def test_format_table5(self):
"""Test 5 of the lib.text.table.format_table() function - no headings."""
# The table data.
contents = [['A', 2], ['B', True]]
# Create the table.
table = format_table(contents=contents)
table_lines = table.split('\n')
# The true table.
true_table = [
" __________ ",
" ",
" A 2 ",
" B True ",
" __________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def test_format_table4(self):
"""Test 4 of the lib.text.table.format_table() function."""
# The table data.
headings = [
[None, 'Long text span test', MULTI_COL, MULTI_COL],
['Column 1', 'Column 2', 'Column 3', 'Column 4']
]
contents = [
['A', 2, 3.4561234124, [1, 2.0]],
['B', 2, 4.567745674, 1e-6]
]
# Create the table.
table = format_table(headings=headings, contents=contents, spacing=True, custom_format=[None, None, '%.3f', None])
table_lines = table.split('\n')
# The true table.
true_table = [
" ___________________________________________ ",
" ",
" Long text span test ",
" ",
" Column 1 Column 2 Column 3 Column 4 ",
" ___________________________________________ ",
" ",
" A 2 3.456 [1, 2.0] ",
" ",
" B 2 4.568 1e-06 ",
" ___________________________________________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def test_format_table3(self):
"""Test 3 of the lib.text.table.format_table() function."""
# The table data.
headings = [
['', 'Long text span test', MULTI_COL],
['Column 1', 'Column 2', 'Column 3']
]
contents = [
['A', '2', '3.456'],
['B', '2', '4.567']
]
# Create the table.
table = format_table(headings=headings, contents=contents, spacing=True)
table_lines = table.split('\n')
# The true table.
true_table = [
" ________________________________ ",
" ",
" Long text span test ",
" ",
" Column 1 Column 2 Column 3 ",
" ________________________________ ",
" ",
" A 2 3.456 ",
" ",
" B 2 4.567 ",
" ________________________________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def test_format_table4(self):
"""Test 4 of the lib.text.table.format_table() function."""
# The table data.
headings = [[None, 'Long text span test', MULTI_COL, MULTI_COL],
['Column 1', 'Column 2', 'Column 3', 'Column 4']]
contents = [['A', 2, 3.4561234124, [1, 2.0]],
['B', 2, 4.567745674, 1e-6]]
# Create the table.
table = format_table(headings=headings,
contents=contents,
spacing=True,
custom_format=[None, None, '%.3f', None])
table_lines = table.split('\n')
# The true table.
true_table = [
" ___________________________________________ ",
" ",
" Long text span test ",
" ",
" Column 1 Column 2 Column 3 Column 4 ",
" ___________________________________________ ",
" ",
" A 2 3.456 [1, 2.0] ",
" ",
" B 2 4.568 1e-06 ",
" ___________________________________________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def test_format_table2(self):
"""Test 2 of the lib.text.table.format_table() function."""
# The table data.
headings = [
['Column 1', 'Column 2']
]
contents = [
['A', '2'],
['B', '2']
]
# Create the table.
table = format_table(headings=headings, contents=contents, max_width=30, spacing=True, debug=True)
table_lines = table.split('\n')
# The true table.
true_table = [
" _____________________ ",
" ",
" Column 1 Column 2 ",
" _____________________ ",
" ",
" A 2 ",
" ",
" B 2 ",
" _____________________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def test_format_table3(self):
"""Test 3 of the lib.text.table.format_table() function."""
# The table data.
headings = [['', 'Long text span test', MULTI_COL],
['Column 1', 'Column 2', 'Column 3']]
contents = [['A', '2', '3.456'], ['B', '2', '4.567']]
# Create the table.
table = format_table(headings=headings,
contents=contents,
spacing=True)
table_lines = table.split('\n')
# The true table.
true_table = [
" ________________________________ ",
" ",
" Long text span test ",
" ",
" Column 1 Column 2 Column 3 ",
" ________________________________ ",
" ",
" A 2 3.456 ",
" ",
" B 2 4.567 ",
" ________________________________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def create_table(label):
"""Format and return the table as text.
