1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
|
#!/usr/bin/env python
import os, tempfile
from unittest import main
from cogent.util.unit_test import TestCase
from cogent import FromFilenameStructureParser
from cogent.struct.selection import einput
from cogent.format import xyzrn
__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 XyzrnTest(TestCase):
"""Tests conversion of PDB files into the informal xyzrn format."""
def setUp(self):
self.structure = FromFilenameStructureParser('data/1A1X.pdb')
self.residues = einput(self.structure, 'R')
self.atoms = einput(self.structure, 'A')
self.residue8 = self.residues.values()[8]
self.atom17 = self.atoms.values()[17]
self.atom23 = self.atoms.values()[23]
def test_write_atom(self):
fd, fn = tempfile.mkstemp()
os.close(fd)
handle = open(fn, 'wb')
xyzrn.XYZRNWriter(handle, [self.atom17])
handle.close()
handle = open(fn, 'rb')
coords_radius = [float(n) for n in handle.read().split()[:4]]
self.atom17.setRadius()
radius = self.atom17.getRadius()
self.assertFloatEqualRel(self.atom17.coords, coords_radius[:3])
self.assertFloatEqualRel(radius, coords_radius[3])
if __name__ == '__main__':
main()
|
