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#!/usr/bin/env python
import os
import numpy as np
try:
from cogent.util.unit_test import TestCase, main
from cogent.parse.pdb import PDBParser
from cogent.struct.selection import einput
except ImportError:
from zenpdb.cogent.util.unit_test import TestCase, main
from zenpdb.cogent.parse.pdb import PDBParser
from zenpdb.cogent.struct.selection import einput
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2009, The Cogent Project"
__contributors__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
class asaTest(TestCase):
"""Tests for surface calculations."""
def setUp(self):
self.arr = np.random.random(3000).reshape((1000, 3))
self.point = np.random.random(3)
self.center = np.array([0.5, 0.5, 0.5])
def test_0import(self):
# sort by name
"""tests if can import _contact cython extension."""
global _contact
from cogent.struct import _contact
assert 'cnt_loop' in dir(_contact)
def test_1import(self):
# sort by name
"""tests if can import contact."""
global contact
from cogent.struct import contact
def test_chains(self):
"""compares contacts diff chains"""
self.input_file = os.path.join('data', '1A1X.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure)
self.assertTrue(res == {})
self.input_file = os.path.join('data', '2E12.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure)
self.assertTrue(res)
self.assertFloatEqual(\
res[('2E12', 0, 'B', ('THR', 17, ' '), ('OG1', ' '))]['CONTACTS']\
[('2E12', 0, 'A', ('ALA', 16, ' '), ('CB', ' '))][0], 5.7914192561064004)
def test_symmetry(self):
"""compares contacts diff symmetry mates"""
self.input_file = os.path.join('data', '2E12.pdb') # one chain
self.input_structure = PDBParser(open(self.input_file))
res = contact.contacts_xtra(self.input_structure, \
symmetry_mode='uc',
contact_mode='diff_sym')
self.assertTrue(res)
self.assertFloatEqual(\
res[('2E12', 0, 'B', ('GLU', 77, ' '), ('OE2', ' '))]['CONTACTS']\
[('2E12', 0, 'B', ('GLU', 57, ' '), ('OE2', ' '))][0], \
5.2156557833123873)
def test_crystal(self):
""""compares contacts diff unit-cell-mates"""
pass
if __name__ == '__main__':
main()
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