class Test(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.thisd = os.path.abspath(os.path.dirname(__file__))
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share, 'testfiles')
cls.tests_dir = tempfile.gettempdir()
@unittest.skipUnless(test_funcs.found_exe("gesamt" + ample_util.EXE_EXT), "gesamt exec missing")
def test_gesamt(self):
gesamt_exe = ample_util.find_exe("gesamt" + ample_util.EXE_EXT)
pdb_list = ['1ujbA.pdb', '2a6pA.pdb', '3c7tA.pdb']
models = [os.path.join(self.ample_share, 'examples', 'homologs', 'input', pdb) for pdb in pdb_list]
work_dir = os.path.join(self.tests_dir, "gesamt_test")
alignment_file = align_gesamt(models, gesamt_exe=gesamt_exe, work_dir=work_dir)
self.assertTrue(os.path.isfile(alignment_file))
# TODO: fix this error on Windows...not sure how this arises
try:
shutil.rmtree(work_dir)
except WindowsError:
pass
@unittest.skipUnless(test_funcs.found_exe("mustang" + ample_util.EXE_EXT), "mustang exec missing")
def test_mustang(self):
mustang_exe = ample_util.find_exe("mustang" + ample_util.EXE_EXT)
pdb_list = ['1ujbA.pdb', '2a6pA.pdb', '3c7tA.pdb']
models = [os.path.join(self.ample_share, 'examples', 'homologs', 'input', pdb) for pdb in pdb_list]
work_dir = os.path.join(self.tests_dir, "mustang_test")
alignment_file = align_mustang(models, mustang_exe=mustang_exe, work_dir=work_dir)
self.assertTrue(os.path.isfile(alignment_file))
shutil.rmtree(work_dir)
"""Test functions for python.shelxe"""
import os
import unittest
from ample import constants
from ample.util import ample_util
from ample.util import shelxe
from ample.testing import test_funcs
@unittest.skipUnless(test_funcs.found_exe("shelxe" + ample_util.EXE_EXT),
"shelxe exec missing")
class Test(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.thisd = os.path.abspath(os.path.dirname(__file__))
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share, 'testfiles')
def test_shelxe_1BYZ(self):
shelxe_exe = ample_util.find_exe('shelxe' + ample_util.EXE_EXT)
pdb = os.path.join(self.testfiles_dir, "1BYZ.pdb")
mtz = os.path.join(self.testfiles_dir, "1BYZ-cad.mtz")
mrPdb = os.path.join(
self.testfiles_dir,
"1BYZ_phaser_loc0_ALL_poly_ala_trunc_0.486615_rad_1_UNMOD.1.pdb")
mrinfo = shelxe.MRinfo(shelxe_exe, pdb, mtz)
mrinfo.analyse(mrPdb)
self.assertEqual(mrinfo.originShift, [0.326, 0.19, 0.275])
# Need MRBUMP to be updated
import glob
import os
import shutil
import unittest
from ample import constants
from ample.testing import test_funcs
from ample.util import ample_util, fast_protein_cluster
@unittest.skip("fast_protein_cluster deprecated")
@unittest.skipUnless(
test_funcs.found_exe("fast_protein_cluster" + ample_util.EXE_EXT), "fast_protein_cluster exec missing"
)
class Test(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.thisd = os.path.abspath(os.path.dirname(__file__))
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share, 'testfiles')
cls.fpc_exe = ample_util.find_exe("fast_protein_cluster" + ample_util.EXE_EXT)
def test_fpc_kmeans_rmsd(self):
os.chdir(self.thisd) # Need as otherwise tests that happen in other directories change os.cwd()
mdir = os.path.join(self.testfiles_dir, "models")
models = glob.glob(mdir + os.sep + "*.pdb")
wdir = 'fpc_test'
if not os.path.isdir(wdir):
os.mkdir(wdir)
fpc = fast_protein_cluster.FPC()
num_clusters = 3
class Test_1(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.thisd = os.path.abspath(os.path.dirname(__file__))
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share, 'testfiles')
