#!/usr/bin/env python # # test_dihedral.py # # Tests the dihedral module. # """Provides tests for functions in the file dihedral.py """ __author__ = "Kristian Rother" __copyright__ = "Copyright 2007-2009 2008, The Cogent Project" __contributors__ = ["Kristian Rother", "Sandra Smit"] __credits__ = ["Janusz Bujnicki", "Nils Goldmann"] __license__ = "GPL" __version__ = "1.4.1" __maintainer__ = "Kristian Rother" __email__ = "krother@rubor.de" __status__ = "Production" from cogent.util.unit_test import main, TestCase from cogent.struct.dihedral import dihedral, scalar, angle, \ DihedralGeometryError, AngleGeometryError from random import random from numpy import array from math import pi, cos, sin class DihedralTests(TestCase): def get_random_array(self): """ Returns a one-dimensional numpy array with three random floats in the range between -5.0 and +5.0. """ return array([(random()-0.5)*10,(random()-0.5)*10,(random()-0.5)*10]) def assertAlmostEqualAngle(self, is_value, should_value, digits=7): """ Checks two angles in degrees whether they are the same within the given number of digits. This has been implemented to make sure that 359.9999991 == 0.0 """ maxv = 359.0 for i in range(digits): maxv += 0.9 * 0.1**i while is_value < 0.0: is_value += 360 while is_value > maxv: is_value -= 360 while should_value < 0.0: should_value += 360 while should_value > maxv: should_value -= 360 self.assertAlmostEqual(is_value,should_value, digits) def test_scalar(self): """Tests the scalar product function for one-dimensional arrays.""" # test one-dimensional arrays self.assertEqual(scalar(array([0]),array([0])),0.0) self.assertEqual(scalar(array([2]),array([3])),6.0) self.assertEqual(scalar(array([0,0]),array([0,0])),0.0) self.assertEqual(scalar(array([-1,-4]),array([1,4])),-17.0) self.assertEqual(scalar(array([1,2]),array([3,4])),11.0) self.assertEqual(scalar(array([-1,-4]),array([-1,4])),-15.0) self.assertEqual(scalar(array([0,0,0]),array([0,0,0])),0.0) self.assertEqual(scalar(array([2.5,0,-1]),array([2.5,0,-1])),7.25) self.assertEqual(scalar(array([1,2,3]),array([0,0,0])),0.0) self.assertEqual(scalar(array([1,2,3]),array([1,2,3])),14.0) self.assertEqual(scalar(array([1,2,3]),array([4,5,6])),32.0) # test two-dimensional arrays (should not be a feature) self.assertNotEqual(scalar(array([[0,0],[0,0]]),\ array([[0,0],[0,0]])),0.0) def test_angle_simple(self): """Tests the angle function for one- and two-dimensional vectors.""" # test two-dimensional vectors (not arrays!) self.assertEqual(angle(array([0,1]),array([1,0])),0.5*pi) self.assertEqual(angle(array([5,0]),array([13,0])),0.0) self.assertEqual(angle(array([2,3]),array([26,39])),0.0) self.assertEqual(angle(array([2,3]),array([-3,2])),0.5*pi) self.assertEqual(angle(array([-5,0]),array([13,0])),pi) # test three-dimensional vectors (not arrays!) self.assertEqual(angle(array([0,0,-1]),array([0,0,1])),pi) self.assertEqual(angle(array([0,15,-1]),array([0,-15,1])),pi) self.assertEqual(angle(array([0,0,7]),array([14,14,0])),0.5*pi) self.assertEqual(angle(array([0,7,7]),array([0,14,14])),0.0) self.assertAlmostEqual(angle(array([100000000.0,0,1]),\ array([1,0,0])),0.0) ## def make_scipy_angles(self): ## """Generates the test data given below. Was commented out ## for getting rid of the library dependency""" ## from Scientific.Geometry import Vector ## for i in range(20): ## v1 = self.get_random_array() ## v2 = self.get_random_array() ## vec1 = Vector(v1[0],v1[1],v1[2]) ## vec2 = Vector(v2[0],v2[1],v2[2]) ## scipy_angle = vec1.angle(vec2) ## out = [(vec1[0],vec1[1],vec1[2]),\ ## (vec2[0],vec2[1],vec2[2]),scipy_angle] ## print out,"," def test_angle_scipy(self): """ Asserts that dihedral and