def peak_data(samples):
print(request.args)
samples = samples.split("/")
if "data" in request.args:
print(request.args.get("data", type=str))
peak = ConsolidatedPeak.from_quoted_string(
request.args.get("data", type=str))
print(peak)
CAS = peak.hits[0].cas
Name = peak.hits[0].name
rt = peak.rt
if CAS.replace("-", '').replace("0", '') == '':
# CAS Number is all zeros
pickle_name = hashlib.md5(Name.encode("utf-8")).hexdigest()
# html_file_name = os.path.join(html_file_directory, f"{pickle_name}_{rt}.html")
if (cache_dir / pickle_name).exists():
with open(cache_dir / pickle_name, "rb") as f:
comp = pickle.load(f)
else:
# if True:
comp = get_compounds(Name, 'name')[0]
# Save to cache
with open(cache_dir / pickle_name, "wb") as f:
pickle.dump(comp, f)
else:
if (cache_dir / CAS).exists():
with open(cache_dir / CAS, "rb") as f:
comp = pickle.load(f)
else:
# if True:
comp = get_compounds(CAS, 'name')[0]
# Save to cache
with open(cache_dir / CAS, "wb") as f:
pickle.dump(comp, f)
return render_template(
"properties_template_2.html",
comp=comp,
peak=peak,
samples=samples,
)
else:
# Legacy mode
index = request.args.get("index", 0, type=int)
filename = request.args.get("filename", '', type=str)
peak_data = []
if filename == '':
return "Please provide a filename with ?filename=", 400
with open(os.path.join(filename), "r") as jsonfile:
for i, peak in enumerate(jsonfile):
if i == index:
peak_data = json.loads(peak)
if not peak_data:
# Index was out of range
return "Peak index out of range", 400
CAS = peak_data["hits"][0]["CAS"]
Name = peak_data["hits"][0]["Name"]
rt = peak_data["average_rt"]
if CAS.replace("-", '').replace("0", '') == '':
# CAS Number is all zeros
pickle_name = hashlib.md5(Name.encode("utf-8")).hexdigest()
# html_file_name = os.path.join(html_file_directory, f"{pickle_name}_{rt}.html")
if (cache_dir / pickle_name).exists():
with open(cache_dir / pickle_name, "rb") as f:
comp = pickle.load(f)
else:
# if True:
comp = get_compounds(Name, 'name')[0]
# Save to cache
with open(cache_dir / pickle_name, "wb") as f:
pickle.dump(comp, f)
else:
if (cache_dir / CAS).exists():
with open(cache_dir / CAS, "rb") as f:
comp = pickle.load(f)
else:
# if True:
comp = get_compounds(CAS, 'name')[0]
# Save to cache
with open(cache_dir / CAS, "wb") as f:
pickle.dump(comp, f)
return render_template(
"properties_template.html",
comp=comp,
data=peak_data,
samples=samples,
)
"621-65-8", "623-26-7", "623-87-0", "626-17-5", "628-96-6", "638-36-8",
"64-18-6", "64-19-7", "644-08-6", "66-25-1", "693-21-0", "71-43-2",
"7440-44-0", "75-05-8", "75-07-0", "76-22-2", "7782-42-5", "78-11-5",
"78-84-2", "78411-60-6", "8006-44-8", "8012-95-1", "83-32-9",
"836-30-6", "84-62-8", "84-66-2", "84-74-2", "84002-64-2", "85-01-8",
"85-98-3", "85209-46-7", "86-30-6", "86-53-3", "86-74-8", "88-72-2",
"88-73-7", "88-74-4", "88-75-5", "88-89-1", "90-02-8", "90-12-0",
"9004-67-5", "9004-70-0", "9005-38-3", "91-15-6", "91-19-0", "91-20-3",
"91-22-5", "91-57-6", "92-24-0", "92-82-0", "939-27-5", "95-13-6",
"95-15-8", "95-16-9", "95-47-6", "95-48-7", "95-63-6", "961-68-2",
"98-01-1", "98-86-2", "98-95-3", "99-08-1", "99-35-4", "99-65-0",
"99-99-0"
]:
try:
comp = get_compounds(cas, 'name')[0]
except:
input(">")
continue
import pprint
print(comp.IUPAC)
print(comp.CAS)
print(comp.cid)
print(comp.inchi)
print(comp.inchikey)
print(comp.canonical_smiles)
print(comp.melting_point)
print(comp.boiling_point)
print(comp.color)
def hit_data(samples):
# print(request.args)
samples = samples.split("/")
maybe_make("cache") # Internal Cache Directory
if "data" in request.args:
# print(request.args.get("data", type=str))
hit = ConsolidatedSearchResult.from_quoted_string(
request.args.get("data", type=str))
# print(hit)
CAS = hit.cas
Name = hit.name
if CAS.replace("-", '').replace("0", '') == '':
# CAS Number is all zeros
pickle_name = hashlib.md5(Name.encode("utf-8")).hexdigest()
# html_file_name = os.path.join(html_file_directory, f"{pickle_name}_{rt}.html")
if (cache_dir / pickle_name).exists():
with open(cache_dir / pickle_name, "rb") as f:
comp = pickle.load(f)
else:
# Check that a connection an be established to PubChem server
try:
urllib.request.urlopen(API_BASE, timeout=2)
except urllib.error.HTTPError as e:
if e.code == 400:
pass
else:
raise e
except urllib.error.URLError:
warnings.warn(
"Unable to connect to PubChem server. Check your internet connection and try again."
