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 = sasmol.SasMol(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 test_1CRN(self):
'''
test a dcd based on a small protein (crambin)
'''
#
pdbFileName = DataPath+'1CRN.pdb'
dcdFileName = moduleDataPath+'test-results/1CRN-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 = sasmol.SasMol(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n',result_coor
os.remove(dcdFileName)
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_frame3(self):
'''
test a dcd with 3 frames based on a 2-aa pdb
write the 3rd frame
'''
#
pdbFileName = DataPath+'2AAD-1to3.pdb'
dcdFileName = moduleDataPath+'test-results/2AAD-1to3-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 2
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 = sasmol.SasMol(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(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 = 1095.772
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 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 = s.SasMol(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 test_rna(self):
'''
test a dcd with 1 frame based on a rna molecule
'''
#
pdbFile = pdbDataPath + 'rna.pdb'
dcdFile = moduleDataPath + 'test-results/rna-writedcdframes.dcd'
start = 0
end = 1
self.o.read_pdb(pdbFile)
self.o.write_dcd_frames(dcdFile, start, end)
o1 = sasmol.SasMol(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), 1)
self.assertEqual(len(result_coor[0]), 10632)
expected_sample_coor = numpy.array([-35.960, 48.536, 72.994],
floattype)
sum_expected_coor = 59505.827
self.assert_list_almost_equal(expected_sample_coor,
result_coor[0][10631], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
def test_1KP8(self):
'''
test a dcd based on a large pdb complex (groel)
'''
#
pdbFileName = DataPath+'1KP8.pdb'
dcdFileName = moduleDataPath+'test-results/1KP8-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 = sasmol.SasMol(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]),57085)
expected_sample_coor = numpy.array([104.484, 26.915, 12.538],floattype)
sum_expected_coor = 6269170.260
self.assert_list_almost_equal(expected_sample_coor,result_coor[0][100], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def test_1ATM_frame2(self):
'''
test a dcd with 2 frames based on a 1-atom pdb
write the 2nd frame
'''
#
pdbFileName = DataPath+'1ATM-1to2.pdb'
dcdFileName = moduleDataPath+'test-results/1ATM-1to2-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 1
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 = sasmol.SasMol(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
expected_coor = numpy.array([[[73.944, 38.799, 41.652]]],floattype)
sum_expected_coor = 154.395
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 test_rna_frame1to10(self):
'''
test a dcd with 10 frames based on a rna molecule
'''
#
pdbFile = pdbDataPath + 'rna-1to10.pdb'
dcdFile = moduleDataPath + 'test-results/rna-1to10-writedcdframes.dcd'
start = 0
end = 10
self.o.read_pdb(pdbFile)
self.o.write_dcd_frames(dcdFile, start, end)
o1 = sasmol.SasMol(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), 10)
self.assertEqual(len(result_coor[9]), 10632)
expected_sample_coor = numpy.array([-6.392, 14.348, 20.914], floattype)
sum_expected_coor = -430804.378
self.assert_list_almost_equal(expected_sample_coor,
result_coor[9][10631], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
def test_1ATM_3(self):
'''
test a dcd with 2 frames based on a 1-atom pdb and write all frames
'''
#
pdbFile = pdbDataPath + '1ATM-1to2.pdb'
dcdFile = moduleDataPath + 'test-results/1ATM-1to2-writedcdframes.dcd'
start = 0
end = 2
self.o.read_pdb(pdbFile)
self.o.write_dcd_frames(dcdFile, start, end)
o1 = sasmol.SasMol(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)
#
expected_coor = numpy.array(
[[[76.944, 41.799, 41.652]], [[73.944, 38.799, 41.652]]],
floattype)
sum_expected_coor = 314.790
print '\nexpected_coor \n', expected_coor
#
self.assert_list_almost_equal(expected_coor, result_coor, self.prcsn)
self.assertAlmostEqual(sum_expected_coor, sum_result_coor, self.prcsn)
def test_2AAD(self):
'''
test a dcd with 3 frames based on a 2-aa pdb
'''