ScientificPython calculate the same angles. """ for v1,v2,scipy_angle in SCIPY_ANGLES: ang = angle(array(v1),array(v2)) self.assertAlmostEqual(ang, scipy_angle) def test_angle_fail(self): """The angle function should fail for zero length vectors.""" # should not work for zero length vectors self.assertRaises(AngleGeometryError,angle,\ array([0,0]),array([0,0])) self.assertRaises(AngleGeometryError,angle,\ array([0,0,0]),array([0,0,0])) def test_dihedral_eight_basic_directions(self): """Checks dihedrals in all 45 degree intervals.""" # using vectors with integer positions. self.assertAlmostEqualAngle(\ dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1, 0]), 0.0) self.assertAlmostEqualAngle(\ dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1,-1]), 45.0) self.assertAlmostEqualAngle(\ dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 0,-1]), 90.0) self.assertAlmostEqualAngle(\ dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1,-1]),135.0) self.assertAlmostEqualAngle(\ dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1, 0]),180.0) self.assertAlmostEqualAngle(\ dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 1, 1]),225.0) self.assertAlmostEqualAngle(\ dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2, 0, 1]),270.0) self.assertAlmostEqualAngle(\ dihedral([-2,-1,0], [-1,0,0], [1,0,0], [2,-1, 1]),315.0) def test_dihedral_rotation(self): """Checks all angles in 0.2 degree intervals.""" # constructs vectors using sin/cos and then calculates dihedrals precision = 5.0 # the higher the better v1 = array([1,0,1]) v2 = array([0,0,1]) v3 = array([0,0,2]) for i in range(int(360*precision)): degrees = i/precision radians = pi*degrees/180.0 opp_degrees = 360-degrees if opp_degrees == 360.0: opp_degrees = 0.0 # construct circular motion of vector v4 = array([cos(radians), sin(radians),2]) self.assertAlmostEqualAngle(dihedral(v4,v3,v2,v1), degrees, 5) # check rotation in the opposite direction self.assertAlmostEqualAngle(dihedral(v1,v2,v3,v4), degrees, 5) def test_dihedral_samples(self): """Checks values measured manually from atoms in PyMOL.""" coordinates = [ [(-1.225,4.621,42.070),(-1.407,4.455,43.516),\ (-2.495,4.892,44.221),(-3.587,5.523,43.715)], [(-2.495,4.892,44.221),(1.513,0.381,40.711),\ (-3.091,4.715,47.723),(-0.567,3.892,44.433)], [(-0.349,5.577,39.446),(-1.559,3.400,41.427),\ (-4.304,5.563,45.998),(-2.495,4.892,44.221)], [(-45.819,84.315,19.372),(-31.124,72.286,14.035),\ (-27.975,58.688,7.025),(-16.238,78.659,23.731)], [(-29.346,66.973,24.152),(-29.977,69.635,24.580),\ (-30.875,68.788,24.663),(-30.668,67.495,24.449)], [(-34.586,84.884,14.064),(-23.351,69.756,11.028),\ (-40.924,69.442,24.630),(-30.875,68.788,24.663)] ] angles = [1.201, 304.621, 295.672, 195.184, 358.699, 246.603] for i in range(len(coordinates)): v1,v2,v3,v4 = coordinates[i] self.assertAlmostEqualAngle(dihedral(v1,v2,v3,v4), angles[i],3) def test_dihedral_linear(self): """The dihedral function should fail for collinear vectors.""" v1 = [1,0,0] v2 = [2,0,0] v3 = [3,0,0] v4 = [4,0,0] # print dihedral(v1,v2,v3,v4) for i in range(100): offset = array([int((random()-0.5)*10),\ int((random()-0.5)*10),\ int((random()-0.5)*10)]) v1 = array([int((random()-0.5)*100),\ int((random()-0.5)*100),\ int((random()-0.5)*100)]) v2 = v1 * int((random()-0.5)*100) + offset v3 = v1 * int((random()-0.5)*100) + offset v4 = v1 * int((random()-0.5)*100) + offset v1 += offset self.assertRaises(DihedralGeometryError,dihedral,v1,v2,v3,v4) def test_dihedral_identical(self): """The dihedral function should fail if two vectors are the same.""" # except for the first and last (the vectors form a triangle), # in which case the dihedral angle should be 0.0 