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Commit 261601c9 authored by Malte Schokolowski's avatar Malte Schokolowski
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#!/usr/bin/env python3
"""
Functions for information retrieval of articles from the ACS journal JCIM
"""
__author__ = "Florian Jochens"
__email__ = "fj@andaco.de"
__status__ = "Production"
#__copyright__ = ""
#__credits__ = ["", "", "", ""]
#__license__ = ""
#__version__ = ""
#__maintainer__ = ""
from bs4 import BeautifulSoup as bs
import requests as req
import sys
from pathlib import Path
class Publication:
#_registry = []
_citations = []
_references = []
def __init__(self, title, publication_date, contributors, doi_url,
subjects = None, num_citations = None):
#self._registry.append(self)
self.title = title
self.publication_date = publication_date
self.contributors = contributors
self.doi_url = doi_url
self.subjects = subjects
self.num_citations = num_citations
#self._citations = []
#self._references = []
class Citation:
def __init__(self, title, journal, contributors, doi_url):
self.title = title
self.journal = journal
self.contributors = contributors
self.doi_url = doi_url
class References:
def __init__(self, title, journal, contributors, doi_url):
self.title = title
self.journal = journal
self.contributors = contributors
self.doi_url = doi_url
def get_article_info(soup):
header = soup.find('div', class_ = 'article_header-left pull-left')
article_title = header.find('span', class_ = 'hlFld-Title').text
publication_date = header.find('span', class_ = 'pub-date-value').text
for link in header.find('div', class_ = 'article_header-doiurl'):
doi_url = link.get('href')
subs = header.find('div', class_ = 'article_header-taxonomy')
subjects = []
for sub in subs.find_all('a'):
subjects.append(sub.get('title'))
cons = header.find('ul', class_ = 'loa')
contributors = []
for con in cons.find_all('span', class_ = 'hlFld-ContribAuthor'):
contributors.append(con.text)
numc = header.find('div', class_ = 'articleMetrics_count')
if not numc.a:
num_citations = 0
else:
num_citations = numc.a.text
pub = Publication(article_title, publication_date, contributors, doi_url,
subjects, num_citations)
return pub
def get_download_url():
export = soup.find('div', class_ = 'cit-download-dropdown_content')
url = 'https://pubs.acs.org'
for link in export.find_all('a'):
if link.get('title') == 'Citation and references':
url += link.get('href')
print(url)
return url
def download(url): # Download citation and references file
if url.find('='):
filename = url.rsplit('=', 1)[1]
path = Path(('./files/' + filename))
if path.is_file():
print("File already exists")
else:
print("File does not exist")
def get_citation_info(pub, num_citations, soup):
pub._citations = []
details = soup.find('ol', class_ = 'cited-content_cbyCitation')
titles = []
for title in details.find_all('span',
class_ = 'cited-content_cbyCitation_article-title'):
titles.append(title.text.replace('.', ''))
journal_names = []
for name in details.find_all('span',
class_ = 'cited-content_cbyCitation_journal-name'):
journal_names.append(name.text)
doi_urls = []
for url in details.find_all('a'):
doi_urls.append(url.get('href'))
contributors = []
for contrib in details.find_all('span',
class_ = 'cited-content_cbyCitation_article-contributors'):
contributors.append(contrib.text)
for i in range(0, int(num_citations)):
pub._citations.append(Citation(titles[i], journal_names[i],
contributors[i], doi_urls[i]))
def print_pub_info(pub):
print(f'''Article title: {pub.title}
Publication date: {pub.publication_date}
DOI-URL: {pub.doi_url}
Subjects:''')
print(*(pub.subjects), sep = ", ")
print('\nContributors:')
print(*(pub.contributors), sep = ", ")
if int(pub.num_citations) > 0:
if int(pub.num_citations) == 1:
print(f'\nThis publication is cited by the following publication:\n')
else:
print(f'\nThis publication is cited by the following {pub.num_citations} publications:\n')
for citation in pub._citations:
print(f'''
Title: {citation.title}
Journal: {citation.journal}
Contributors: {citation.contributors}
DOI-URL: {citation.doi_url}
''')
else:
print('\nThis publication is not cited by any other publication.')
def input(url):
html_text = req.get(url).text
soup = bs(html_text, 'html.parser')
pub = get_article_info(soup)
if int(pub.num_citations) > 0:
get_citation_info(pub, int(pub.num_citations), soup)
return pub
#if len(sys.argv) != 2:
# sys.stderr.write('Usage: {} <url>\n'.format(sys.argv[0]))
# exit(1)
#url = sys.argv[1]
#pub = input(url)
#print_pub_info(pub)
verarbeitung/json_text.json
+ 1
− 1
Edit View file @ 261601c9
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Baeschlin"], "year": "November 3, 2020", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/acs.jmedchem.0c01332", "group": "height", "citations": 8}, {"name": "Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms", "author": ["Robert Schmidt", "Emanuel S. R. Ehmki", "Farina Ohm", "Hans-Christian Ehrlich", "Andriy Mashychev", "Matthias Rarey"], "year": "May 23, 2019", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.9b00250", "group": "height", "citations": 12}, {"name": "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings", "author": ["Jerome Eberhardt", "Diogo Santos-Martins", "Andreas F. Tillack", "Stefano Forli"], "year": "July 19, 2021", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.1c00203", "group": "input", "citations": 1}, {"name": "Accelerating AutoDock4 with GPUs and Gradient-Based Local Search", "author": ["Diogo Santos-Martins", "Leonardo Solis-Vasquez", "Andreas F Tillack", "Michel F Sanner", "Andreas Koch", "Stefano Forli"], "year": "January 6, 2021", "journal": "Journal of Chemical Theory and Computation", "doi": "https://doi.org/10.1021/acs.jctc.0c01006", "group": "depth", "citations": 14}, {"name": "Docking Flexible Cyclic Peptides with AutoDock CrankPep", "author": ["Yuqi Zhang", "Michel F. Sanner"], "year": "September 11, 2019", "journal": "Journal of Chemical Theory and Computation", "doi": "https://doi.org/10.1021/acs.jctc.9b00557", "group": "depth", "citations": 9}, {"name": "Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise", "author": ["David Ryan Koes", "Matthew P. Baumgartner", "Carlos J. Camacho"], "year": "February 4, 2013", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/ci300604z", "group": "depth", "citations": 100}, {"name": "Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking", "author": ["Anita K. Nivedha", "David F. Thieker", "Spandana Makeneni", "Huimin Hu", "Robert J. 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Sayle"], "year": "October 29, 2020", "journal": "Journal of Chemical Information and Modeling", "doi": "https://doi.org/10.1021/acs.jcim.0c00675", "group": "depth", "citations": 25}, {"name": "Structural Biology-Inspired Discovery of Novel KRAS\u2013PDE\u03b4 Inhibitors", "author": ["Yan Jiang", "Chunlin Zhuang", "Long Chen", "Junjie Lu", "Guoqiang Dong", "Zhenyuan Miao", "Wannian Zhang", "Jian Li", "Chunquan Sheng"], "year": "September 20, 2017", "journal": "Journal of Medicinal Chemistry", "doi": "https://doi.org/10.1021/acs.jmedchem.7b01243", "group": "depth", "citations": 12}, {"name": "Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking", "author": ["Michael M. Mysinger", "Michael Carchia", "John. J. Irwin", "Brian K. 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\ No newline at end of file
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\ No newline at end of file
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