable-setuid-sandbox']
})
.then(async browser => {
const page = await browser.newPage()
page.setDefaultNavigationTimeout(0)
let infoList = []
let drugs
for (let what of whats) {
for (let gene of genes) {
await page.waitForTimeout(2000)
await page.goto(`https://go.drugbank.com/pharmaco/${what}?q%5Bg%5B0%5D%5D%5Bm%5D=or&q%5Bg%5B0%5D%5D%5Bdrug_approved_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_nutraceutical_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_illicit_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_investigational_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_withdrawn_true%5D=all&q%5Bg%5B0%5D%5D%5Bdrug_experimental_true%5D=all&q%5Bg%5B1%5D%5D%5Bm%5D=or&q%5Bg%5B1%5D%5D%5Bdrug_available_in_us_true%5D=all&q%5Bg%5B1%5D%5D%5Bdrug_available_in_ca_true%5D=all&q%5Bg%5B1%5D%5D%5Bdrug_available_in_eu_true%5D=all&commit=Apply+Filter&q%5Bdrug_precise_names_name_cont%5D=&q%5Bgene_symbol_eq%5D=${gene}&q%5Bgene_id_eq%5D=&q%5Bchange_eq%5D=${change}&q%5Binteraction_cont%5D=&q%5Bchromosome_location_cont%5D=`)
await page.waitForSelector('.table-gene-regulations, .table-protein-regulations', {timeout:0})
drugs = await page.$eval('body', getPharmaco)
console.log(drugs.length, gene, what)
if (drugs.length) {
drugs = await Promise.all(drugs.map(async drug => ({
...drug,
articles: await Promise.all(drug.references.map(async article => await getArticle(article)))
}
)))
const info = drugs.map(drug => ({
gene,
what,
geneId: drug.geneId,
geneChange: drug.change,
chromosome: drug.chromosome,
drugName: drug.name,
drugId: drug.id,
drugGrups: drug.groups.join(";!"),
drugInteraction: drug.interaction,
drugArticlesId: drug.references.join(";!"),
drugArticlesTitles: drug.articles.map(atricle => atricle.title).join(";!"),
drugArticlesPubmedId:drug.articles.map(atricle => atricle.pubMedId).join(";!"),
drugArticlesAbstracts:drug.articles.map(atricle => atricle.abstract).join(":!")
}))
infoList = infoList.concat(info)
}
}
}
saveToTSV(infoList, 'pharmaco.tsv')
await browser.close()
})
}
const runDrugBankBEProteinsOnly = async(entityList) => {
const infoList = await Promise.all(entityList.map(async entity => {
// console.log(entity)
if (!entity) return {}
const bioEnity = await getBioEnity(entity)
// console.log(bioEnity)
return {
id: bioEnity.id,
name: bioEnity.name,
// proteinsNames: bioEnity.proteins.map(i => i?.name || '').join(';!'),
// proteinsID: bioEnity.proteins.map(i => i?.id || '').join(';!')