@param label: The unique table label.
@type label: str
@return: The formatted table.
@rtype: str
"""
# Get the table.
table = uf_tables.get_table(label)
# Initialise some variables.
text = ''
num_rows = len(table.cells)
num_cols = len(table.headings)
# Generate and return the table.
return format_table(headings=[table.headings], contents=table.cells, max_width=status.text_width, spacing=table.spacing, debug=status.debug)
def test_format_table6(self):
"""Test 6 of the lib.text.table.format_table() function - no headings."""
# The table data.
headings = [['Model', 'k', 'chi2', 'AIC', 'Average position', MULTI_COL, MULTI_COL, 'Motional eigenframe', MULTI_COL, MULTI_COL, 'Order parameters (deg)', MULTI_COL, MULTI_COL], [None, None, None, None, 'a', 'b', 'g', 'a', 'b/th', 'g/ph', 'thx', 'thy', 'smax']]
contents = [['Rigid', 6, 1611.0583844357488, 1623.0583844357488, 2.7928187044509789, 6.241673451655573, 3.3350126302921255, None, None, None, None, None, None], ['Rotor', 9, 1393.0628812874404, 1411.0628812874404, 2.3720778521835015, 6.2511294411496241, 3.7347870727084764, None, 1.3782156252713658, 5.5998324326753401, None, None, 36.651271107544183], ['Iso cone, torsionless', 9, 1407.9014811061686, 1425.9014811061686, 2.2550248034078395, 6.2368882019396619, 3.891108977360032, None, 0.25090427716293384, 1.590485101074278, 21.287274572663485, None, None], ['Iso cone', 10, 1400.3558737738815, 1420.3558737738815, 2.8146957276396858, 6.2597080483925627, 3.2956149488567879, None, 1.3956123975976844, 5.5817149266639987, 10.300677006193942, None, 32.387495822632452], ['Pseudo ellipse, torsionless', 11, 1386.6214759007082, 1408.6214759007082, 2.6253119819082835, 6.2528446735668872, 3.4989380500907097, 2.692632830571366, 0.43833843941243616, 1.3038063115520346, 33.512494725673051, 15.888178532164503, None], ['Pseudo ellipse', 12, 1378.8893702060313, 1402.8893702060313, 2.7403158840045716, 6.259192518336242, 3.3759530521363121, 6.1651101516049849, 1.3600775439064279, 5.5851511636460813, 13.646328409458231, 0.74265383200964785, 31.027675419200627]]
# Create the table.
table = format_table(headings=headings, contents=contents, custom_format=[None, None, "%.2f", "%.2f", "%.3f", "%.3f", "%.3f", "%.3f", "%.3f", "%.3f", "%.2f", "%.2f", "%.2f"])
table_lines = table.split('\n')
# The true table.
true_table = [
" _______________________________________________________________________________________________________________________________ ",
" ",
" Model k chi2 AIC Average position Motional eigenframe Order parameters (deg) ",
" a b g a b/th g/ph thx thy smax ",
" _______________________________________________________________________________________________________________________________ ",
" ",
" Rigid 6 1611.06 1623.06 2.793 6.242 3.335 ",
" Rotor 9 1393.06 1411.06 2.372 6.251 3.735 1.378 5.600 36.65 ",
" Iso cone, torsionless 9 1407.90 1425.90 2.255 6.237 3.891 0.251 1.590 21.29 ",
" Iso cone 10 1400.36 1420.36 2.815 6.260 3.296 1.396 5.582 10.30 32.39 ",
" Pseudo ellipse, torsionless 11 1386.62 1408.62 2.625 6.253 3.499 2.693 0.438 1.304 33.51 15.89 ",
" Pseudo ellipse 12 1378.89 1402.89 2.740 6.259 3.376 6.165 1.360 5.585 13.65 0.74 31.03 ",
" _______________________________________________________________________________________________________________________________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def test_format_table2(self):
"""Test 2 of the lib.text.table.format_table() function."""
