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# -*- coding: utf-8 -*-
"""
test_compound
~~~~~~~~~~~~~
Test the Compound object.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import logging
import os
import pytest
import requests
from chemspipy import ChemSpider, Compound
logging.basicConfig(level=logging.WARN, format='%(levelname)s:%(name)s:(%(threadName)-10s):%(message)s')
logging.getLogger('chemspipy').setLevel(logging.DEBUG)
# API key is retrieved from environment variables
CHEMSPIDER_API_KEY = os.environ['CHEMSPIDER_API_KEY']
cs = ChemSpider(CHEMSPIDER_API_KEY)
def test_get_compound():
"""Test getting a compound by ChemSpider ID."""
compound = cs.get_compound(2157)
assert isinstance(compound, Compound)
assert compound.record_id == 2157
with pytest.deprecated_call():
assert compound.csid == 2157
compound = cs.get_compound('2157')
assert isinstance(compound, Compound)
assert compound.record_id == 2157
with pytest.deprecated_call():
assert compound.csid == 2157
def test_get_compounds():
"""Test getting multiple compounds by ChemSpider ID."""
compounds = cs.get_compounds([2157, 13837760])
assert [c.csid for c in compounds], [2157 == 13837760]
for c in compounds:
assert 'http://' in c.image_url
assert c.average_mass > 0
def test_compound_init():
"""Test instantiating a Compound directly."""
compound = Compound(cs, 2157)
assert compound.csid == 2157
def test_compound_equality():
"""Test equality test by ChemSpider ID."""
c1 = cs.get_compound(13837760)
c2 = cs.get_compound(2157)
c3 = cs.get_compound(2157)
assert c1 != c2
assert c2 == c3
def test_compound_repr():
"""Test Compound object repr."""
assert repr(cs.get_compound(1234)) == 'Compound(1234)'
def test_image_url():
"""Test image_url returns a valid URL."""
url = cs.get_compound(2157).image_url
response = requests.get(url)
assert 'http://www.chemspider.com/ImagesHandler.ashx?id=' in url
assert response.status_code == 200
def test_molecular_formula():
"""Test Compound property molecular_formula."""
compound = cs.get_compound(2157)
assert compound.molecular_formula == 'C_{9}H_{8}O_{4}'
# Ensure value is the same on subsequent access from cache
assert compound.molecular_formula == 'C_{9}H_{8}O_{4}'
def test_smiles():
"""Test Compound property smiles."""
compound = cs.get_compound(2157)
assert compound.smiles == 'CC(=O)Oc1ccccc1C(=O)O'
# Ensure value is the same on subsequent access from cache
assert compound.smiles == 'CC(=O)Oc1ccccc1C(=O)O'
def test_inchi():
"""Test Compound property inchi."""
compound = cs.get_compound(2157)
assert compound.inchi == 'InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)'
# Ensure value is the same on subsequent access from cache
assert compound.inchi == 'InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)'
def test_stdinchi():
"""Test Compound property stdinchi."""
compound = cs.get_compound(2157)
with pytest.deprecated_call():
assert compound.stdinchi == 'InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)'
# Ensure value is the same on subsequent access from cache
assert compound.stdinchi == 'InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)'
def test_inchikey():
"""Test Compound property inchikey."""
compound = cs.get_compound(2157)
assert compound.inchikey == 'BSYNRYMUTXBXSQ-UHFFFAOYSA-N'
# Ensure value is the same on subsequent access from cache
assert compound.inchikey == 'BSYNRYMUTXBXSQ-UHFFFAOYSA-N'
def test_stdinchikey():
"""Test Compound property stdinchikey."""
compound = cs.get_compound(2157)
with pytest.deprecated_call():
assert compound.stdinchikey == 'BSYNRYMUTXBXSQ-UHFFFAOYSA-N'
# Ensure value is the same on subsequent access from cache
assert compound.stdinchikey == 'BSYNRYMUTXBXSQ-UHFFFAOYSA-N'
def test_masses():
"""Test Compound property average_mass, molecular_weight, monoisotopic_mass, nominal_mass."""
compound = cs.get_compound(2157)
assert 180 < compound.average_mass < 180.2
assert 180 < compound.molecular_weight < 180.2
assert 180 < compound.monoisotopic_mass < 180.2
assert compound.nominal_mass == 180
def test_name():
"""Test Compound property common_name."""
compound = cs.get_compound(2157)
assert compound.common_name == 'Aspirin'
def test_molfiles():
"""Test Compound property mol2d, mol3d, mol_raw."""
compound = cs.get_compound(2157)
assert 'V2000' in compound.mol_2d
assert 'V2000' in compound.mol_3d
def test_image():
"""Test Compound property image."""
compound = cs.get_compound(2157)
assert compound.image[:8] == b'\x89PNG\x0d\x0a\x1a\x0a' # PNG magic number
def test_external_references():
"""Test Compound property external_references."""
compound = cs.get_compound(97809)
assert len(compound.external_references) > 50
for xref in compound.external_references:
assert 'externalId' in xref
assert 'externalUrl' in xref
assert 'source' in xref
assert 'sourceUrl' in xref
|
