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#!/usr/bin/env python
import os
try:
from cogent.util.unit_test import TestCase, main
from cogent.struct.selection import einput
from cogent.parse.pdb import PDBParser
from cogent.parse.stride import stride_parser
from cogent.app.stride import Stride, stride_xtra
except ImportError:
from zenpdb.cogent.util.unit_test import TestCase, main
from zenpdb.cogent.struct.selection import einput
from zenpdb.cogent.parse.pdb import PDBParser
from zenpdb.cogent.parse.stride import stride_parser
from zenpdb.cogent.app.stride import Stride, stride_xtra
__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 StrideParseTest(TestCase):
"""Tests for Stride application controller."""
def setUp(self):
input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(input_file))
stride_app = Stride()
res = stride_app(self.input_structure)
self.lines = res['StdOut'].readlines()
def test_stride_parser(self):
"""tests if output is parsed fully"""
id_xtra = stride_parser(self.lines)
assert len(id_xtra) < len(self.input_structure[(0,)][('A',)]) + \
len(self.input_structure[(0,)][('B',)])
self.input_structure[(0,)][('A',)].remove_hetero()
self.input_structure[(0,)][('B',)].remove_hetero()
assert len(id_xtra) == len(self.input_structure[(0,)][('A',)]) + \
len(self.input_structure[(0,)][('B',)])
def test_stride_xtra(self):
"""tests if residues get annotated with parsed data."""
stride_xtra(self.input_structure)
self.assertEquals(\
self.input_structure[(0,)][('A',)][(('H_HOH', 138, ' '),)].xtra, {})
self.assertAlmostEquals(\
self.input_structure[(0,)][('A',)][(('ILE', 86, ' '),)].xtra['STRIDE_ASA'], 13.9)
self.input_structure[(0,)][('A',)].remove_hetero()
self.input_structure[(0,)][('B',)].remove_hetero()
all_residues = einput(self.input_structure, 'R')
a = all_residues.data_children('STRIDE_ASA', xtra=True, forgiving=False)
if __name__ == '__main__':
main()
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