# The table data.
headings = [['Column 1', 'Column 2']]
contents = [['A', '2'], ['B', '2']]
# Create the table.
table = format_table(headings=headings,
contents=contents,
max_width=30,
spacing=True,
debug=True)
table_lines = table.split('\n')
# The true table.
true_table = [
" _____________________ ",
" ",
" Column 1 Column 2 ",
" _____________________ ",
" ",
" A 2 ",
" ",
" B 2 ",
" _____________________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def __repr__(self):
"""The string representation of the object.
Rather than using the standard Python conventions (either the string representation of the value or the "<...desc...>" notation), a rich-formatted description of the object is given.
"""
# Intro.
text = "Interatomic data container list:\n"
# The data.
table = []
for i in range(len(self)):
table.append([
i, self[i]._hash, self[i].spin_id1, self[i].spin_id2,
self[i]._spin_hash1, self[i]._spin_hash2
])
text += format_table(headings=[[
"Index", "Hash", "Spin ID 1", "Spin ID 2", "Spin hash 1",
"Spin hash 2"
]],
contents=table)
return text
def create_table(label):
"""Format and return the table as text.
@param label: The unique table label.
@type label: str
@return: The formatted table.
@rtype: str
"""
# Get the table.
table = uf_tables.get_table(label)
# Initialise some variables.
text = ''
num_rows = len(table.cells)
num_cols = len(table.headings)
# Generate and return the table.
return format_table(headings=[table.headings],
contents=table.cells,
max_width=status.text_width,
spacing=table.spacing,
debug=status.debug)
def test_format_table5(self):
"""Test 5 of the lib.text.table.format_table() function - no headings."""
# The table data.
contents = [
['A', 2],
['B', True]
]
# Create the table.
table = format_table(contents=contents)
table_lines = table.split('\n')
# The true table.
true_table = [
" __________ ",
" ",
" A 2 ",
" B True ",
" __________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def test_format_table6(self):
"""Test 6 of the lib.text.table.format_table() function - no headings."""
# The table data.
headings = [[
'Model', 'k', 'chi2', 'AIC', 'Average position', MULTI_COL,
MULTI_COL, 'Motional eigenframe', MULTI_COL, MULTI_COL,
'Order parameters (deg)', MULTI_COL, MULTI_COL
],
[
None, None, None, None, 'a', 'b', 'g', 'a', 'b/th',
'g/ph', 'thx', 'thy', 'smax'
]]
contents = [
[
'Rigid', 6, 1611.0583844357488, 1623.0583844357488,
2.7928187044509789, 6.241673451655573, 3.3350126302921255,
None, None, None, None, None, None
],
[
'Rotor', 9, 1393.0628812874404, 1411.0628812874404,
2.3720778521835015, 6.2511294411496241, 3.7347870727084764,
None, 1.3782156252713658, 5.5998324326753401, None, None,
36.651271107544183
],
[
'Iso cone, torsionless', 9, 1407.9014811061686,
1425.9014811061686, 2.2550248034078395, 6.2368882019396619,
3.891108977360032, None, 0.25090427716293384,
1.590485101074278, 21.287274572663485, None, None
],
[
'Iso cone', 10, 1400.3558737738815, 1420.3558737738815,
2.8146957276396858, 6.2597080483925627, 3.2956149488567879,
None, 1.3956123975976844, 5.5817149266639987,
10.300677006193942, None, 32.387495822632452
],
[
'Pseudo ellipse, torsionless', 11, 1386.6214759007082,
1408.6214759007082, 2.6253119819082835, 6.2528446735668872,
3.4989380500907097, 2.692632830571366, 0.43833843941243616,
1.3038063115520346, 33.512494725673051, 15.888178532164503,
None
],
[
'Pseudo ellipse', 12, 1378.8893702060313, 1402.8893702060313,
2.7403158840045716, 6.259192518336242, 3.3759530521363121,
6.1651101516049849, 1.3600775439064279, 5.5851511636460813,
13.646328409458231, 0.74265383200964785, 31.027675419200627
]
]
