#! /usr/bin/env python from testutils import McellTest from testutils import get_output_dir from testutils import cleandir from testutils import crange from reaction_output import RequireCountConstraints from reaction_output import RequireCountEquilibrium from reaction_output import RequireCounts from macromol_test_types import InvalidMacromolParserTest import unittest import math def distance(p1, p2): v = (p1[0] - p2[0], p1[1] - p2[1], p1[2] - p2[2]) return math.sqrt(v[0]*v[0] + v[1]*v[1] + v[2]*v[2]) worst_match = -1.0 def match_position(positions, dist, eps, pos): for i in positions: d = distance(i, pos) deviate = abs(d - dist) if deviate < eps: global worst_match if deviate > worst_match: worst_match = deviate return True return False class CheckListReleasePositions(object): def __init__(self, file, eps=3.0e-2): self.filename = file self.epsilon = eps self.positions = ((-0.5, -0.5, -0.5), (-0.5, -0.5, 0.5), (-0.5, 0.5, -0.5), (-0.5, 0.5, 0.5), ( 0.5, -0.5, -0.5), ( 0.5, -0.5, 0.5), ( 0.5, 0.5, -0.5), ( 0.5, 0.5, 0.5), ( 0, -0.5, -0.5), ( 0, -0.5, 0.5), ( 0, 0.5, -0.5), ( 0, 0.5, 0.5), (-0.5, 0, -0.5), (-0.5, 0, 0.5), ( 0.5, 0, -0.5), ( 0.5, 0, 0.5), (-0.5, -0.5, 0), (-0.5, 0.5, 0), ( 0.5, -0.5, 0), ( 0.5, 0.5, 0), ( 0, 0, -0.5), ( 0, 0, 0.5), ( 0, -0.5, 0), ( 0, 0.5, 0), (-0.5, 0, 0), ( 0.5, 0, 0)) def check(self): num_complexes = 0 num_subunits = 0 for line in open(self.filename): id, amp_id, x, y, z, ox, oy, oz = line.split() x = float(x) y = float(y) z = float(z) pos = (x, y, z) if id == '1': assert match_position(self.positions, 0, self.epsilon, pos), 'Found macromolecule at unexpected location (%.15g, %.15g, %.15g)' % pos num_complexes += 1 else: assert match_position(self.positions, 0.11, self.epsilon, pos), 'Found subunit at unexpected location (%.15g, %.15g, %.15g)' % pos num_subunits += 1 assert num_complexes == len(self.positions), 'Got an unexpected number of macromolecules in the ASCII viz output file.' assert num_subunits == 12*len(self.positions), 'Got an unexpected number of subunits in the ASCII viz output file.' ################################################################### # Test cases for macromol parser error handling ################################################################### class TestMacromolParseInvalid(unittest.TestCase): pass def make_invalid_test(i): methname = "test%02d" % i filename = "invalid-%02d.mdl" % i func = lambda self: InvalidMacromolParserTest(filename).invoke(get_output_dir()) setattr(TestMacromolParseInvalid, methname, func) ## Bulk generate invalid test cases 1...40 for i in crange(1, 40): make_invalid_test(i) ################################################################### # Test cases for numeric validation of macromolecules ################################################################### class TestMacromolNumeric(unittest.TestCase): def test_volume_mixed(self): t = McellTest("macromols", "01-macro.mdl", ["-quiet"]) t.add_extra_check(RequireCountConstraints("dat/01-macro/counts.dat", [(1, 1, 1, 1, 0, 0, 0), # 180 (0, 1, -1, 0, 0, 0, 0), # 0 (1, 1, 0, 0, -1, 0, 0), # 0 (0, 0, 1, 1, 0, -1, 0), # 0 (0, 1, 0, 1, 0, 0, 1)], # 800 [180, 0, 0, 0, 800], header=True)) t.add_extra_check(RequireCountEquilibrium("dat/01-macro/counts.dat", [62.2, 30.0, 30.0, 57.8, 92.1, 87.9, 712.1], [ 3.0, 1.5, 1.5, 3.0, 4.5, 4.5, 10.0], min_time=0.001, header=True)) t.invoke(get_output_dir()) def test_surface(self): t = McellTest("macromols", "02-macro_surface.mdl", ["-quiet"]) t.add_extra_check(RequireCountConstraints("dat/02-macro_surface/counts.dat", # xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd x d u x d u # 00 I 01 I 10 I 11 I U B C [(1, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 180, 800], header=True)) e00 = 15.5348 e01 = 7.4969 e11 = 14.4715 t.add_extra_check(RequireCountEquilibrium("dat/02-macro_surface/counts.dat", # xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd # 00 I [4*e00, 2*e00, 2*e00, 2*e00, 2*e00, e00, e00, e00, e00, 4*e00, 2*e00, 2*e00, 4*e00+2*e01, 4*e00+2*e01, 2*e00+e01, 2*e00+e01, 2*e00+e01, 2*e00+e01, # xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd # 01 I 4*e01, 2*e01, 2*e01, 2*e01, 2*e01, e01, e01, e01, e01, 4*e01, 2*e01, 2*e01, 4*e01+2*e00, 4*e01+2*e00, 2*e01+e00, 2*e01+e00, 2*e01+e00, 2*e01+e00, # xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd # 10 I 4*e01, 2*e01, 2*e01, 2*e01, 2*e01, e01, e01, e01, e01, 4*e01, 2*e01, 2*e01, 4*e01+2*e11, 4*e01+2*e11, 2*e01+e11, 2*e01+e11, 2*e01+e11, 2*e01+e11, # xx ux dx xu xd ud du uu dd xx ux dx xu xd ud du uu dd # 11 I 4*e11, 2*e11, 2*e11, 2*e11, 2*e11, e11, e11, e11, e11, 4*e11, 2*e11, 2*e11, 4*e11+2*e01, 4*e11+2*e01, 2*e11+e01, 2*e11+e01, 2*e11+e01, 2*e11+e01, # x d u x d u # U B C 4*e00+4*e01, 2*e00+2*e01, 2*e00+2*e01, 4*e11+4*e01, 2*e11+2*e01, 