Mercurial > repos > bitlab > plidflow

comparison PLIDflow/scripts/scrapPubChem.py @ 6:795e11fac81b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Included new tools for standardization
author bitlab
date Wed, 22 Apr 2020 06:12:00 -0400
parents
children
comparison
equal deleted inserted replaced
5:97f12f7cc852 6:795e11fac81b
1 from requests import Session
2 from robobrowser import RoboBrowser
3 from pprint import pprint
4 from bs4 import BeautifulSoup
5 from time import sleep
6 import random
7 import json
8 import csv
9 import time
10 import re
11 import gc
12 import time
13 import sys
14
15 def main():
16 # User information
17
18
19 # REMEMBER TO PUT THE INPUT ARGUMENT WITH DOUBLE QUOTES
20 if (len(sys.argv) != 2):
21 print >> sys.stderr, "ERROR: Missing input chain"
22 exit()
23
24 chain = str(sys.argv[1])
25
26 finished = 0
27
28 while finished == 0:
29
30 try:
31
32 #chain = 'Nc1nc(NC2CC2)c2ncn([C@@H]3C[C@H](CO)C=C3)c2n1'
33 url = 'https://pubchem.ncbi.nlm.nih.gov/standardize/standardize.cgi'
34
35 # Create session and browser
36 session = Session()
37 browser = RoboBrowser(session=session,history=False, parser="html5lib")
38 browser.open(url)
39
40 form = browser.get_form(action=re.compile(r'standardize'))
41
42 #print(form.fields)
43
44 form['structure'] = 'smiles'
45 form['structuresmiles'] = chain
46
47 #print(len(list(form.submit_fields.items(multi=True))))
48 #print(list(form.submit_fields.items(multi=True)))
49 #print(' FORM action1 name: ', list(form.submit_fields.items(multi=True))[0])
50 #print(' FORM action1 name: ', list(form.submit_fields.items(multi=True))[1])
51
52 submit_field = form['submitjob']
53 submit_field.value = 'Authorize'
54 #print(form)
55 res = browser.submit_form(form, submit=submit_field)
56 parsedbrowser = str(browser.parsed)
57 #print(parsedbrowser)
58
59 parsedbrowser = parsedbrowser.replace("<html>", "")
60 parsedbrowser = parsedbrowser.replace("<head>", "")
61 parsedbrowser = parsedbrowser.replace("</head>", "")
62 parsedbrowser = parsedbrowser.replace("</html>", "")
63 parsedbrowser = parsedbrowser.replace("<body>", "")
64 parsedbrowser = parsedbrowser.replace("</body>", "")
65
66 badpos = parsedbrowser.find('Output Log:')
67 if(badpos != -1):
68 print >> sys.stderr, parsedbrowser[badpos:]
69 else:
70 parsedbrowser = parsedbrowser.replace("\n", "")
71 print(parsedbrowser)
72
73
74
75 del browser
76 gc.collect()
77
78 finished = 1
79
80
81 except Exception as ex:
82
83 finished = 0
84 time.sleep(5)
85
86
87
88
89
90
91
92 if __name__ == "__main__":
93 main()
94