# Create the table.
table = format_table(headings=headings,
contents=contents,
custom_format=[
None, None, "%.2f", "%.2f", "%.3f", "%.3f",
"%.3f", "%.3f", "%.3f", "%.3f", "%.2f",
"%.2f", "%.2f"
])
table_lines = table.split('\n')
# The true table.
true_table = [
" _______________________________________________________________________________________________________________________________ ",
" ",
" Model k chi2 AIC Average position Motional eigenframe Order parameters (deg) ",
" a b g a b/th g/ph thx thy smax ",
" _______________________________________________________________________________________________________________________________ ",
" ",
" Rigid 6 1611.06 1623.06 2.793 6.242 3.335 ",
" Rotor 9 1393.06 1411.06 2.372 6.251 3.735 1.378 5.600 36.65 ",
" Iso cone, torsionless 9 1407.90 1425.90 2.255 6.237 3.891 0.251 1.590 21.29 ",
" Iso cone 10 1400.36 1420.36 2.815 6.260 3.296 1.396 5.582 10.30 32.39 ",
" Pseudo ellipse, torsionless 11 1386.62 1408.62 2.625 6.253 3.499 2.693 0.438 1.304 33.51 15.89 ",
" Pseudo ellipse 12 1378.89 1402.89 2.740 6.259 3.376 6.165 1.360 5.585 13.65 0.74 31.03 ",
" _______________________________________________________________________________________________________________________________ ",
" ",
"" # This is because split combined with a final \n character.
]
# Printout.
print("The formatted table:")
for i in range(len(table_lines)):
print("'%s'" % table_lines[i])
print("\nWhat the table should look like:")
for i in range(len(true_table)):
print("'%s'" % true_table[i])
# Check the table.
self.assertEqual(len(true_table), len(table_lines))
for i in range(len(table_lines)):
self.assertEqual(true_table[i], table_lines[i])
def tensor_info_table(type=None,
tm=None,
Diso=None,
Da=None,
Dpar=None,
Dper=None,
Dratio=None,
Dr=None,
Dx=None,
Dy=None,
Dz=None,
theta=None,
phi=None,
alpha=None,
beta=None,
gamma=None,
fixed=None):
"""Print out details of the diffusion tensor.
@keyword type: The diffusion tensor type - one of 'sphere', 'spheroid', or 'ellipsoid'.
@type type: str
@keyword tm: The isotropic correlation time in seconds.
@type tm: float
@keyword Diso: The isotropic diffusion rate.
@type Diso: float
@keyword Da: The anisotropic component of the tensor.
@type Da: float or None
@keyword Dpar: The parallel component of the spheroidal diffusion tensor.
@type Dpar: float or None
@keyword Dper: The perpendicular component of the spheroidal diffusion tensor.
@type Dper: float or None
@keyword Dratio: The ratio of Dpar and Dper.
@type Dratio: float or None
@keyword Dr: The rhombic component of the diffusion tensor.
@type Dr: float or None
@keyword Dx: The x component of the ellipsoid.
@type Dx: float or None
@keyword Dy: The y component of the ellipsoid.
@type Dy: float or None
@keyword Dz: The z component of the ellipsoid.
@type Dz: float or None
@keyword theta: The azimuthal angle in radians.
@type theta: float or None
@keyword phi: The polar angle in radians.
@type phi: float or None
@keyword alpha: The Euler angle alpha in radians using the z-y-z convention.
@type alpha: float or None
@keyword beta: The Euler angle beta in radians using the z-y-z convention.
@type beta: float or None
@keyword gamma: The Euler angle gamma in radians using the z-y-z convention.