2*e11+2*e01, 800 - (4*e11+4*e01)], [1.8]*18 + [1.2]*36 + [1.8]*18 + [1.2]*6 + [2.4], min_time=0.05, header=True)) t.invoke(get_output_dir()) def test_list_release(self): t = McellTest("macromols", "03-macro_surface_listrelease.mdl", ["-quiet"]) t.add_extra_check(RequireCounts('counts.txt', [[0, 26, 312, 208, 26, 52]], header="# Iteration_# complexes subunits 00 01 11")) t.add_extra_check(CheckListReleasePositions('molecules.ascii.0.dat')) t.invoke(get_output_dir()) def test_surface_init(self): t = McellTest("macromols", "04-macro_surface_init.mdl", ["-quiet"]) # XXX: Will have to change a few numbers in the next two validity checks # once placement of macromols on surface classes is working. t.add_extra_check(RequireCountConstraints("counts.txt", [(12, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 0 (subunits per complex) ( 0, 1, -1, -2, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 0 (total subunits vs. per-orientation) ( 0, 0, 0, 0, 0, -1, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 0 (00 vs. 01 orientation on top) ( 0, 0, 0, 0, 0, 0, 0, 0, -1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 0 (00 vs. 01 orientation on bottom) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 0 (00 vs. 01 orientation on left) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 2, 0, 0, 0, 0, 0, 0, 0), # 0 (00 vs. 01 orientation on right) ( 0, 0, 0, 0, 0, 0, 2, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 0 (11 vs. 01 orientation on top) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 8, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 0 (11 vs. 01 orientation on bottom) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 0 (11 vs. 01 orientation on left) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8, -1, 0, 0, 0, 0, 0, 0), # 0 (11 vs. 01 orientation on right) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -10, 1, 0, 0, 0), # 0 (00+11 vs. 01 orientation on front) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, -10, 1), # 0 (00+11 vs. 01 orientation on back) ( 0, 0, 1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0), # 0 (total 00 subunits vs. per-face) ( 0, 0, 0, 1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0), # 0 (total 01 subunits vs. per-face) ( 0, 0, 0, 0, 1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, -1), # 0 (total 11 subunits vs. per-face) # ( 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # BROKEN: 20 (01 subunits on top face) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), # 20 (01 subunits on bottom face) ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0), # 200 (01 subunits on right face) # ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0), # BROKEN: 25 (01 subunits on top face) ], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 20, 200], header=True)) # BROKEN: placement on surface class does nothing # expect_t = 20 # expect_l = 200 # expect_f = 25 expect_t = 0 expect_l = 0 expect_f = 0 expect_bo = 20 expect_r = 200 expect_ba = 200 expect_00 = 8*expect_t + 2*expect_bo + 8*expect_l + 2*expect_r + 5*expect_f + 5*expect_ba expect_01 = expect_t + expect_bo + expect_l + expect_r + expect_f + expect_ba expect_11 = 2*expect_t + 8*expect_bo + 2*expect_l + 8*expect_r + 5*expect_f + 5*expect_ba expect_total = expect_t + expect_l + expect_f + expect_bo + expect_r + expect_ba expect_subunits = 12*expect_total t.add_extra_check(RequireCountEquilibrium("counts.txt", [expect_total, expect_subunits, expect_00, expect_01, expect_11, 8*expect_t, expect_t, 2*expect_t, 2*expect_bo, expect_bo, 8*expect_bo, 8*expect_l, expect_l, 2*expect_l, 2*expect_r, expect_r, 8*expect_r, 5*expect_f, expect_f, 5*expect_f, 5*expect_ba, expect_ba, 5*expect_ba], [expect_total / 10, expect_subunits/10, expect_00/10, expect_01/10, expect_11/10, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 1+expect_l, 1+expect_l/8, 1+expect_l/4, 0.1, 0.1, 0.1, 1+expect_f, 0.1, 1+expect_f, expect_ba, expect_ba/10, expect_ba], header=True)) t.invoke(get_output_dir()) ################################################################### # Generate a test suite for all invalid mdl files ################################################################### def errorsuite(): return unittest.makeSuite(TestMacromolParseInvalid, "test") ################################################################### # Generate a test suite for all numeric tests ################################################################### def numericsuite(): return unittest.makeSuite(TestMacromolNumeric, "test") ################################################################### # Default use of this file will invoke all tests ################################################################### if __name__ == "__main__": cleandir(get_output_dir()) unittest.main()