diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index ddc3a465a231c32219bf33e1b4eea375cdc0b4ca..c901b9408447b30971c89d97d8b2ec8f30ecfa61 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -1,4 +1,5 @@
import unittest, os
+import ost
from ost import io
from ost.mol.alg.qsscoring import *
@@ -10,13 +11,115 @@ def _LoadFile(file_name):
class TestQSscore(unittest.TestCase):
+ # TESTS base
+
+ def test_QSscoreEntity(self):
+ # use smallest test structure...
+ ent = _LoadFile('3ia3.1.pdb')
+ ent.SetName("my_ent")
+ # create clean one
+ qs_ent = QSscoreEntity(ent)
+ self.assertTrue(qs_ent.is_valid)
+ # check naming
+ qs_ent.SetName("my_qs_ent")
+ self.assertEqual(qs_ent.original_name, "my_ent")
+ self.assertEqual(qs_ent.GetName(), "my_qs_ent")
+ # check cleanup
+ self.assertEqual(sorted(ch.name for ch in qs_ent.ent.chains), ['A', 'B'])
+ self.assertEqual(qs_ent.removed_chains, ['_'])
+ self.assertFalse(qs_ent.calpha_only)
+ # check CA entity
+ ca_ent = qs_ent.ca_entity
+ self.assertEqual(sorted(ch.name for ch in ca_ent.chains), ['A', 'B'])
+ self.assertEqual(ca_ent.residue_count, ca_ent.atom_count)
+ self.assertEqual(ca_ent.Select('aname=CA').atom_count, ca_ent.atom_count)
+ self.assertEqual(sorted(qs_ent.ca_chains.keys()), ['A', 'B'])
+ for ch in ca_ent.chains:
+ self.assertEqual(''.join([r.one_letter_code for r in ch.residues]),
+ str(qs_ent.ca_chains[ch.name]))
+ # check chem groups
+ self.assertEqual(sorted(qs_ent.chem_groups), [['A'], ['B']])
+ # check contacts
+ self.assertEqual(len(qs_ent.contacts['A']['B']), 45)
+ self.assertAlmostEqual(qs_ent.contacts['A']['B'][23][127], 10.069, 2)
+ self.assertEqual(len(qs_ent.contacts_ca['A']['B']), 42)
+ self.assertAlmostEqual(qs_ent.contacts_ca['A']['B'][23][127], 10.471, 2)
+ # check contact filtering
+ old_contacts = qs_ent.contacts.copy()
+ old_contacts_ca = qs_ent.contacts_ca.copy()
+ qs_ent.contacts = old_contacts
+ self.assertEqual(qs_ent.contacts, old_contacts)
+ qs_ent.contacts_ca = old_contacts_ca
+ self.assertEqual(qs_ent.contacts_ca, old_contacts_ca)
+ dummy_contacts = {'A': {'B': {1: {2: 3.0, 4: 5.0}},
+ 'C': {10: {20: 30.0, 40: 50.0}}},
+ 'B': {'C': {100: {200: 300.0, 400: 500.0}}}}
+ qs_ent.contacts = dummy_contacts
+ self.assertEqual(qs_ent.contacts, {'A': {'B': {1: {2: 3.0, 4: 5.0}}}})
+ self.assertEqual(qs_ent.contacts_ca, old_contacts_ca)
+ qs_ent.contacts = old_contacts
+ qs_ent.contacts_ca = dummy_contacts
+ self.assertEqual(qs_ent.contacts, old_contacts)
+ self.assertEqual(qs_ent.contacts_ca, {'A': {'B': {1: {2: 3.0, 4: 5.0}}}})
+
+ # check chain removal for non-amino acid chains
+ ent_extra = ent.Copy()
+ edi = ent_extra.EditXCS()
+ # classic ligand chain
+ ch = edi.InsertChain('C')
+ for _ in range(30):
+ r = edi.AppendResidue(ch, 'HOH')
+ edi.InsertAtom(r, 'O', ost.geom.Vec3())
+ # DNA chain
+ ch = edi.InsertChain('D')
+ for _ in range(30):
+ r = edi.AppendResidue(ch, 'A')
+ edi.InsertAtom(r, 'P', ost.geom.Vec3())
