diff --git a/ippisite/ippidb/tests.py b/ippisite/ippidb/tests.py
index cd0914b0c3702b189c47be16f79bc76c9ea6e616..2c2d02a6d01dd840c602d6b62c201f2761ca1865 100644
--- a/ippisite/ippidb/tests.py
+++ b/ippisite/ippidb/tests.py
@@ -8,7 +8,6 @@ from django.contrib.auth import get_user_model
from django.core.management import call_command
from django.test import TestCase
from django.urls import reverse
-from openbabel import vectorUnsignedInt, OBFingerprint
import requests
@@ -26,7 +25,6 @@ from .models import (
PcaBiplotData,
)
from .models import DrugBankCompound, Protein
-from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey, smi2sdf
class MolSmiTestCase(TestCase):
@@ -44,12 +42,6 @@ class MolSmiTestCase(TestCase):
" 0 0 0 0 0 0 0 0\nM END\n"
)
- def test_mol2smi(self):
- self.assertEqual(mol2smi(self.mol), self.smiles)
-
- def test_smi2mol2smi(self):
- self.assertTrue(re.compile(self.mol).match(smi2mol(self.smiles)))
-
def test_view_smi2mol_valid(self):
url = reverse("smi2mol")
response = self.client.get(url, {"smiString": self.smiles})
@@ -89,94 +81,6 @@ class MolSmiTestCase(TestCase):
self.assertEqual(response.status_code, 400)
-class SmiInchi(TestCase):
- """
- Test INCHI and INCHIKEY generation functions
- """
-
- def setUp(self):
- self.smiles_str = (
- "CC(C)C(=O)C1=C(C(=C(C(=C1)C(=O)C2=CC=C(C=C2)" "OC3=CC=CC=C3)O)O)O"
- )
- self.inchi_str = (
- "InChI=1S/C23H20O6/c1-13(2)19(24)17-12-18(22"
- "(27)23(28)21(17)26)20(25)14-8-10-16(11-9-14)29-15-6-4-3-"
- "5-7-15/h3-13,26-28H,1-2H3"
- )
- self.inchikey_str = "CVVQMBDTMYUWTR-UHFFFAOYSA-N"
-
- def test_smi2inchi(self):
- self.assertEqual(smi2inchi(self.smiles_str), self.inchi_str)
-
- def test_smi2inchikey(self):
- self.assertEqual(smi2inchikey(self.smiles_str), self.inchikey_str)
-
-
-class FingerPrinterTestCase(TestCase):
- """
- Test FingerPrinter class
- """
-
- def setUp(self):
- self.fingerprinter = FingerPrinter("FP4")
- self.smiles = "CC"
- self.fp = vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
- self.smiles_dict = {1: "CC", 2: "CCC"}
- self.fp_dict = {
- 1: vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
- 2: vectorUnsignedInt([3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
- }
- self.tanimoto_dict = {1: 1.0, 2: 0.5}
-
- def test_fingerprints_available(self):
- # test that all necessary fingerprints are available
- self.assertIsNotNone(OBFingerprint.FindFingerprint("FP2"))
- self.assertIsNotNone(OBFingerprint.FindFingerprint("FP4"))
- self.assertIsNotNone(OBFingerprint.FindFingerprint("ECFP4"))
-
- def assertEqualVUI(self, vui_one, vui_two):
- return self.assertEqual(list(vui_one), list(vui_two))
-
- def assertEqualVUIdict(self, vuidict_one, vuidict_two):
- vuidict_one = {id_: list(vui) for id_, vui in vuidict_one.items()}
- vuidict_two = {id_: list(vui) for id_, vui in vuidict_two.items()}
- return self.assertEqual(vuidict_one, vuidict_two)
-
- def test_fp(self):
- self.assertEqualVUI(self.fingerprinter.fp(self.smiles), self.fp)
-
- def test_fp_dict(self):
