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#!/usr/bin/env python
import os, tempfile
try:
from cogent.util.unit_test import TestCase, main
from cogent.parse.pdb import PDBParser
from cogent.format.pdb import PDBWriter
from cogent.struct.selection import einput
from cogent.struct.manipulation import copy, clean_ical, \
expand_symmetry, expand_crystal
except ImportError:
from zenpdb.cogent.util.unit_test import TestCase, main
from zenpdb.cogent.parse.pdb import PDBParser
from cogent.format.pdb import PDBWriter
from zenpdb.cogent.struct.selection import einput
from zenpdb.cogent.struct.manipulation import copy, clean_ical, \
exapnd_symmetry, expand_crystal
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
class ManipulationTest(TestCase):
"""tests manipulationg entities"""
def setUp(self):
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
def test_clean_ical(self):
"""tests the clean ical function which cleans structures."""
chainB = self.input_structure.table['C'][('2E12', 0, 'B')]
leu25 = self.input_structure.table['R'][('2E12', 0, 'B', \
('LEU', 25, ' '))]
leu25icA = copy(leu25)
self.assertTrue(leu25icA.parent is None)
self.assertTrue(leu25icA is not leu25)
self.assertTrue(leu25icA[(('N', ' '),)] is not leu25[(('N', ' '),)])
leu25icA.setIc('A')
self.assertEquals(leu25icA.getId(), (('LEU', 25, 'A'),))
chainB.addChild(leu25icA)
self.assertFalse(chainB[(('LEU', 25, 'A'),)] is \
chainB[(('LEU', 25, ' '),)])
self.assertEquals(clean_ical(self.input_structure), \
([], [('2E12', 0, 'B', ('LEU', 25, 'A'))]))
clean_ical(self.input_structure, pretend=False)
self.assertTrue(chainB[(('LEU', 25, 'A'),)] is leu25icA)
self.assertFalse((('LEU', 25, 'A'),) in chainB.keys())
self.assertFalse((('LEU', 25, 'A'),) in chainB)
self.assertTrue((('LEU', 25, 'A'),) in chainB.keys(unmask=True))
self.input_structure.setUnmasked(force=True)
self.assertEquals(clean_ical(self.input_structure), \
([], [('2E12', 0, 'B', ('LEU', 25, 'A'))]))
clean_ical(self.input_structure, pretend=False, mask=False)
self.assertFalse((('LEU', 25, 'A'),) in chainB.keys())
self.assertFalse((('LEU', 25, 'A'),) in chainB)
self.assertFalse((('LEU', 25, 'A'),) in chainB.keys(unmask=True))
def test_0expand_symmetry(self):
"""tests the expansion of a asu to a unit-cell."""
global fn
mh = expand_symmetry(self.input_structure[(0,)])
fd, fn = tempfile.mkstemp('.pdb')
os.close(fd)
fh = open(fn, 'w')
PDBWriter(fh, mh, self.input_structure.raw_header)
fh.close()
def test_1expand_crystal(self):
"""tests the expansion of a unit-cell to a crystal"""
fh = open(fn, 'r')
input_structure = PDBParser(fh)
self.assertTrue(input_structure.values(), 4) # 4 models
sh = expand_crystal(input_structure)
self.assertTrue(len(sh) == 27)
fd, fn2 = tempfile.mkstemp('.pdb')
os.close(fd)
fh = open(fn2, 'w')
a1 = einput(input_structure, 'A')
a2 = einput(sh.values()[3], 'A')
k = a1.values()[99].getFull_id()
name = sh.values()[3].name
a1c = a1[k].coords
a2c = a2[(name,) + k[1:]].coords
self.assertTrue(len(a1), len(a2))
self.assertRaises(AssertionError, self.assertFloatEqual, a1c, a2c)
PDBWriter(fh, sh)
fh.close()
os.unlink(fn)
os.unlink(fn2)
if __name__ == '__main__':
main()
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