/usr/share/psi/python/pubchem.py is in psi4-data 1:0.3-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
#@END LICENSE
#
from __future__ import print_function
"""Queries the PubChem database using a compound name (i.e. 1,3,5-hexatriene)
to obtain a molecule string that can be passed to Molecule. ::
results = getPubChemObj("1,3,5-hexatriene")
Results is an array of results from PubChem matches to your query.
for entry in results:
entry["CID"] => PubChem compound identifer
entry["IUPAC"] => IUPAC name for the resulting compound
entry["PubChemObj"] => instance of PubChemObj for this compound
entry["PubChemObj"].getMoleculeString() => returns a string compatible
with PSI4's Molecule creation
"""
try:
# Python 2 syntax
from urllib2 import urlopen
from urllib2 import quote
from urllib2 import URLError
except ImportError:
# Python 3 syntax
from urllib.request import urlopen
from urllib.parse import quote
from urllib.error import URLError
import xml.etree.ElementTree as ET
import time
import gzip
import re
import sys
import os
class PubChemObj(object):
def __init__(self, cid, mf, iupac):
self.url = 'http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi'
self.cid = cid
self.mf = mf
self.iupac = iupac
self.natom = 0
self.dataSDF = ''
def __str__(self):
return "%17d %s\n" % (self.cid, self.iupac)
def getSDF(self):
"""Function to return the SDF (structure-data file) of the PubChem object."""
if (len(self.dataSDF) == 0):
def extract_xml_keyval(xml, key):
""" A useful helper function for parsing a single key from XML. """
try:
# Python 2.6 (ElementTree 1.2 API)
matches = xml.getiterator(key)
except:
# Python 2.7 (ElementTree 1.3 API)
matches = list(xml.iter(key))
if len(matches) == 0:
return None
elif len(matches) == 1:
return matches[0].text
else:
print(matches)
raise TooManyMatchesException
url = "http://pubchem.ncbi.nlm.nih.gov/pug/pug.cgi"
initial_request = """
<PCT-Data>
<PCT-Data_input>
<PCT-InputData>
<PCT-InputData_download>
<PCT-Download>
<PCT-Download_uids>
<PCT-QueryUids>
<PCT-QueryUids_ids>
<PCT-ID-List>
<PCT-ID-List_db>pccompound</PCT-ID-List_db>
<PCT-ID-List_uids>
<PCT-ID-List_uids_E>%d</PCT-ID-List_uids_E>
</PCT-ID-List_uids>
</PCT-ID-List>
</PCT-QueryUids_ids>
</PCT-QueryUids>
</PCT-Download_uids>
<PCT-Download_format value="sdf"/>
<PCT-Download_use-3d value="true"/>
<PCT-Download_n-3d-conformers>%d</PCT-Download_n-3d-conformers>
</PCT-Download>
</PCT-InputData_download>
</PCT-InputData>
</PCT-Data_input>
</PCT-Data>
""" % (self.cid, 1)
print("\tPosting PubChem request for CID %d" % self.cid)
server_response = urlopen(url, initial_request).read()
xml = ET.fromstring(server_response)
for attempt in range(4):
if attempt == 3:
raise PubChemTimeoutError
# Look for a download location in the XML response
download_url = extract_xml_keyval(xml, 'PCT-Download-URL_url')
if download_url:
print("\tDownloading from PubChem...")
# We have a download location; gogetit
file_name = '_psi4_pubchem_temp_download_.tgz'
response = urlopen(download_url)
data = response.read()
fh = open(file_name, 'wb')
fh.write(data)
fh.close()
unzipped = gzip.open(file_name)
self.dataSDF = unzipped.read()
unzipped.close()
try:
os.remove(file_name)
except:
pass
print("\tDone!")
break
# We didn't find a download location yet.
if attempt == 0:
# If this is the first try, take a ticket
ticket = extract_xml_keyval(xml, 'PCT-Waiting_reqid')
#print("ticket = " + ticket)
statusrequest = """<PCT-Data>
<PCT-Data_input>
<PCT-InputData>
<PCT-InputData_request>
<PCT-Request>
<PCT-Request_reqid>%d</PCT-Request_reqid>
<PCT-Request_type value="status"/>
</PCT-Request>
</PCT-InputData_request>
</PCT-InputData>
</PCT-Data_input>
</PCT-Data>
""" % int(ticket)
if ticket:
# Wait 10 seconds...
print("\tPubChem result not available yet, will try again in 10 seconds...")
time.sleep(10)
# ...and ask for an update on the progress
server_response = urlopen(url, statusrequest).read()
xml = ET.fromstring(server_response)
#print(server_response)
else:
# We can't find a ticket number, or a download location. Bail.
raise PubChemDownloadError
return self.dataSDF
def name(self):
"""Function to return the IUPAC name of the PubChem object."""
return self.iupac
def getCartesian(self):
"""Function to return a string of the atom symbol and XYZ
coordinates of the PubChem object.