- self.assertEqualVUIdict(
- self.fingerprinter.fp_dict(self.smiles_dict), self.fp_dict
- )
-
- def test_tanimoto_fps(self):
- self.assertEqual(
- self.fingerprinter.tanimoto_fps(self.smiles, self.fp_dict),
- self.tanimoto_dict,
- )
-
- def test_tanimoto_smiles(self):
- self.assertEqual(
- self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
- self.tanimoto_dict,
- )
-
-
-class FingerPrinterTestCaseCompound1ECFP4(TestCase):
- def setUp(self):
- self.fingerprinter = FingerPrinter("ECFP4")
- self.smiles = "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"
- self.smiles_dict = {1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)" "c(O)c1O"}
- self.tanimoto_dict = {1: 1.0}
-
- def test_tanimoto_smiles(self):
- self.assertEqual(
- self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
- self.tanimoto_dict,
- )
-
-
def create_dummy_compound(id_, smiles):
c = Compound()
c.id = id_
@@ -918,30 +822,6 @@ class TestConvertSMILESToIUPAC(TestCase):
)
-class TestConvertSMILESToSDF(TestCase):
- """
- Test converting a smiles to SDF using openbabel
- """
-
- def test_valid(self):
- smiles_to_sdfs = {
- "C": [
- "1",
- " OpenBabel04142011372D",
- "",
- " 1 0 0 0 0 0 0 0 0 0999 V2000",
- " 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0",
- "M END",
- "$$$$",
- ]
- }
- for smiles, expected_lines in smiles_to_sdfs.items():
- result = smi2sdf({1: smiles})
- result_lines = result.split("\n")
- for line_idx in [0, 2, 3, 4, 5, 6]:
- self.assertEqual(result_lines[line_idx], expected_lines[line_idx])
-
-
class DuplicateGeneNameTestCase(TestCase):
def test_works(self):
models.Protein.objects.get_or_create(uniprot_id="P12497")
diff --git a/ippisite/ippidb/tests_utils.py b/ippisite/ippidb/tests_utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..0865028b482683279168d132f32822a20bc645c6
--- /dev/null
+++ b/ippisite/ippidb/tests_utils.py
@@ -0,0 +1,143 @@
+"""
+iPPI-DB unit tests
+"""
+import re
+
+from django.test import TestCase
+from openbabel import vectorUnsignedInt, OBFingerprint
+
+from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey, smi2sdf
+
+
+class MolSmiTestCase(TestCase):
+ """
+ Test MOL to SMILES and SMILES to MOL format conversion functions
+ """
+
+ def setUp(self):
+ self.smiles = "C"
+ # the MOL version is also a valid regexp to validate arbitrary name in
+ # the openbabel-generated version
+ self.mol = (
+ "\n OpenBabel[0-9]{11}D\n\n 1 0 0 0 0 0 0 0 "
+ " 0 0999 V2000\n 1.0000 0.0000 0.0000 C 0 0 0 0 "
+ " 0 0 0 0 0 0 0 0\nM END\n"
+ )
+
+ def test_mol2smi(self):
+ self.assertEqual(mol2smi(self.mol), self.smiles)
+
+ def test_smi2mol2smi(self):
+ self.assertTrue(re.compile(self.mol).match(smi2mol(self.smiles)))
+
+
+class SmiInchiTestCase(TestCase):
+ """
+ Test INCHI and INCHIKEY generation functions
+ """
+
+ def setUp(self):
+ self.smiles_str = (
+ "CC(C)C(=O)C1=C(C(=C(C(=C1)C(=O)C2=CC=C(C=C2)" "OC3=CC=CC=C3)O)O)O"
+ )
+ self.inchi_str = (
+ "InChI=1S/C23H20O6/c1-13(2)19(24)17-12-18(22"
