mcell/mdl/testsuite/macromols/test_macromols.py

#! /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,  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,  1,  0, -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,  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,  1,  0, -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,  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,  1,  0,  0,  0, -1,  0, -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,  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,  1,  0,  0,  0, -1,  0, -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,  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),
                             (1,  0,  0,  0,  0,  0,  0,  0,  0, -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,  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,  1,  0,  0,  0,  0,  0,  0,  0,  0, -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,  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,  1,  0,  0,  0,  0,  0,  0,  0,  0, -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,  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),
                             (1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),
                             (1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),
                             (0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),
                             (0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),
                             (0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0),
                             (0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0,  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,  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,  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,  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,  1,  0,  0, -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,  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,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0,  0),
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0),
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  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,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0,  0,  0),
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0, -1,  0, -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,  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,  1,  0,  0,  0, -1,  0, -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,  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,  1,  0,  0,  0,  0,  0,  0,  0,  0, -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,  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,  1,  0,  0,  0,  0,  0,  0,  0,  0, -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,  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,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0,  0),
                             (1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0,  0),
                             (0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0,  0,  0,  0,  0),
                             (0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -1,  0),
                             (0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0, -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,  0,  0,  0,  0,  0,  0),
                             (1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  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,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  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, 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()