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# coding=utf-8
"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
test_basic_functions.py - Unit Tests for basic functionality.
"""
# Python Standard Library
import unittest
import numpy
import random
# Own modules
from plip.structure.preparation import PDBComplex
from plip.basic.supplemental import euclidean3d, vector, vecangle, projection
from plip.basic.supplemental import normalize_vector, cluster_doubles, centroid
class TestLigandSupport(unittest.TestCase):
"""Test for support of different ligands"""
def test_dna_rna(self):
"""Test if DNA and RNA is correctly processed as ligands"""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1tf6.pdb')
# DNA ligand four times consisting of 31 parts (composite)
self.assertEqual([len(ligand.members) for ligand in tmpmol.ligands].count(31), 4)
for ligset in [set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands]:
if len(ligset) == 4:
# DNA only contains four bases
self.assertEqual(ligset, {'DG', 'DC', 'DA', 'DT'})
class TestMapping(unittest.TestCase):
"""Test"""
def test_ids(self):
"""Test if the atom IDs are correctly mapped from internal to original PDB."""
tmpmol = PDBComplex()
tmpmol.load_pdb('./pdb/1vsn.pdb')
bsid = 'NFT:A:283'
for ligand in tmpmol.ligands:
if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid:
tmpmol.characterize_complex(ligand)
s = tmpmol.interaction_sets[bsid]
for contact in s.hydrophobic_contacts:
if contact.restype == 'ALA' and contact.resnr == 133:
self.assertEqual(contact.ligatom_orig_idx, 1636)
self.assertEqual(contact.bsatom_orig_idx, 994)
if contact.restype == 'ASP' and contact.resnr == 61:
self.assertEqual(contact.ligatom_orig_idx, 1639)
self.assertEqual(contact.bsatom_orig_idx, 448)
for contact in s.hbonds_ldon + s.hbonds_pdon:
if contact.restype == 'GLN' and contact.resnr == 19:
self.assertEqual(contact.a_orig_idx, 1649)
self.assertEqual(contact.d_orig_idx, 153)
if contact.restype == 'CYS' and contact.resnr == 25:
self.assertEqual(contact.a_orig_idx, 1649)
self.assertEqual(contact.d_orig_idx, 183)
if contact.restype == 'ASN' and contact.resnr == 158:
self.assertEqual(contact.d_orig_idx, 1629)
self.assertEqual(contact.a_orig_idx, 1199)
for contact in s.halogen_bonds:
if contact.restype == 'TYR' and contact.resnr == 67:
self.assertEqual(contact.don.x_orig_idx, 1627)
self.assertEqual(contact.acc.o_orig_idx, 485)
if contact.restype == 'LEU' and contact.resnr == 157:
self.assertEqual(contact.don.x_orig_idx, 1628)
self.assertEqual(contact.acc.o_orig_idx, 1191)
class GeometryTest(unittest.TestCase):
"""Tests for geometrical calculations in PLIP"""
def vector_magnitude(self, v):
return numpy.sqrt(sum(x**2 for x in v))
# noinspection PyUnusedLocal
def setUp(self):
"""Generate random data for the tests"""
# Generate two random n-dimensional float vectors, with -100 <= n <= 100 and values 0 <= i <= 1
dim = random.randint(1, 100)
self.rnd_vec = [random.uniform(-100, 100) for i in range(dim)]
def test_euclidean(self):
"""Tests for mathematics.euclidean"""
# Are the results correct?
self.assertEqual(euclidean3d([0.0, 0.0, 0.0], [0.0, 0.0, 0.0]), 0)
self.assertEqual(euclidean3d([2.0, 3.0, 4.0], [2.0, 3.0, 4.0]), 0)
self.assertEqual(euclidean3d([4.0, 5.0, 6.0], [4.0, 5.0, 8.0]), 2.0)
# Does the function take vectors or tuples as an input? What about integers?
self.assertEqual(euclidean3d((4.0, 5.0, 6.0), [4.0, 5.0, 8.0]), 2.0)
self.assertEqual(euclidean3d((4.0, 5.0, 6.0), (4.0, 5.0, 8.0)), 2.0)
self.assertEqual(euclidean3d((4, 5, 6), (4.0, 5.0, 8.0)), 2.0)
# Is the output a float?
self.assertIsInstance(euclidean3d([2.0, 3.0, 4.0], [2.0, 3.0, 4.0]), float)
def test_vector(self):
"""Tests for mathematics.vector"""
# Are the results correct?
self.assertEqual(list(vector([1, 1, 1], [0, 1, 0])), [-1, 0, -1])
self.assertEqual(list(vector([0, 0, 10], [0, 0, 4])), [0, 0, -6])
# Do I get an Numpy Array?
self.assertIsInstance(vector([1, 1, 1], [0, 1, 0]), numpy.ndarray)
# Do I get 'None' if the points have different dimensions?
self.assertEqual(vector([1, 1, 1], [0, 1, 0, 1]), None)
def test_vecangle(self):
"""Tests for mathematics.vecangle"""
# Are the results correct?
self.assertEqual(vecangle([3, 4], [-8, 6], deg=False), numpy.radians(90.0))
self.assertEqual(vecangle([3, 4], [-8, 6]), 90.0)
self.assertAlmostEqual(vecangle([-1, -1], [1, 1], deg=False), numpy.pi)
# Correct if both vectors are equal?
self.assertEqual(vecangle([3, 3], [3, 3]), 0.0)
def test_centroid(self):
"""Tests for mathematics.centroid"""
# Are the results correct?
self.assertEqual(centroid([[0, 0, 0], [2, 2, 2]]), [1.0, 1.0, 1.0])
self.assertEqual(centroid([[-5, 1, 2], [10, 2, 2]]), [2.5, 1.5, 2.0])
def test_normalize_vector(self):
"""Tests for mathematics.normalize_vector"""
# Are the results correct?
self.assertAlmostEqual(self.vector_magnitude(normalize_vector(self.rnd_vec)), 1)
def test_projection(self):
"""Tests for mathematics.projection"""
# Are the results correct?
self.assertEqual(projection([-1, 0, 0], [3, 3, 3], [1, 1, 1]), [3, 1, 1])
def test_cluster_doubles(self):
"""Tests for mathematics.cluster_doubles"""
# Are the results correct?
self.assertEqual(set(cluster_doubles([(1, 3), (4, 1), (5, 6), (7, 5)])), {(1, 3, 4), (5, 6, 7)})
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