def test_radius_cctbx(self):
# Test we can reproduce the original thresholds
radius = 8
clusterer = subcluster.CctbxClusterer()
# Only select a few as is very slow
pdb_list = [
os.path.join(self.testfiles_dir, "models", pdb) for pdb in [
'1_S_00000001.pdb', '1_S_00000002.pdb', '1_S_00000003.pdb',
'1_S_00000004.pdb'
]
]
clusterer.generate_distance_matrix(pdb_list)
cluster_files1 = [
os.path.basename(x) for x in clusterer.cluster_by_radius(radius)
]
ref = ['1_S_00000002.pdb', '1_S_00000004.pdb']
self.assertItemsEqual(ref, cluster_files1)
@unittest.skipUnless(test_funcs.found_exe("gesamt" + ample_util.EXE_EXT),
"gesamt exec missing")
def test_gesamt_matrix_generic(self):
# Test we can reproduce the original thresholds
gesamt_exe = ample_util.find_exe("gesamt" + ample_util.EXE_EXT)
clusterer = subcluster.GesamtClusterer(executable=gesamt_exe)
pdb_list = glob.glob(
os.path.join(self.testfiles_dir, "models", '*.pdb'))
clusterer._generate_distance_matrix_generic(pdb_list, purge_all=True)
# Test two files manually
index1 = 2
index2 = 25
f1 = pdb_list[index1]
f2 = pdb_list[index2]
# Run gesamt to get the score between the two
logfile = 'gesamt.log'
ample_util.run_command([gesamt_exe, f1, f2], logfile=logfile)
qscore = None
with open(logfile) as f:
for l in f.readlines():
if l.startswith(' Q-score'):
qscore = float(l.split()[2])
self.assertIsNotNone(qscore, "No q-score found")
# read score matrix
matrix = []
with open(subcluster.SCORE_MATRIX_NAME) as f:
for l in f.readlines():
if not l.strip(): continue
fields = l.split()
matrix.append(
(int(fields[0]), int(fields[1]), float(fields[2])))
# Make sure the score matches
for l in matrix:
if l[0] == index1 and l[1] == index2:
# Gesamt log and out file formats have different precisions
self.assertAlmostEqual(
l[2], qscore, 3,
"Q-scores differ: {0} - {1}".format(l[2], qscore))
os.unlink(logfile)
os.unlink(subcluster.SCORE_MATRIX_NAME)
os.unlink(subcluster.FILE_LIST_NAME)
return
@unittest.skipUnless(test_funcs.found_exe("gesamt" + ample_util.EXE_EXT),
"gesamt exec missing")
def test_radius_gesamt(self):
# Test we can reproduce the original thresholds
gesamt_exe = ample_util.find_exe("gesamt" + ample_util.EXE_EXT)
clusterer = subcluster.GesamtClusterer(executable=gesamt_exe)
pdb_list = glob.glob(
os.path.join(self.testfiles_dir, "models", '*.pdb'))
radius = 4
clusterer.generate_distance_matrix(pdb_list)
cluster_files1 = [
os.path.basename(x) for x in clusterer.cluster_by_radius(radius)
]
ref = [
'1_S_00000002.pdb', '1_S_00000004.pdb', '1_S_00000005.pdb',
'2_S_00000001.pdb', '2_S_00000005.pdb', '3_S_00000003.pdb',
'3_S_00000004.pdb', '3_S_00000006.pdb', '4_S_00000002.pdb',
'4_S_00000005.pdb', '5_S_00000004.pdb', '5_S_00000005.pdb'
]
self.assertItemsEqual(ref, cluster_files1)
#clusterer.dump_pdb_matrix('foo')
return
def test_radius_lsqkab(self):
# Test we can reproduce the original thresholds
clusterer = subcluster.LsqkabClusterer()
pdb_list = glob.glob(
os.path.join(self.testfiles_dir, "models", '*.pdb'))
clusterer.generate_distance_matrix(pdb_list)
clusterer.dump_pdb_matrix('lsqkab.matrix')
os.unlink('lsqkab.matrix')
return
@unittest.skipUnless(
test_funcs.found_exe("maxcluster" + ample_util.EXE_EXT),
"maxcluster exec missing")
def test_radius_maxcluster(self):
# Test we can reproduce the original thresholds
maxcluster_exe = ample_util.find_exe('maxcluster' + ample_util.EXE_EXT)
radius = 4
clusterer = subcluster.MaxClusterer(maxcluster_exe)
pdb_list = glob.glob(
os.path.join(self.testfiles_dir, "models", '*.pdb'))
