"""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"].get_molecule_string() => returns a string compatible
with Psi4's Molecule creation
"""
import json
import re
from ..exceptions import ValidationError
from .regex import DECIMAL
class PubChemObj:
def __init__(self, cid, mf, iupac, charge):
self.url = "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi"
self.cid = cid
self.mf = mf
self.iupac = iupac
self.molecular_charge = charge
self.natom = 0
self.dataSDF = ""
def __str__(self):
return "%17d %s\n" % (self.cid, self.iupac)
def get_sdf(self):
"""Function to return the SDF (structure-data file) of the PubChem object."""
from urllib.request import urlopen, Request
from urllib.parse import quote
from urllib.error import URLError
if len(self.dataSDF) == 0:
url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{}/SDF?record_type=3d".format(
quote(str(self.cid))
)
req = Request(url, headers={"Accept": "chemical/x-mdl-sdfile"})
try:
self.dataSDF = urlopen(req).read().decode("utf-8")
except URLError as e:
msg = "Unable to open\n\n%s\n\ndue to the error\n\n%s\n\n" % (url, e)
msg += "It is possible that 3D information does not exist for this molecule in the PubChem database\n"
print(msg)
raise ValidationError(msg)
return self.dataSDF
def name(self):
"""Function to return the IUPAC name of the PubChem object."""
return self.iupac
def get_cartesian(self):
"""Function to return a string of the atom symbol and XYZ
coordinates of the PubChem object.
"""
try:
sdf_text = self.get_sdf()
except Exception as e:
raise ValidationError(e.message)
# 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$", sdf_text, re.MULTILINE)
self.natom = 0
if m:
self.natom = int(m.group(1))
if self.natom == 0:
raise ValidationError(
"PubChem: Cannot find the number of atoms. 3D data doesn't appear\n"
+ "to be available for %s.\n" % self.iupac
)
lines = re.split("\n", sdf_text)
# 3.7320 -0.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
atom_re = re.compile(
r"^\s*" + DECIMAL + r"\s+" + DECIMAL + r"\s+" + DECIMAL + r"\s*(\w+)(?:\s+\d+){12}", re.VERBOSE
)
molecule_string = "PubchemInput\n"
atom_count = 0
for line in lines:
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 get_molecule_string(self):
"""Function to obtain a molecule string through
get_cartesian() or fail.
"""
try:
return self.get_cartesian()
except Exception as e:
return e.message
def get_pubchem_results(name):
"""Function to query the PubChem database for molecules matching the
input string. Builds a PubChemObj object if found.
"""
from urllib.request import urlopen
from urllib.parse import quote
from urllib.error import URLError
if name.isdigit():
print("\tSearching PubChem database for CID {}".format(name))
url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{}/property/IUPACName,MolecularFormula,Charge/JSON".format(
quote(name)
)
else:
if name.endswith("*"):
name = name[:-1]
loose = True
else:
loose = False
print(
"\tSearching PubChem database for {} ({} returned)".format(
name, "all matches" if loose else "single best match"
)
)
url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{}/property/IUPACName,MolecularFormula,Charge/JSON?name_type={}".format(
quote(name), "word" if loose else "complete"
)
try:
response = urlopen(url)
except URLError as e:
# travis urllib.error.HTTPError: HTTP Error 503: Service Unavailable
raise ValidationError(
"""\tPubchemError\n%s\n\treceived when trying to open\n\t%s\n\tCheck your internet connection, and the above URL, and try again.\n"""
% (str(e), url)
) from e
data = json.loads(response.read().decode("utf-8"))
results = []
for d in data["PropertyTable"]["Properties"]:
if "IUPACName" not in d:
continue
pubobj = PubChemObj(d["CID"], d["IUPACName"], d["IUPACName"], d["Charge"])
results.append(pubobj)
print("\tFound {} result(s)".format(len(results)))
return results
if __name__ == "__main__":
# * comment "..exceptions" line above
# * sulfonate below has no 3D structure available
# * XYZ printing for tropolone* suppressed b/c too many and some have no 3D
for inp in [
"1-methoxy-4-[(E)-prop-1-enyl]benzene",
"4-[bis(4-hydroxyphenyl)methyl]phenol",
"tropolone",
"tropolone*",
"sodium benzenesulfonate",
]: # pragma: no cover
obj = get_pubchem_results(inp)
for r in obj:
print(r, end="")
if inp != "tropolone*":
print(r.get_molecule_string())
