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#!/usr/bin/env python
import os
import numpy as np
from numpy import sum
from cogent.util.unit_test import TestCase, main
from cogent.app.util import ApplicationNotFoundError
from cogent.parse.pdb import PDBParser
from cogent.struct.selection import einput
from cogent.maths.stats.test import correlation
__author__ = "Marcin Cieslik"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__contributors__ = ["Marcin Cieslik"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Marcin Cieslik"
__email__ = "mpc4p@virginia.edu"
__status__ = "Development"
class DummyFile(object):
def __init__(self, some_string):
self.some_string = some_string
slist = self.some_string.split('\n')
self.some_string_list = [i + '\n' for i in slist]
def readlines(self):
return self.some_string_list
def close(self):
pass
test_file_water = """
HETATM 1185 O HOH 268 141.577 14.676 13.168 1.00 54.76 O
HETATM 1186 O HOH 269 137.019 17.606 19.854 1.00 33.36 O
HETATM 1187 O HOH 270 149.639 55.203 4.611 1.00 49.01 O
HETATM 1188 O HOH 271 156.238 32.191 -4.204 1.00 64.53 O
CONECT 453 685
CONECT 685 453
MASTER 357 0 0 1 10 0 0 6 1187 1 2 12
END
"""
dummy_water = DummyFile(test_file_water)
class asaTest(TestCase):
"""Tests for surface calculations."""
def setUp(self):
self.arr = np.random.random(3000).reshape((1000, 3))
self.point = np.random.random(3)
self.center = np.array([0.5, 0.5, 0.5])
def test_0import(self):
# sort by name
"""tests if can import _asa cython extension."""
global _asa
from cogent.struct import _asa
assert 'asa_loop' in dir(_asa)
def test_1import(self):
# sort by name
"""tests if can import asa."""
global asa
from cogent.struct import asa
def test_asa_loop(self):
"""tests if inner asa_loop (cython) performs correctly"""
self.lcoords = np.array([[-4., 0, 0], [0, 0, 0], [4, 0, 0], [10, 0, 0]])
self.qcoords = np.array([[0., 0, 0], [4., 0, 0]])
self.lradii = np.array([2., 3.])
self.qradii = np.array([3., 2.])
#spoints, np.ndarray[DTYPE_t, ndim =1] box,\
# DTYPE_t probe, unsigned int bucket_size, MAXSYM =200000)
self.spoints = np.array([[1., 0., 0.], [-1., 0., 0.], [0., 1., 0.], \
[0., -1., 0.], [0., 0., 1.], [0., 0., -1.]])
output = _asa.asa_loop(self.qcoords, self.lcoords, self.qradii, \
self.lradii, self.spoints, \
np.array([-100., -100., -100., 100., 100., 100.]), 1., 10)
self.assertFloatEqual(output, np.array([ 75.39822369, 41.88790205]))
def test_asa_xtra(self):
"""test internal asa"""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
self.assertRaises(ValueError, asa.asa_xtra, self.input_structure, mode='a')
result = asa.asa_xtra(self.input_structure)
a = einput(self.input_structure, 'A')
for i in range(len(result)):
self.assertEquals(result.values()[i]['ASA'], a[result.keys()[i]].xtra['ASA'])
r = einput(self.input_structure, 'R')
for water in r.selectChildren('H_HOH', 'eq', 'name').values():
self.assertFalse('ASA' in water.xtra)
for residue in r.selectChildren('H_HOH', 'ne', 'name').values():
for a in residue:
self.assertTrue('ASA' in a.xtra)
result = asa.asa_xtra(self.input_structure, xtra_key='SASA')
for residue in r.selectChildren('H_HOH', 'ne', 'name').values():
for a in residue:
a.xtra['ASA'] == a.xtra['SASA']
def test_asa_xtra_stride(self):
"""test asa via stride"""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
try:
result = asa.asa_xtra(self.input_structure, 'stride')
except ApplicationNotFoundError:
return
self.assertAlmostEqual(self.input_structure[(0,)][('B',)]\
[(('LEU', 35, ' '),)].xtra['STRIDE_ASA'], 17.20)
def test_compare(self):
"""compares internal asa to stride."""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
try:
asa.asa_xtra(self.input_structure, mode='stride')
except ApplicationNotFoundError:
return
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
residues = einput(self.input_structure, 'R')
asa1 = []
asa2 = []
for residue in residues.selectChildren('H_HOH', 'ne', 'name').values():
asa1.append(residue.xtra['ASA'])
asa2.append(residue.xtra['STRIDE_ASA'])
self.assertAlmostEqual(correlation(asa1, asa2)[1], 0.)
def test_uc(self):
"""compares asa within unit cell."""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
asa.asa_xtra(self.input_structure, symmetry_mode='uc', xtra_key='ASA_UC')
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
self.input_structure.propagateData(sum, 'A', 'ASA_UC', xtra=True)
residues = einput(self.input_structure, 'R')
x = residues[('2E12', 0, 'B', ('GLU', 77, ' '))].xtra.values()
self.assertTrue(x[0] != x[1])
def test_crystal(self):
"""compares asa within unit cell."""
self.input_file = os.path.join('data', '2E12.pdb')
self.input_structure = PDBParser(open(self.input_file))
asa.asa_xtra(self.input_structure, symmetry_mode='uc', crystal_mode=2, xtra_key='ASA_XTAL')
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
self.input_structure.propagateData(sum, 'A', 'ASA_XTAL', xtra=True)
residues = einput(self.input_structure, 'R')
r1 = residues[('2E12', 0, 'A', ('ALA', 42, ' '))]
r2 = residues[('2E12', 0, 'A', ('VAL', 8, ' '))]
r3 = residues[('2E12', 0, 'A', ('LEU', 25, ' '))]
self.assertFloatEqual(r1.xtra.values(), \
[32.041070749038823, 32.041070749038823])
self.assertFloatEqual(r3.xtra.values(), \
[0., 0.])
self.assertFloatEqual(r2.xtra.values(), \
[28.873559956056916, 0.0])
def test__prepare_entities(self):
self.input_structure = PDBParser(dummy_water)
self.assertRaises(ValueError, asa._prepare_entities, self.input_structure)
def _test_bio(self):
"""compares asa within a bio unit."""
self.input_file = os.path.join('data', '1A1X.pdb')
self.input_structure = PDBParser(open(self.input_file))
asa.asa_xtra(self.input_structure, symmetry_mode='bio', xtra_key='ASA_BIO')
asa.asa_xtra(self.input_structure)
self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
self.input_structure.propagateData(sum, 'A', 'ASA_BIO', xtra=True)
residues = einput(self.input_structure, 'R')
r1 = residues[('1A1X', 0, 'A', ('GLU', 37, ' '))]
r2 = residues[('1A1X', 0, 'A', ('TRP', 15, ' '))]
self.assertFloatEqual(r1.xtra.values(), \
[20.583191467544726, 78.996394472066541])
self.assertFloatEqual(r2.xtra.values(), \
[136.41436710386989, 136.41436710386989])
if __name__ == '__main__':
main()
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