def test_rna_frame1to10_frame10(self):
'''
test a dcd based on a rna molecule of 10 frames
write the 10th frame
'''
#
# #
pdbFileName = DataPath + 'rna-1to10.pdb'
dcdFileName = moduleDataPath + 'test-results/rna-1to10-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 9
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = system.Molecule(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n', result_coor
self.assertEqual(len(result_coor[0]), 10632)
expected_sample_coor = numpy.array([-6.392, 14.348, 20.914], floattype)
sum_expected_coor = -42837.531
self.assert_list_almost_equal(expected_sample_coor,
result_coor[0][10631], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def generate(fin='rna.pdb', fout='rna.dcd', frames=1000):
path = os.path.dirname(os.path.realpath(__file__))
fin = os.path.join(path, '../', 'data', 'pdb_common', fin)
if not os.path.exists(fin):
raise Exception, fin + ' does not exist while generating huge rna dcd files'
return
#fout = os.path.join(path,'../','data','dcd_common',fout)
fout = os.path.join('/tmp/', fout)
if os.path.exists(fout):
return
o = system.Molecule(0)
o.read_pdb(fin)
outfile = dcdio.open_dcd_write(fout)
nset = frames
natoms = o._coor[0, :, 0].shape[0]
istart = 0
nsavc = 1
delta = 1.0
o.write_dcd_header(outfile, frames)
tx = o.coor()[0, :, 0].astype(np.float32)
ty = o.coor()[0, :, 1].astype(np.float32)
tz = o.coor()[0, :, 2].astype(np.float32)
for i in range(frames):
dcdio.write_dcdstep(outfile, tx, ty, tz, i + 1)
o.close_dcd_write(outfile)
def main(pdb_fname, dcd_fname='', in_dir='', out_dir='', restart=False):
'''
calculate the pair-distance distribution
'''
full_pdb_fname = os.path.join(in_dir, pdb_fname)
assert os.path.exists(full_pdb_fname), 'No such file: {}'.format(
full_pdb_fname)
mol = system.Molecule(full_pdb_fname)
if dcd_fname:
full_dcd_fname = os.path.join(in_dir, dcd_fname)
assert os.path.exists(full_dcd_fname), 'No such file: {}'.format(
full_dcd_fname)
dcd_file = mol.open_dcd_read(full_dcd_fname)
n_frames = dcd_file[2]
out_prefix = dcd_fname[:-4]
else:
n_frames = 1
out_prefix = pdb_fname[:-4]
if out_dir:
mkdir_p(out_dir)
out_prefix = os.path.join(out_dir, out_prefix)
tic = time.time()
n_start = 0
if restart:
fnames = glob.glob(os.path.join(out_dir, '*.pr'))
if fnames:
fnames.sort()
n_start = int(fnames[-1].replace('{}_'.format(out_prefix),
'')[:-3])
for i in xrange(n_start):
mol.read_dcd_step(dcd_file, i)
for i in xrange(n_start, n_frames):
mol.read_dcd_step(dcd_file, i)
pr = calc_pr_numba(mol.coor()[0])
# output the result
out_fname = '{}_{:05d}.pr'.format(out_prefix, i + 1)
np.savetxt(out_fname, pr, fmt='%d', delimiter=',')
toc = time.time() - tic
if n_start < n_frames:
logging.info('calculated P(r) for {} structures in {} s'.format(
n_frames - n_start, toc))
logging.info('{} s for each structure'.format(toc /
(n_frames - n_start)))
else:
logging.info('Output already exists. To recalculate, '
'run using `restart=False``')
mol.close_dcd_read(dcd_file[0])
def setUp(self):
self.centertmp = operate.Move.center
self.m = Mocker()
operate.Move.center = self.m.mock()
operate.Move.center(ARGS)
self.m.result(None)
self.m.count(0, None)
self.m.replay()
self.o = system.Molecule(0)
def test_id(self):
'''
test initializer with id
'''
#
id = 3
o = system.Molecule(id)
self.assertEqual(o.id(), id)
self.assertEqual(o.total_mass(), 0.0)
self.assertEqual(o.natoms(), 0)
self.assertEqual(o.mass(), None)
self.assertEqual(o.coor(), None)
self.assertEqual(o.com(), None)
def setUp(self):
self.o = system.Molecule(0)
charmm_names = self.o.charmm_names()
hl = charmm_names['hydrogen']
cl = charmm_names['carbon']
nl = charmm_names['nitrogen']
ol = charmm_names['oxygen']
sl = charmm_names['sulfur']
pl = charmm_names['phosphorus']
otherl = charmm_names['other']
(self.hl, self.cl, self.nl, self.ol, self.sl, self.pl,
self.otherl) = (hl, cl, nl, ol, sl, pl, otherl)
def test_1CRN(self):
'''
test a dcd from a small protein of crambin
'''
#
pdbFile = pdbDataPath + '1CRN.pdb'
dcdFile = moduleDataPath + 'test-results/1CRN-writedcd.dcd'
self.o.read_pdb(pdbFile)
self.o.write_dcd(dcdFile)
o1 = system.Molecule(0)
o1.read_dcd(dcdFile)
result_coor = o1.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n', result_coor, '\nsum of result_coor\n', sum_result_coor
os.remove(dcdFile)
#
self.assertEqual(len(result_coor[0]), 327)
expected_sample_coor = numpy.array([9.555, 2.856, 3.730], floattype)
sum_expected_coor = 8509.587
self.assert_list_almost_equal(expected_sample_coor,
result_coor[0][100], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
def test_2AAD_frame1(self):
'''
test a dcd with 3 frames based on a 2-aa pdb
write the 1st frame
'''
#
pdbFileName = DataPath + '2AAD-1to3.pdb'
dcdFileName = moduleDataPath + 'test-results/2AAD-1to3-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 0
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = system.Molecule(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor\n', result_coor
expected_coor = numpy.array(
[[[73.944, 41.799, 41.652], [74.229, 42.563, 40.456],
[75.667, 43.093, 40.463], [76.264, 43.279, 39.401],
[73.210, 43.734, 40.336], [71.856, 43.168, 39.926],
[73.677, 44.782, 39.354], [70.721, 44.177, 39.946],
[76.231, 43.330, 41.647], [77.592, 43.852, 41.730],
[78.617, 42.820, 42.184], [79.712, 43.169, 42.656],
[77.671, 45.097, 42.648], [77.054, 44.816, 43.910],
[76.970, 46.273, 42.000]]], floattype)
sum_expected_coor = 2407.676
self.assert_list_almost_equal(expected_coor, result_coor, self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def setUp(self):
self.o1 = system.Molecule(0)
self.o2 = system.Molecule(0)
self.o1Sub = system.Molecule(0)
self.o2Sub = system.Molecule(0)
def setUp(self):
self.o = system.Molecule(0)
(self.protein, self.dna, self.rna, self.nucleic,
self.water) = self.o.get_resnames()
def setUp(self):
self.o = system.Molecule(0)
self.amino_acid_sld = self.o.amino_acid_sld()
def setUp(self):
self.o=system.Molecule(0)
self.standard_atomic_weight = self.o.amu()