#!/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 2007-2012, The Cogent Project" __contributors__ = ["Marcin Cieslik"] __license__ = "GPL" __version__ = "1.5.3" __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_uc2(self): self.input_file = os.path.join('data', '1LJO.pdb') self.input_structure = PDBParser(open(self.input_file)) asa.asa_xtra(self.input_structure, symmetry_mode='uc', 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[('1LJO', 0, 'A', ('ARG', 65, ' '))] r2 = residues[('1LJO', 0, 'A', ('ASN', 46, ' '))] self.assertFloatEqual(r1.xtra.values(), [128.94081270529105, 22.807700865674093]) self.assertFloatEqual(r2.xtra.values(), [115.35738419425566, 115.35738419425566]) 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()