+ edi.UpdateICS()
+ # ensure both removed
+ qs_ent_test = QSscoreEntity(ent_extra)
+ self.assertEqual(sorted(qs_ent_test.removed_chains), ['C', 'D', '_'])
+
+ # invalid structures: monomers (or less) before or after cleaning
+ ost.PushVerbosityLevel(-1)
+ # empty view
+ ent_empty = ent.CreateEmptyView()
+ qs_ent_invalid = QSscoreEntity(ent_empty)
+ self.assertFalse(qs_ent_invalid.is_valid)
+ # monomer
+ ent_mono = ent.Select('cname=A')
+ qs_ent_invalid = QSscoreEntity(ent_mono)
+ self.assertFalse(qs_ent_invalid.is_valid)
+ # short chain removed
+ ent_short = ent.Select('cname=A or rnum<20')
+ qs_ent_invalid = QSscoreEntity(ent_short)
+ self.assertFalse(qs_ent_invalid.is_valid)
+ self.assertEqual(sorted(qs_ent_invalid.removed_chains), ['B', '_'])
+ # non-AA chain removal
+ ent_non_AA = ent_extra.Select('cname=A,C,D')
+ qs_ent_invalid = QSscoreEntity(ent_non_AA)
+ self.assertFalse(qs_ent_invalid.is_valid)
+ self.assertEqual(sorted(qs_ent_invalid.removed_chains), ['C', 'D'])
+ ost.PopVerbosityLevel()
+
+ # exception when scoring with invalid QSscoreEntity
+ with self.assertRaises(QSscoreError):
+ qs_scorer_tst = QSscorer(qs_ent_invalid, qs_ent)
+ qs_scorer_tst.global_score
+ with self.assertRaises(QSscoreError):
+ qs_scorer_tst = QSscorer(qs_ent, qs_ent_invalid)
+ qs_scorer_tst.global_score
+
+
+ # TESTS HETERO
+
def test_HeteroCase1(self):
# additional chains
ent_1 = _LoadFile('4ux8.1.pdb') # A2 B2 C2, symmetry: C2
ent_2 = _LoadFile('3fub.2.pdb') # A2 B2 , symmetry: C2
qs_scorer = QSscorer(ent_1, ent_2)
# check properties
- self.assertEqual(qs_scorer.calpha_only, False)
+ self.assertFalse(qs_scorer.calpha_only)
# check mappings
self.assertEqual(qs_scorer.chem_mapping,
{('D', 'F'): ('B', 'D'), ('C', 'E'): ('A', 'C')})
@@ -36,7 +139,7 @@ class TestQSscore(unittest.TestCase):
ent_2 = _LoadFile('3fub.au.pdb')
qs_scorer = QSscorer(ent_1, ent_2)
# check properties
- self.assertEqual(qs_scorer.calpha_only, False)
+ self.assertFalse(qs_scorer.calpha_only)
# check mappings
self.assertEqual(qs_scorer.chem_mapping,
{('C', 'E'): ('A', 'C'), ('D', 'F'): ('D', 'B')})
@@ -81,11 +184,17 @@ class TestQSscore(unittest.TestCase):
qs_scorer = QSscorer(ent_1, ent_2)
self.assertAlmostEqual(qs_scorer.global_score, 0.980, 2)
self.assertAlmostEqual(qs_scorer.best_score, 0.980, 2)
+ # check properties
+ self.assertFalse(qs_scorer.calpha_only)
+ # check mappings
+ self.assertEqual(qs_scorer.chem_mapping, {('A',): ('B',), ('B',): ('A',)})
+ self.assertEqual(qs_scorer.chain_mapping, {'A': 'B', 'B': 'A'})
# check if CA-only scoring is close to this
ent_2_ca = ent_2.Select('aname=CA')
# use QSscoreEntity to go faster
qs_scorer_ca = QSscorer(qs_scorer.qs_ent_1, ent_2_ca)
+ self.assertTrue(qs_scorer_ca.calpha_only)
self.assertAlmostEqual(qs_scorer_ca.global_score, qs_scorer.global_score, 2)
self.assertAlmostEqual(qs_scorer_ca.best_score, qs_scorer.best_score, 2)
# throw exception for messed up chains without CA atoms