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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.annotation import xtradata
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.annotation import xtradata
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 AnnotationTest(TestCase):
"""tests if annotation get into xtra."""
def setUp(self):
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
def test_xtradata(self):
"""tests if an full_id's in the data dict are correctly parsed."""
structure = einput(self.input_structure, 'S')[('2E12',)]
model = einput(self.input_structure, 'M')[('2E12', 0)]
chain = einput(self.input_structure, 'C')[('2E12', 0, 'B')]
residue = einput(self.input_structure, 'R')[('2E12', 0, 'B', ('LEU', 24, ' '))]
atom = einput(self.input_structure, 'A')[('2E12', 0, 'B', ('LEU', 24, ' '), ('CD1', ' '))]
data_model = {(None, 0):{'model':1}}
xtradata(data_model, structure)
self.assertEquals(model.xtra, {'model': 1})
data_chain = {(None, None, 'B'):{'chain':1}}
xtradata(data_chain, model)
self.assertEquals(chain.xtra, {'chain': 1})
data_chain = {(None, 0, 'B'):{'chain': 2}}
xtradata(data_chain, structure)
self.assertEquals(chain.xtra['chain'], 2)
data_residue = {(None, None, 'B', ('LEU', 24, ' ')):{'residue':1}}
xtradata(data_residue, model)
self.assertEquals(residue.xtra, {'residue': 1})
data_residue = {(None, 0, 'B', ('LEU', 24, ' ')):{'residue':2}}
xtradata(data_residue, structure)
self.assertEquals(residue.xtra, {'residue': 2})
if __name__ == '__main__':
main()
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