+ "(27)23(28)21(17)26)20(25)14-8-10-16(11-9-14)29-15-6-4-3-"
+ "5-7-15/h3-13,26-28H,1-2H3"
+ )
+ self.inchikey_str = "CVVQMBDTMYUWTR-UHFFFAOYSA-N"
+
+ def test_smi2inchi(self):
+ self.assertEqual(smi2inchi(self.smiles_str), self.inchi_str)
+
+ def test_smi2inchikey(self):
+ self.assertEqual(smi2inchikey(self.smiles_str), self.inchikey_str)
+
+
+class FingerPrinterTestCase(TestCase):
+ """
+ Test FingerPrinter class
+ """
+
+ def setUp(self):
+ self.fingerprinter = FingerPrinter("FP4")
+ self.smiles = "CC"
+ self.fp = vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
+ self.smiles_dict = {1: "CC", 2: "CCC"}
+ self.fp_dict = {
+ 1: vectorUnsignedInt([1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
+ 2: vectorUnsignedInt([3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]),
+ }
+ self.tanimoto_dict = {1: 1.0, 2: 0.5}
+
+ def test_fingerprints_available(self):
+ # test that all necessary fingerprints are available
+ self.assertIsNotNone(OBFingerprint.FindFingerprint("FP2"))
+ self.assertIsNotNone(OBFingerprint.FindFingerprint("FP4"))
+ self.assertIsNotNone(OBFingerprint.FindFingerprint("ECFP4"))
+
+ def assertEqualVUI(self, vui_one, vui_two):
+ return self.assertEqual(list(vui_one), list(vui_two))
+
+ def assertEqualVUIdict(self, vuidict_one, vuidict_two):
+ vuidict_one = {id_: list(vui) for id_, vui in vuidict_one.items()}
+ vuidict_two = {id_: list(vui) for id_, vui in vuidict_two.items()}
+ return self.assertEqual(vuidict_one, vuidict_two)
+
+ def test_fp(self):
+ self.assertEqualVUI(self.fingerprinter.fp(self.smiles), self.fp)
+
+ def test_fp_dict(self):
+ self.assertEqualVUIdict(
+ self.fingerprinter.fp_dict(self.smiles_dict), self.fp_dict
+ )
+
+ def test_tanimoto_fps(self):
+ self.assertEqual(
+ self.fingerprinter.tanimoto_fps(self.smiles, self.fp_dict),
+ self.tanimoto_dict,
+ )
+
+ def test_tanimoto_smiles(self):
+ self.assertEqual(
+ self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
+ self.tanimoto_dict,
+ )
+
+
+class FingerPrinterTestCaseCompound1ECFP4(TestCase):
+ def setUp(self):
+ self.fingerprinter = FingerPrinter("ECFP4")
+ self.smiles = "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)c(O)c1O"
+ self.smiles_dict = {1: "CC(C)C(=O)c1cc(C(=O)c2ccc(Oc3ccccc3)cc2)c(O)" "c(O)c1O"}
+ self.tanimoto_dict = {1: 1.0}
+
+ def test_tanimoto_smiles(self):
+ self.assertEqual(
+ self.fingerprinter.tanimoto_smiles(self.smiles, self.smiles_dict),
+ self.tanimoto_dict,
+ )
+
+
+class ConvertSMILESToSDFTestCase(TestCase):
+ """
+ Test converting a smiles to SDF using openbabel
+ """
+
+ def setUp(self):
+ self.smiles = "C"
+ # the MOL version is also a valid regexp to validate arbitrary name in
+ # the openbabel-generated version
+ self.sdf = (
+ "1\n"
+ " OpenBabel[0-9]{11}D\n"
+ "\n"
+ " 1 0 0 0 0 0 0 0 0 0999 V2000\n"
+ " 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
+ "M END\n"
+ "\$\$\$\$\n"
+ )
+
+ def test_valid(self):
+ result = smi2sdf({1: self.smiles})
+ self.assertTrue(re.compile(self.sdf).search(result))