)
return render_template(
"properties_template_offline.html",
hit=hit,
samples=samples,
)
try:
comp = get_compounds(CAS, 'name')[0]
except IndexError:
comp = None
# Save to cache
with open(cache_dir / pickle_name, "wb") as f:
pickle.dump(comp, f)
else:
if (cache_dir / CAS).exists():
with open(cache_dir / CAS, "rb") as f:
comp = pickle.load(f)
else:
# if True:
try:
comp = get_compounds(CAS, 'name')[0]
except IndexError:
comp = None
# Save to cache
with open(cache_dir / CAS, "wb") as f:
pickle.dump(comp, f)
# TODO: Combine information from hit.reference_data and comp, e.g. synonyms
return render_template(
"properties_template_2.html",
comp=comp,
hit=hit,
samples=samples,
)
else:
# Legacy mode
index = request.args.get("index", 0, type=int)
filename = request.args.get("filename", '', type=str)
peak_data = []
if filename == '':
return "Please provide a filename with ?filename=", 400
with open(os.path.join(filename), "r") as jsonfile:
for i, peak in enumerate(jsonfile):
if i == index:
peak_data = json.loads(peak)
if not peak_data:
# Index was out of range
return "Peak index out of range", 400
CAS = peak_data["hits"][0]["CAS"]
Name = peak_data["hits"][0]["Name"]
rt = peak_data["average_rt"]
if CAS.replace("-", '').replace("0", '') == '':
# CAS Number is all zeros
pickle_name = hashlib.md5(Name.encode("utf-8")).hexdigest()
# html_file_name = os.path.join(html_file_directory, f"{pickle_name}_{rt}.html")
if (cache_dir / pickle_name).exists():
with open(cache_dir / pickle_name, "rb") as f:
comp = pickle.load(f)
else:
# if True:
comp = get_compounds(Name, 'name')[0]
# Save to cache
with open(cache_dir / pickle_name, "wb") as f:
pickle.dump(comp, f)
else:
if (cache_dir / CAS).exists():
with open(cache_dir / CAS, "rb") as f:
comp = pickle.load(f)
else:
# if True:
comp = get_compounds(CAS, 'name')[0]
# Save to cache
with open(cache_dir / CAS, "wb") as f:
pickle.dump(comp, f)
return render_template(
"properties_template.html",
comp=comp,
data=peak_data,
samples=samples,
)
"""Test for PubChemPy"""
from chemistry_tools.lookup import get_compounds
from decimal import Decimal
comp = get_compounds("diphenylamine", 'name')[0]
import pprint
pprint.pprint(comp._physical_properties)
print(f"CID: {'Passed!' if comp.cid == 11487 else 'Failed!'}")
print(f"CAS Number: {'Passed!' if comp.CAS == '122-39-4' else 'Failed!'}")
print(
f"Formula: {'Passed!' if comp.molecular_formula == 'C12H11N' else 'Failed!'}"
)
print(
f"IUPAC: {'Passed!' if comp.IUPAC['String'] == 'N-phenylaniline' else 'Failed!'}"
)
print(
f"InChI: {'Passed!' if comp.inchi == 'InChI=1S/C12H11N/c1-3-7-11(8-4-1)13-12-9-5-2-6-10-12/h1-10,13H' else 'Failed!'}"
)
print(
f"InChIKey: {'Passed!' if comp.inchikey == 'DMBHHRLKUKUOEG-UHFFFAOYSA-N' else 'Failed!'}"
)
print(
f"Canonical SMILES: {'Passed!' if comp.canonical_smiles == 'C1=CC=C(C=C1)NC2=CC=CC=C2' else 'Failed!'}"
)
print(
f"Isomeric SMILES: {'Passed!' if True == False else 'Failed!'}") # TODO
print(
f"SMILES: {'Passed!' if comp.smiles == 'C1=CC=C(C=C1)NC2=CC=CC=C2' else 'Failed!'}"