}
}))
saveToTSVWithFlat(infoList, 'BEProteinsOnly.tsv')
}
const getCID = async(smiles) =>{
console.log(smiles)
let url = `https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/${smiles}/JSON`
console.log(url)
const res = await fetchAsync(url)
// const document = parse(res)
let cid
try {
cid = JSON.parse(res)["PC_Compounds"][0]['id']['id']['cid'] || ''
} catch {
cid = ''
}
console.log(cid)
return {
smiles,
cid
}
}
const findCIDbySmiles = async(smilesList) => {
let infoList = []
console.log(smilesList)
for (let smiles of smilesList) {
console.log(smiles)
if (!smiles) infoList.push({})
else infoList.push(await getCID(smiles))
}
saveToTSVWithFlat(infoList, 'cids.tsv')
}
const runDrugBankEntities = async(entityList) => {
entityList.map(async entity => {
const bioEnity = await getBioEnity(entity)
console.log(bioEnity)
const proteins = await Promise.all(
bioEnity.proteins.map(async protein => await getProtein(protein.id))
)
console.log(proteins)
})
}
const runDrugBankProteinsForBE = async (entityList) => {
let infoList = []
for (const entity of entityList) {
console.log(entity)
if (entity) {
const bioEnity = await getBioEnity(entity)
// console.log({bioEnity})
const proteins = await Promise.all(
bioEnity.proteins.map(async protein => protein.id ? await getProtein(protein.id) : {})
)
// console.log({proteins})
const result = proteins.map(protein => {
const {drugs, articles, pfamDomainFunction, synonyms, GO, ...newObj} = protein
return {
BEid: entity,
...newObj,
synonyms: synonyms.join(";!"),
'articles.ids': articles.map(article => article?.id || '').join(";!"),
'articles.titles': articles.map(article => article?.title || '').join(";!"),
'pfamDomainFunction.ids': pfamDomainFunction.map(funct => funct?.id || '').join(";!"),
'pfamDomainFunction.titles': pfamDomainFunction.map(funct => funct?.title || '').join(";!"),
'GO.Components': GO.GOComponents.join(";!"),
'GO.Processes': GO.GOProcesses.join(";!"),
'GO.Functions': GO.GOFunctions.join(";!")
}})
// console.log({result})
infoList = infoList.concat(result)
}
}
console.log({infoList})
saveToTSVWithFlat(infoList, './data/ProteinsForBE.tsv')
}
const runDrugBankProteins = async (proteinList) =>{
const proteins = await Promise.all(proteinList.map(async protein => (protein ? await getProtein(protein) : {})))
const result = proteins.map(protein => {
const {drugs, articles, pfamDomainFunction, synonyms, GO, ...newObj} = protein
return {
...newObj,
synonyms: synonyms.join(";!"),
'articles.ids': articles.map(article => article?.id || '').join(";!"),
'articles.titles': articles.map(article => article?.title || '').join(";!"),
'pfamDomainFunction.ids': pfamDomainFunction.map(funct => funct?.id || '').join(";!"),
'pfamDomainFunction.titles': pfamDomainFunction.map(funct => funct?.title || '').join(";!"),
'GO.Components': GO.GOComponents.join(";!"),
'GO.Processes': GO.GOProcesses.join(";!"),
'GO.Functions': GO.GOFunctions.join(";!")
}})
console.log({result})
saveToTSVWithFlat(result, './data/Proteins.tsv')
}
const runDrugBankDrugsForBEandProteins = async(entityList) => {
let infoList = []
for (const entity of entityList) {
console.log(entity)
if (entity) {
const bioEnity = await getBioEnity(entity)
// console.log(bioEnity)
const BEDrugs = bioEnity.drugs.map(drug => ({
BEId: entity,
proteinId: '',
...drug
}))
// console.log({BEDrugs})
infoList = infoList.concat(BEDrugs)
bioEnity.proteins.forEach(async protein => {
const proteins = await getProtein(protein.id)
// console.log(proteins)
const proteinDrugs = proteins.drugs.map(drug => ({
BEId: entity,
proteinId: protein.id,
...drug
}))
// console.log({proteinDrugs})
infoList = infoList.concat(proteinDrugs)
})
}
}
// console.log({infoList})
saveToTSVWithFlat(infoList, './data/DrugsForBEandProteins.tsv')