clusterer.generate_distance_matrix(pdb_list)
cluster_files1 = [
os.path.basename(x) for x in clusterer.cluster_by_radius(radius)
]
ref = [
'4_S_00000003.pdb', '2_S_00000005.pdb', '2_S_00000001.pdb',
'3_S_00000006.pdb', '5_S_00000005.pdb', '3_S_00000003.pdb',
'1_S_00000004.pdb', '4_S_00000005.pdb', '3_S_00000004.pdb',
'1_S_00000002.pdb', '5_S_00000004.pdb', '4_S_00000002.pdb',
'1_S_00000005.pdb'
]
self.assertItemsEqual(ref, cluster_files1)
os.unlink('files.list')
os.unlink('maxcluster.log')
@unittest.skipUnless(
test_funcs.found_exe("maxcluster" + ample_util.EXE_EXT),
"maxcluster exec missing")
def test_cluster_score(self):
maxcluster_exe = ample_util.find_exe('maxcluster' + ample_util.EXE_EXT)
radius = 4
clusterer = subcluster.MaxClusterer(maxcluster_exe)
pdb_list = glob.glob(
os.path.join(self.testfiles_dir, "models", '*.pdb'))
clusterer.generate_distance_matrix(pdb_list)
clusterer.cluster_by_radius(radius)
variance = clusterer.cluster_score
ref = 4.748
self.assertLessEqual(
abs(ref - variance), 0.001,
"Incorrect variance: {0} -> {1}".format(variance, ref))
"""Test functions for python.shelxe"""
import os
import unittest
from ample import constants
from ample.util import ample_util
from ample.util import shelxe
from ample.testing import test_funcs
@unittest.skipUnless(test_funcs.found_exe("shelxe" + ample_util.EXE_EXT), "shelxe exec missing")
class Test(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.thisd = os.path.abspath( os.path.dirname( __file__ ) )
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share,'testfiles')
def test_shelxe_1BYZ(self):
shelxe_exe = ample_util.find_exe('shelxe' + ample_util.EXE_EXT)
pdb = os.path.join(self.testfiles_dir, "1BYZ.pdb")
mtz = os.path.join(self.testfiles_dir, "1BYZ-cad.mtz")
mrPdb = os.path.join(self.testfiles_dir,
"1BYZ_phaser_loc0_ALL_poly_ala_trunc_0.486615_rad_1_UNMOD.1.pdb")
mrinfo = shelxe.MRinfo(shelxe_exe, pdb, mtz)
mrinfo.analyse(mrPdb, cleanup=True)
self.assertEqual(mrinfo.originShift,[0.326, 0.19, 0.275])
# Need MRBUMP to be updated
#self.assertEqual(mrinfo.MPE,78.5)
self.assertEqual(mrinfo.wMPE,74.5)
import glob
import os
import shutil
import sys
import tempfile
import unittest
from ample import constants
from ample.util import ample_util
from ample.util import pdb_edit
from ample.util import theseus
from ample.testing import test_funcs
@unittest.skipUnless(test_funcs.found_exe("theseus" + ample_util.EXE_EXT),
"theseus not found")
class Test(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share, 'testfiles')
cls.tests_dir = tempfile.gettempdir()
cls.theseus_exe = ample_util.find_exe("theseus" + ample_util.EXE_EXT)
def test_align_models(self):
## BUG - hlfsimko
# CAUSES PROBLEMS ON MAC BECAUSE OF SYM LINK IN root on Mac OS X
tests_dir = os.environ["HOMEPATH"] if sys.platform.startswith("win") \
else os.environ["HOME"]
work_dir = os.path.join(tests_dir, 'theseus_align')
models = glob.glob(os.path.join(self.testfiles_dir, 'models', '*.pdb'))
import glob
import os
import shutil
import tempfile
import unittest
from ample import constants
from ample.testing import test_funcs
from ample.util import ample_util
from ample.util import spicker
@unittest.skip("unreliable test cases")
@unittest.skipUnless(test_funcs.found_exe("spicker" + ample_util.EXE_EXT), "spicker exec missing")
class Test(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.thisd = os.path.abspath( os.path.dirname( __file__ ) )
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share, 'testfiles')
cls.tests_dir = tempfile.gettempdir()