for i in range(100): v1 = self.get_random_array() v2 = self.get_random_array() v3 = self.get_random_array() self.assertRaises(DihedralGeometryError,dihedral,v1,v1,v2,v3) self.assertRaises(DihedralGeometryError,dihedral,v1,v2,v1,v3) self.assertRaises(DihedralGeometryError,dihedral,v1,v2,v2,v3) self.assertRaises(DihedralGeometryError,dihedral,v1,v2,v3,v3) self.assertRaises(DihedralGeometryError,dihedral,v1,v3,v2,v3) # now the triangular case # make sure that 359.999998 is equal to 0.0 torsion = dihedral(v1,v2,v3,v1) + 0.000001 if torsion > 360.0: torsion -= 360.0 self.assertAlmostEqualAngle(torsion,0.0,5) SCIPY_ANGLES = [ [(-4.4891521637990852, -1.2310927013330153, -0.96969777583098771), (4.2147455310344171, -3.5069051036633514, 2.2430685816310305), 2.2088870817461759] , [(0.13959847081794097, 1.7204537912940399, -1.9303780516641089), (0.35412687539602361, -2.9493521724340743, -4.865941405480644), 1.2704043143950585] , [(2.3192363837822327, -3.6376441859213848, -2.2337816400479813), (-1.0271253661119029, -2.5736009846920425, -4.1470855710278975), 0.83609068310373857] , [(-0.38347986357358477, -4.1453876196041719, -2.1354583394773785), (0.27416747968044608, -2.5747732838982551, -0.68554680652905264), 0.28348352552436806] , [(-2.4928231204363449, 1.9263125976608209, -0.34275964486924715), (0.6721152528064811, 1.5270465172130598, -3.5720133753579564), 1.3701121510959966] , [(-1.50101403139692, 2.3218275982958292, 1.044582416480222), (-3.044743729573085, 2.0655933798619532, 2.9037849925327897), 0.46218988498537578] , [(4.9648826388927603, -1.7439743270051977, 1.0432135258334796), (-3.3694557299188608, 3.7697639370274052, 2.6962018714965055), 2.3004031013653625] , [(-3.3337033325729051, -0.79660906888508021, -3.4875326261817454), (1.4735023133671066, -0.066399047153666846, 0.94171530437632489), 2.8293957790283595] , [(-2.1249404252000517, 2.7456001658201568, 1.6891202129451799), (-0.66412553435299504, 3.371012200444512, -1.1548086037901306), 0.89846374464990042] , [(3.3993205618602018, 1.2047703532166887, -1.5839949555795063), (-4.6759756026580863, -2.8551222890449646, 4.888270217692785), 2.7825564894291754] , [(-3.966467296275785, 0.75617096138383189, -3.1711352932360248), (2.1054362220912326, 4.2867761689586601, -0.65739369331424213), 1.6933117193742961] , [(0.44413554305522851, 4.6000690382282361, -3.8338383756621819), (-2.4947413565865029, 1.8136080147734013, -4.0295344084655405), 0.73110709489481174] , [(-1.0971777991639065, -3.3166205797568815, 2.7098739534055563), (2.1536566381847289, 4.7817155120086055, -0.068554664323454695), 2.4878958372925202] , [(2.2696914760438136, 4.8841630875833673, 4.9524177412608861), (1.2249510822623111, 0.73008672334971658, 1.131607772478449), 0.45741431674591532] , [(-2.4456899797216938, 4.7894200033986447, -2.839449354837468), (0.95035116225980154, 4.2179212878828238, -1.801158217734109), 0.63144509227951684] , [(-4.6954041297179474, -2.8326266911591391, -1.1804869511610427), (3.2585456362256924, -2.2325171051479265, -2.0527260317826901), 1.8363466110668369] , [(2.1416146613604283, 3.8577375591718677, 3.1463493245087939), (-0.32185887240442468, 2.2163051363839505, 2.4704882512058224), 0.52534998201320993] , [(-2.8493351354335941, -3.8203784990110954, 2.4657357720402273), (-2.7799043389229383, 4.358406526726669, -2.8319872383058744), 2.0906833125217235] , [(2.274223250163784, -3.6086250253596406, 1.7143006579401876), (3.2763334328544347, -0.89908959703552171, -4.4068824993431557), 1.4477009361020545] , [(0.66737672421842809, -3.4628508908383848, 3.9044108358095366), (-1.9078974719893915, -0.53231141116878433, 1.3323584972786728), 1.0932781951137689] , ] if __name__== '__main__': main()