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#!/usr/bin/env python
import os
try:
from cogent.util.unit_test import TestCase, main
from cogent.parse.pdb import PDBParser
from cogent.struct.selection import einput, select
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, select
__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 AnnotationTest(TestCase):
"""tests selecting entities"""
def setUp(self):
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
def test_einput(self):
"""tests einput."""
structures = einput(self.input_structure, 'S')
models = einput(self.input_structure, 'M')
chains = einput(self.input_structure, 'C')
residues = einput(self.input_structure, 'R')
atoms = einput(self.input_structure, 'A')
self.assertEquals(structures.level, 'H')
self.assertEquals(models.level, 'S')
self.assertEquals(chains.level, 'M')
self.assertEquals(residues.level, 'C')
self.assertEquals(atoms.level, 'R')
atoms2 = einput(models, 'A')
self.assertEquals(atoms, atoms2)
atoms3 = einput(chains, 'A')
self.assertEquals(atoms, atoms3)
structures2 = einput(atoms, 'S')
self.assertEquals(self.input_structure, structures2.values()[0])
residues2 = einput(atoms, 'R')
self.assertEquals(residues, residues2)
def test_select(self):
"""tests select."""
water = select(self.input_structure, 'R', 'H_HOH', 'eq', 'name')
for residue in water:
self.assertTrue(residue.name == 'H_HOH')
non_water = select(self.input_structure, 'R', 'H_HOH', 'ne', 'name')
for residue in non_water:
self.assertTrue(residue.name != 'H_HOH')
if __name__ == '__main__':
main()
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