cls.spicker_exe = ample_util.find_exe('spicker' + ample_util.EXE_EXT)
def test_spicker(self):
mdir = os.path.join(self.testfiles_dir, "models")
models = glob.glob(mdir + os.sep + "*.pdb")
work_dir = os.path.join(self.tests_dir, "spicker")
if os.path.isdir(work_dir): shutil.rmtree(work_dir)
os.mkdir(work_dir)
spickerer = spicker.Spickerer(spicker_exe=self.spicker_exe)
import glob
import os
import shutil
import unittest
from ample import constants
from ample.testing import test_funcs
from ample.util import ample_util
from ample.util import fast_protein_cluster
@unittest.skip("fast_protein_cluster deprecated")
@unittest.skipUnless(test_funcs.found_exe("fast_protein_cluster" + ample_util.EXE_EXT), "fast_protein_cluster exec missing")
class Test(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.thisd = os.path.abspath( os.path.dirname( __file__ ) )
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share,'testfiles')
cls.fpc_exe = ample_util.find_exe("fast_protein_cluster" + ample_util.EXE_EXT)
def test_fpc_kmeans_rmsd(self):
os.chdir(self.thisd) # Need as otherwise tests that happen in other directories change os.cwd()
mdir=os.path.join(self.testfiles_dir,"models")
models=glob.glob(mdir+os.sep+"*.pdb")
wdir='fpc_test'
if not os.path.isdir(wdir): os.mkdir(wdir)
fpc=fast_protein_cluster.FPC()
num_clusters=3
score_type='rmsd'
"""Test functions for util.tm_util"""
import unittest
from ample.testing import test_funcs
from ample.util import ample_util, tm_util
@unittest.skipUnless(test_funcs.found_exe("TMscore" + ample_util.EXE_EXT), "TMscore exec missing")
class TestTM(unittest.TestCase):
def test_gaps_1(self):
gaps = tm_util.TMscore("TMscore", wdir=".")._find_gaps("AAAA---AA--AA")
ref_gaps = [False, False, False, False, True, True, True, False, False, True, True, False, False]
self.assertEqual(ref_gaps, gaps)
def test_gaps_2(self):
gaps = tm_util.TMscore("TMscore", wdir=".")._find_gaps("---AA--AA")
ref_gaps = [True, True, True, False, False, True, True, False, False]
self.assertEqual(ref_gaps, gaps)
def test_gaps_3(self):
gaps = tm_util.TMscore("TMscore", wdir=".")._find_gaps("-AAA--")
ref_gaps = [True, False, False, False, True, True]
self.assertEqual(ref_gaps, gaps)
if __name__ == "__main__":
unittest.main()
@unittest.skipUnless(test_funcs.found_exe("maxcluster" + ample_util.EXE_EXT), "maxcluster exec missing")
def test_cluster_score(self):
maxcluster_exe = ample_util.find_exe('maxcluster' + ample_util.EXE_EXT)
radius = 4
clusterer = subcluster.MaxClusterer(maxcluster_exe)
pdb_list = glob.glob(os.path.join(self.testfiles_dir, "models",'*.pdb'))
clusterer.generate_distance_matrix(pdb_list)
clusterer.cluster_by_radius(radius)
variance = clusterer.cluster_score
ref = 4.748
self.assertLessEqual(abs(ref-variance), 0.001, "Incorrect variance: {0} -> {1}".format(variance, ref))
@unittest.skipUnless(test_funcs.found_exe("fast_protein_cluster" + ample_util.EXE_EXT), "fast_protein_cluster exec missing")
class Test_2(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.thisd = os.path.abspath( os.path.dirname( __file__ ))
cls.ample_share = constants.SHARE_DIR
cls.testfiles_dir = os.path.join(cls.ample_share, 'testfiles')
cls.fpc_exe = ample_util.find_exe("fast_protein_cluster" + ample_util.EXE_EXT)
def test_indices_fpc(self):
# Test we can reproduce the original thresholds
radius = 4
clusterer = subcluster.FpcClusterer(self.fpc_exe)
pdb_list = glob.glob(os.path.join(self.testfiles_dir, "models",'*.pdb'))
clusterer.generate_distance_matrix(pdb_list)