"""
try:
sdfText = self.getSDF()
except Exception as e:
raise e
# Find
# NA NB CONSTANT
# 14 13 0 0 0 0 0 0 0999 V2000
m = re.search(r'^\s*(\d+)\s+(?:\d+\s+){8}V2000$', sdfText, re.MULTILINE)
self.natom = 0
if (m):
self.natom = int(m.group(1))
if (self.natom == 0):
raise Exception("PubchemError\n Cannot find the number of atoms. 3D data doesn't appear\n" +
"to be available for %s.\n" % self.iupac)
lines = re.split('\n', sdfText)
# 3.7320 -0.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
NUMBER = "((?:[-+]?\\d*\\.\\d+(?:[DdEe][-+]?\\d+)?)|(?:[-+]?\\d+\\.\\d*(?:[DdEe][-+]?\\d+)?))"
atom_re = re.compile(r'^\s*' + NUMBER + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*(\w+)(?:\s+\d+){12}')
molecule_string = "PubchemInput\n"
atom_count = 0
for line in lines:
if (not line or line.isspace()):
continue
atom_match = atom_re.match(line)
if atom_match:
x = float(atom_match.group(1))
y = float(atom_match.group(2))
z = float(atom_match.group(3))
sym = atom_match.group(4)
atom_count = atom_count + 1
molecule_string += "%s %10.6f %10.6f %10.6f\n" % (sym, x, y, z)
if (atom_count == self.natom):
break
return molecule_string
def getXYZFile(self):
"""Function to obtain preferentially a molecule string
through getCartesian() or a query string otherwise.
"""
try:
temp = self.getCartesian()
except Exception as e:
raise
molstr = "%d\n%s\n%s" % (self.natom, self.iupac, temp)
return molstr
def getMoleculeString(self):
"""Function to obtain a molecule string through
getCartesian() or fail.
"""
try:
return self.getCartesian()
except Exception as e:
return e.message
def getPubChemResults(name):
"""Function to query the PubChem database for molecules matching the
input string. Builds a PubChem object if found.
"""
url = 'http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=%s&format=text' % quote(name)
print("\tSearching PubChem database for %s" % (name))
try:
loc = urlopen(url)
except URLError as e:
msg = "\tPubchemError\n%s\n\treceived when trying to open\n\t%s\n" % (str(e), url)
msg += "\tCheck your internet connection, and the above URL, and try again.\n"
raise Exception(msg)
data = loc.read()
ans = []
l = data.find(b"<pre>")
l = data.find(b"\n", l)
i = 1
while(True):
l = data.find(str("%d. " % i).encode(sys.getdefaultencoding()), l)
if l == -1:
break
tag = b"MF: "
l = data.find(tag, l) + len(tag)
mf = data[l:data.find(b'\n', l)].decode(sys.getdefaultencoding())
tag = b"IUPAC name: "
l = data.find(tag, l) + len(tag)
iupac = data[l:data.find(b'\n', l)].decode(sys.getdefaultencoding())
tag = b"CID:"
l = data.find(tag, l) + len(tag)
#if l == 4:
# break
cid = int(data[l:data.find(b"\n", l)])
l = data.find(b'\t', l) + 1
pubobj = PubChemObj(cid, mf, iupac)
ans.append(pubobj)
i += 1
print("\tFound %d results" % (len(ans)))
return ans
if __name__ == "__main__":
try:
#obj = getPubChemResults("1-methoxy-4-[(E)-prop-1-enyl]benzene")
#obj = getPubChemResults("sodium benzenesulfonate")
obj = getPubChemResults("4-[bis(4-hydroxyphenyl)methyl]phenol")
except Exception as e:
print(e.message)
for r in obj:
print(r)
print(r.getMoleculeString())
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