}
const runDrugBankDrugsForProteins = async(proteinsList) => {
let infoList = []
for (const protein of proteinsList) {
if (protein) {
const proteins = await getProtein(protein)
// console.log(proteins)
const proteinDrugs = proteins.drugs.map(drug => ({
BEId: '',
proteinId: protein,
...drug
}))
// console.log({proteinDrugs})
infoList = infoList.concat(proteinDrugs)
}
}
console.log({infoList})
saveToTSVWithFlat(infoList, './data/DrugsForProteins.tsv')
}
const runDrugBankArticles = async(articleList) => {
const res = await getArticle('A20386')
console.log(res)
}
const runDrugBankDrugs = async(drugList) => {
console.log(drugList.length)
let res = []
const chankSize = 200
const chanksNumber = Math.floor(drugList.length / chankSize)
for (let i = 0; i <= chanksNumber; i++) {
console.log(i*chankSize,(i+1)*chankSize)
let list = drugList.slice(i*chankSize,(i+1)*chankSize)
let tempRes = await Promise.all(list.map(async drugId => await getDrug(drugId)))
// console.log(tempRes)
res = res.concat(tempRes)
}
console.log(res)
res = res.map(i => {
if (!i) return {}
const {targets, enzymes, pathways, ...newObj} = i
return {
...newObj,
'pathways.names': pathways.map(ii => ii.name).join(';!'),
'pathways.links': pathways.map(ii => ii.link).join(';!'),
'enzymes.names': enzymes.map(ii => ii.name).join(';!'),
'targets.names': targets.map(ii => ii.name).join(';!'),
'enzymes.PIds': enzymes.map(ii => ii.PId).join(';!'),
'targets.PIds': targets.map(ii => ii.PId).join(';!'),
'targets.genes': targets.map(ii => ii.gene).join(';!'),
'enzymes.genes': enzymes.map(ii => ii.gene).join(';!'),
}
})
// console.log(res)
res = res.map(i => flat(i))
// console.log(res)
let headerSet = new Set()
res.forEach(i => Object.keys(i).forEach(ii => headerSet.add(ii)))
headerSet = Array.from(headerSet).sort()
// console.log(headerSet)
const header = headerSet.join('\t')
const rows = res.map(i => headerSet.map(ii => {
// console.log(i[ii], typeof i[ii], ii)
if (!i[ii]) return ''
if ((typeof i[ii] !== 'string') && (typeof i[ii] !== 'number')) return ''
return i[ii].toString().replace(/(?:\r\n|\r|\n)/g,'').trim()
}).join('\t'))
// console.log(rows.length)
const toSave = [header].concat(rows).join('\n')
fs.writeFile('./data/drugsInfo.tsv', toSave, (error) => {console.log(error)})
}
const downloadDrugMol = async (row) => {
if (!row.length) { return {} }
const id = row.split('.')[0]
const drugBankId = row.split('.')[1]
let res = await fetchAsync(`https://go.drugbank.com/structures/small_molecule_drugs/${drugBankId}.mol`)
let molSuccess = res.length > 0 && res !== 'error code: 1015'
if (molSuccess) {
fs.writeFile(`./data/ligands/mol/${row}.mol`, res, (error)=>{})
}
console.log(id, drugBankId)
// console.log({molSuccess})
res = await fetchAsync(`https://go.drugbank.com/structures/small_molecule_drugs/${drugBankId}.pdb`)
let pdbSuccess = res.length > 0 && res !== 'error code: 1015'
if (pdbSuccess) {
fs.writeFile(`./data/ligands/pdb/${row}.pdb`, res, (error)=>{})
}
res = await fetchAsync(`https://go.drugbank.com/structures/small_molecule_drugs/${drugBankId}.sdf?type=3d`)
let sdfSuccess = res.length > 0 && res !== 'error code: 1015'
if (sdfSuccess) {
fs.writeFile(`./data/ligands/3Dsdf/${row}.sdf`, res, (error)=>{})
}
return {
id,
drugBankId,
molSuccess,
pdbSuccess,
sdfSuccess
}
}
const downloadDrugBankMols = async (drugList) => {
// console.log(drugList.length)
let res = []
const chankSize = 100
const chanksNumber = Math.floor(drugList.length / chankSize)
for (let i = 0; i <= chanksNumber; i++) {
console.log(i*chankSize,(i+1)*chankSize)
let list = drugList.slice(i*chankSize,(i+1)*chankSize)
let tempRes = await Promise.all(list.map(async drugId => await downloadDrugMol(drugId)))
// console.log(tempRes)
res = res.concat(tempRes)
