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#!/usr/bin/env python
import os, tempfile
from cogent.util.unit_test import TestCase, main
from cogent.parse.pdb import PDBParser
from cogent.app.msms import Msms, surface_xtra
from cogent.struct.selection import einput
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
class MsmsTest(TestCase):
"""Tests for Msms application controller"""
def setUp(self):
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
def test_stdout_input_from_entity(self):
"""Test Stride when input is an entity"""
s = Msms()
res = s(self.input_structure)
self.assertEqual(res['ExitStatus'], 0)
stdout = res['StdOut'].read()
assert stdout.find('1634 spheres 0 collision only, radii 1.600 to 1.850') != -1
assert not res['StdOut'].read()
assert res['ExitStatus'] == 0
assert list(sorted(res.keys())) == list(sorted(['FaceFile', 'StdOut', 'AreaFile', 'StdErr', 'VertFile', 'ExitStatus']))
af = res['AreaFile'].readlines()
assert len(af) == 1635, len(af)
ff = res['FaceFile'].readlines()
assert ff[1].strip() == "#faces #sphere density probe_r"
assert ff[2].strip() == "25310 1634 1.00 1.50" or \
ff[2].strip() == "51712 1634 1.00 1.50"
assert len(ff) == 25313 or len(ff) == 51715
vf = res['VertFile'].readlines()
assert vf[1] == '#vertex #sphere density probe_r\n'
assert vf[2].strip() == '12657 1634 1.00 1.50' or \
vf[2].strip() == '25858 1634 1.00 1.50'
assert len(vf) == 12660 or len(vf) == 25861
res.cleanUp()
def test_surface_xtra(self):
res = surface_xtra(self.input_structure)
assert res.shape == (12658, 3) or res.shape == (25859, 3)
assert res is self.input_structure.xtra['MSMS_SURFACE']
chains = einput(self.input_structure, 'C')
chainA, chainB = chains.sortedvalues()
resA = surface_xtra(chainA)
assert len(resA) == 6223 or len(resA) == 12965
resB = surface_xtra(chainB)
assert len(resB) == 6620 or len(resB) == 13390
assert chainB.xtra['MSMS_SURFACE'] is resB is \
self.input_structure[(0,)][('B',)].xtra['MSMS_SURFACE']
if __name__ == '__main__':
main()
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