#
pdbFile = pdbDataPath + '2AAD-1to3.pdb'
dcdFile = moduleDataPath + 'test-results/2AAD-1to3-writedcdframes.dcd'
start = 0
end = 3
self.o.read_pdb(pdbFile)
self.o.write_dcd_frames(dcdFile, start, end)
o1 = sasmol.SasMol(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)
#
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]],\
[[ -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]],\
[[ 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 = 3644.294
print '\nexpected_coor \n', expected_coor
#
self.assert_list_almost_equal(expected_coor, result_coor, self.prcsn)
self.assertAlmostEqual(sum_expected_coor, sum_result_coor, self.prcsn)
def test_1KP8(self):
'''
test a dcd from a protein complex of greol
'''
#
pdbFile = pdbDataPath + '1KP8.pdb'
dcdFile = moduleDataPath + 'test-results/1KP8-writedcdframes.dcd'
start = 0
end = 1
self.o.read_pdb(pdbFile)
self.o.write_dcd_frames(dcdFile, start, end)
o1 = sasmol.SasMol(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]), 57085)
expected_sample_coor = numpy.array([104.484, 26.915, 12.538],
floattype)
sum_expected_coor = 6269170.260
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_pass(self):
'''
test corr bypass since there is nothing here
'''
#
id = 3
o = sasmol.SasMol(id)
o.molcharge()
def test_find_u_rotate_pdb(self):
m1 = sasmol.SasMol(0)
m2 = sasmol.SasMol(1)
m1.read_pdb(PdbPath + "1CRN.pdb")
m2.read_pdb(modulePdbPath + "1CRN-rot.pdb")
coor_sub_m1 = m1.coor()[0]
coor_sub_m2 = m2.coor()[0]
u = sasmath.find_u(coor_sub_m1, coor_sub_m2)
result = numpy.array(
(numpy.matrix(u) * (numpy.matrix(coor_sub_m2).T)).T, numpy.float)
#print numpy.dot(result.reshape(1,-1)[0],coor_sub_m1.reshape(1,-1)[0])/numpy.sqrt(numpy.dot(coor_sub_m1.reshape(1,-1)[0],coor_sub_m1.reshape(1,-1)[0])*numpy.dot(result.reshape(1,-1)[0],result.reshape(1,-1)[0]))
#m3 = sasmol.SasMol(2)
#m3.read_pdb('1CRN.pdb')
#m3._coor[0,:]=result
#m3.writepdb('1CRN-result.pdb',0,'w')
self.assertEqual(len(result), len(coor_sub_m1))
for i in range(len(coor_sub_m1)):
self.assert_list_almost_equal(list(result[i]), coor_sub_m1[i])
def setUp(self):
self.centertmp = sasop.Move.center
self.m = Mocker()
sasop.Move.center = self.m.mock()
sasop.Move.center(ARGS)
self.m.result(None)
self.m.count(0, None)
self.m.replay()
self.o = sasmol.SasMol(0)
def setUp(self):
self.m = Mocker()
self.back_masscheck = sasop.Move.masscheck
sasop.Move.masscheck = self.m.mock()
sasop.Move.masscheck(ARGS)
self.m.result(None)
self.m.count(0, None)
self.m.replay()
self.o = sasmol.SasMol(0)
def split_dcd(pdb_full_name, dcd_full_name, n_cpus, starting_dir):
mol = sasmol.SasMol(0)
mol.read_pdb(pdb_full_name)
dcd_file = mol.open_dcd_read(dcd_full_name)
total_frames = dcd_file[2]
n_atoms = dcd_file[1]
_, copy_mask = mol.get_subset_mask('all')
n_frames_sub = np.array([total_frames / n_cpus] * n_cpus, dtype=int)
n_frames_sub[:total_frames % n_cpus] += 1
last_frame = 0
sub_dirs = []
sub_dcd_names = []
first_last = []
for cpu in xrange(1, n_cpus + 1):
sub_dir = op.join(starting_dir, 'sub%s' % str(cpu).zfill(2))
sub_dirs.append(sub_dir)
mkdir_p(sub_dir)
sub_mol = sasmol.SasMol(0)
mol.copy_molecule_using_mask(sub_mol, copy_mask, 0)
with cd(sub_dir):
dcd_out_name = 'sub%s.dcd' % str(cpu).zfill(2)
sub_dcd_names.append(dcd_out_name)
first = last_frame
last = last_frame + n_frames_sub[cpu - 1]
dcd_out_file = sub_mol.open_dcd_write(dcd_out_name)
for (i, frame) in enumerate(xrange(first, last)):
sub_mol.read_dcd_step(dcd_file, frame)
sub_mol.write_dcd_step(dcd_out_file, 0, i + 1)
sub_mol.close_dcd_write(dcd_out_file)
first_last.append([first, last])
last_frame += n_frames_sub[cpu - 1]
return sub_dirs, sub_dcd_names, first_last
def test_id(self):
'''
test initializer with id
'''
#
id = 3
o = sasmol.SasMol(id)
self.assertEqual(o.id(), id)
self.assertEqual(o.totalmass(), 0.0)
self.assertEqual(o.natoms(), 0)
self.assertEqual(o.mass(), None)
self.assertEqual(o.coor(), None)
self.assertEqual(o.com(), None)
self.assertEqual(o.name(), 'Mol_None')
def get_dna_bp_and_axes(bp_mask,
dna_ids,
dna_mol,
bp_mol=None,
dna_id_type='segname'):
if not bp_mol:
bp_mol = sasmol.SasMol(0)
error = dna_mol.copy_molecule_using_mask(bp_mol, bp_mask, 0)
else:
error, bp_coor = dna_mol.get_coor_using_mask(0, bp_mask)
bp_mol.setCoor(bp_coor)
bp_origin, bp_axes = get_dna_bp_reference_frame(dna_ids, bp_mol,
dna_id_type)
return bp_origin, bp_axes, bp_mol
def calculate_pr(pdbfile, dcdfile, input_nbins, bin_width):
m = sasmol.SasMol(0)
m.read_pdb(pdbfile)
nbins = get_number_of_bins_from_structure(m, input_nbins)
print 'nbins = ', nbins
m.read_dcd(dcdfile)
nf = m.number_of_frames()
print 'nf = ', nf
coor = m.coor()
print 'coor[0][0] = ', coor[0][0]
print 'coor[0][-1] = ', coor[0][-1]
natoms = m.natoms()
print 'natoms = ', natoms
if flag:
npairs = (natoms * (natoms - 1)) / 2
all_distances = numpy.zeros(npairs, numpy.float32)
for i in xrange(nf):
distances = prc.prc(coor[i])
all_distances += numpy.array(distances)
if i == 0:
print 'one_distance[0] = ', distances[0]
print '.',
print 'all_distances[0] = ', all_distances[0] / nf
print 'calling pr_parallel'
print 'python: coor[0][0][0] = ', coor[0][0][0]
dist = pr_parallel.pr_parallel(coor, nf, natoms, nbins, bin_width)
print '\nback in python\n\n'
outfile = open('dist.txt', 'w')
for val in dist:
outfile.write('%f\n' % val)
outfile.close()
def read_pdb_prep_pair(prep_filename, pdb_filename):
"""
Load structure, topology and naming information from PDB and atomic
charges from antechamber ac file.
Args:
prep_filename (str): Path to the library (prep) file
pdb_filename (str): Path to the PDB containing atomic coordinates
and names
Returns:
amber_utils.AmberPrep: Information derived from prep file
sasmol.SasMol: Information read from PDB file
"""
prep = AmberPrep(prep_filename)
structure = sasmol.SasMol(0)
structure.read_pdb(pdb_filename)
structure.setFilename(pdb_filename)
if len(structure.resnames()) != 1:
raise Exception("More than one residue in PDB: {0:s}".format(pdb_filename))
# Sometimes building ligands files end up with inconsistent atom name
# capitilization - we will upper case everything
upper_names = []
structure_names = structure.name()
for idx in range(structure.natoms()):
upper_names.append(structure_names[idx].upper())
structure.setName(upper_names)
invalid = check_prep_structure_consistency(prep, structure)
if invalid:
raise Exception(invalid)
return prep, structure
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 = sasmol.SasMol(0)
mol.read_pdb(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(os.path.join(in_dir, full_dcd_fname))
n_frames = dcd_file[2]
out_prefix = dcd_fname[:-4]
else:
n_frame = 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()
for i in xrange(n_frames):
mol.read_dcd_step(dcd_file, i)
pr = calc_pr_python(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
logging.info('calculated P(r) for {} structures in {} s'.format(
n_frames, toc))
logging.info('{} s for each structure'.format(toc / n_frames))
mol.close_dcd_read(dcd_file[0])
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 = sasmol.SasMol(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 split_dcd_to_pdbs(pdb_full_fname, dcd_full_fname, starting_dir):
mol = sasmol.SasMol(0)
mol.read_pdb(pdb_full_fname)
dcd_file = mol.open_dcd_read(dcd_full_fname)
total_frames = dcd_file[2]
n_atoms = dcd_file[1]
sub_dirs = []
pdb_out_fname = 'temp_0.pdb'
for i in xrange(total_frames):
sub_dir = op.join(starting_dir, 'sub{}'.format(str(i + 1).zfill(5)))
sub_dirs.append(sub_dir)
mkdir_p(sub_dir)
with cd(sub_dir):
mol.read_dcd_step(dcd_file, 0)
mol.write_pdb(pdb_out_fname, 0, 'w')
return sub_dirs
import sasmol.sasmol as sasmol
# setup the samol object
mol = sasmol.SasMol(0)
out_filename = "dna_sl.txt"
f = open(out_filename, 'w')
atomic = sasmol.sasproperties.Atomic()
dsl = atomic.dna_sl()
for key, item in dsl.items():
print key, item
f.write('%3s' ' ' '%s' '\n' % (key, item))
f.close()
def setUp(self):
self.o = sasmol.SasMol(0)
def setUp(self):
self.o=sasmol.SasMol(0)
self.standard_atomic_weight = self.o.amu()
def setUp(self):
self.o = sasmol.SasMol(0)
self.o_result = sasmol.SasMol(1)
self.o_expected = sasmol.SasMol(2)
def setUp(self):
self.m = Mocker()
self.o=sasmol.SasMol(0)
def setUp(self):
self.o1 = sasmol.SasMol(0)
self.o2 = sasmol.SasMol(1)
self.o3 = sasmol.SasMol(2)
def setUp(self):
self.o = sasmol.SasMol(0)
self.prcsn = 3