await new Promise(resolve => setTimeout(resolve, 10000));
}
// console.log(res)
let headerSet = new Set()
res.forEach(i => Object.keys(i).forEach(ii => headerSet.add(ii)))
headerSet = Array.from(headerSet).sort()
// console.log(headerSet)
const header = headerSet.join('\t')
const rows = res.map(i => headerSet.map(ii => (
i[ii]?.toString() || ''
)).join('\t'))
// console.log(rows.length)
const toSave = [header].concat(rows).join('\n')
fs.writeFile('./data/ligandsInfo.tsv', toSave, (error) => {console.log(error)})
}
const downloadPubchemMol = async (row) => {
if (!row.length) { return {} }
const id = row.split('.')[0]
const pubchemId = row.split('.')[1]
let res = await fetchAsync(`https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/${pubchemId}/record/SDF/?record_type=3d&response_type=save&response_basename=${row}`)
let sdfSuccess = res.length > 0 && res !== 'error code: 1015' && res.substring(0, 7) !== 'Status:'
if (sdfSuccess) {
fs.writeFile(`./data/ligands/3Dsdf/${row}.sdf`, res, (error)=>{})
}
console.log(id, pubchemId)
// console.log({sdfSuccess})
// console.log({res})
return {
id,
pubchemId,
sdfSuccess
}
}
const downloadPubchemMols = async (drugList) => {
// console.log(drugList.length)
let res = []
const chankSize = 100
const chanksNumber = Math.floor(drugList.length / chankSize)
for (let i = 0; i <= chanksNumber; i++) {
console.log(i*chankSize,(i+1)*chankSize)
let list = drugList.slice(i*chankSize,(i+1)*chankSize)
let tempRes = await Promise.all(list.map(async drugId => await downloadPubchemMol(drugId)))
// console.log(tempRes)
res = res.concat(tempRes)
await new Promise(resolve => setTimeout(resolve, 10000));
}
// console.log(res)
let headerSet = new Set()
res.forEach(i => Object.keys(i).forEach(ii => headerSet.add(ii)))
headerSet = Array.from(headerSet).sort()
// console.log(headerSet)
const header = headerSet.join('\t')
const rows = res.map(i => headerSet.map(ii => (
i[ii]?.toString() || ''
)).join('\t'))
// console.log(rows.length)
const toSave = [header].concat(rows).join('\n')
fs.writeFile('./data/ligandsInfo.tsv', toSave, (error) => {console.log(error)})
}
const downloadZincMol = async (row) => {
if (!row.length) { return {} }
const id = row.split('.')[0]
const zincId = row.split('.')[1]
let res = await fetchAsync(`https://zinc.docking.org/substances/${zincId}.sdf`)
let sdfSuccess = res.length > 0 && res !== 'error code: 1015' && res.substring(0, 1) !== 0 && !res.includes('This is not the page you were looking for.')
if (sdfSuccess) {
fs.writeFile(`./data/ligands/test/${row}.sdf`, res, (error)=>{})
}
console.log(id, zincId)
// console.log({sdfSuccess})
// console.log({res})
return {
id,
zincId,
sdfSuccess
}
}
const downloadZincMols = async (drugList) => {
// console.log(drugList.length)
let res = []
const chankSize = 100
const chanksNumber = Math.floor(drugList.length / chankSize)
for (let i = 0; i <= chanksNumber; i++) {
console.log(i*chankSize,(i+1)*chankSize)
let list = drugList.slice(i*chankSize,(i+1)*chankSize)
let tempRes = await Promise.all(list.map(async drugId => await downloadZincMol(drugId)))
// console.log(tempRes)
res = res.concat(tempRes)
await new Promise(resolve => setTimeout(resolve, 10000));
}
// console.log(res)
let headerSet = new Set()
res.forEach(i => Object.keys(i).forEach(ii => headerSet.add(ii)))
headerSet = Array.from(headerSet).sort()
// console.log(headerSet)
const header = headerSet.join('\t')
const rows = res.map(i => headerSet.map(ii => (
i[ii]?.toString() || ''
)).join('\t'))
// console.log(rows.length)
const toSave = [header].concat(rows).join('\n')
fs.writeFile('./data/ligandsInfo.tsv', toSave, (error) => {console.log(error)})
}
const downloadPubchemMolFromPage = async (row) => {
if (!row.length) { return {} }
const id = row.split('.')[0]