@type gamma: float or None
"""
# Build the data for a table.
contents = [["Diffusion type", type]]
contents.append(["tm (s)", tm])
contents.append(["Diso (rad/s)", Diso])
if Da != None:
contents.append(["Da (rad/s)", Da])
if Dpar != None:
contents.append(["Dpar (rad/s)", Dpar])
if Dper != None:
contents.append(["Dper (rad/s)", Dper])
if Dratio != None:
contents.append(["Dratio", Dratio])
if Dr != None:
contents.append(["Dr", Dr])
if Dx != None:
contents.append(["Dx (rad/s)", Dx])
if Dy != None:
contents.append(["Dy (rad/s)", Dy])
if Dz != None:
contents.append(["Dz (rad/s)", Dz])
if theta != None:
contents.append(["theta (rad)", theta])
if phi != None:
contents.append(["phi (rad)", phi])
if alpha != None:
contents.append(["alpha (rad)", alpha])
if beta != None:
contents.append(["beta (rad)", beta])
if gamma != None:
contents.append(["gamma (rad)", gamma])
if fixed != None:
contents.append(["Fixed flag", fixed])
# Print out the table.
print(format_table(contents=contents))
def tensor_info_table(type=None, tm=None, Diso=None, Da=None, Dpar=None, Dper=None, Dratio=None, Dr=None, Dx=None, Dy=None, Dz=None, theta=None, phi=None, alpha=None, beta=None, gamma=None, fixed=None):
"""Print out details of the diffusion tensor.
@keyword type: The diffusion tensor type - one of 'sphere', 'spheroid', or 'ellipsoid'.
@type type: str
@keyword tm: The isotropic correlation time in seconds.
@type tm: float
@keyword Diso: The isotropic diffusion rate.
@type Diso: float
@keyword Da: The anisotropic component of the tensor.
@type Da: float or None
@keyword Dpar: The parallel component of the spheroidal diffusion tensor.
@type Dpar: float or None
@keyword Dper: The perpendicular component of the spheroidal diffusion tensor.
@type Dper: float or None
@keyword Dratio: The ratio of Dpar and Dper.
@type Dratio: float or None
@keyword Dr: The rhombic component of the diffusion tensor.
@type Dr: float or None
@keyword Dx: The x component of the ellipsoid.
@type Dx: float or None
@keyword Dy: The y component of the ellipsoid.
@type Dy: float or None
@keyword Dz: The z component of the ellipsoid.
@type Dz: float or None
@keyword theta: The azimuthal angle in radians.
@type theta: float or None
@keyword phi: The polar angle in radians.
@type phi: float or None
@keyword alpha: The Euler angle alpha in radians using the z-y-z convention.
@type alpha: float or None
@keyword beta: The Euler angle beta in radians using the z-y-z convention.
@type beta: float or None
@keyword gamma: The Euler angle gamma in radians using the z-y-z convention.
@type gamma: float or None
"""
# Build the data for a table.
contents = [["Diffusion type", type]]
contents.append(["tm (s)", tm])
contents.append(["Diso (rad/s)", Diso])
if Da != None:
contents.append(["Da (rad/s)", Da])
if Dpar != None:
contents.append(["Dpar (rad/s)", Dpar])
if Dper != None:
contents.append(["Dper (rad/s)", Dper])
if Dratio != None:
contents.append(["Dratio", Dratio])
if Dr != None:
contents.append(["Dr", Dr])
if Dx != None:
contents.append(["Dx (rad/s)", Dx])
if Dy != None:
contents.append(["Dy (rad/s)", Dy])
if Dz != None:
contents.append(["Dz (rad/s)", Dz])
if theta != None:
contents.append(["theta (rad)", theta])
if phi != None:
contents.append(["phi (rad)", phi])
if alpha != None:
contents.append(["alpha (rad)", alpha])
if beta != None:
contents.append(["beta (rad)", beta])
if gamma != None:
contents.append(["gamma (rad)", gamma])
if fixed != None:
contents.append(["Fixed flag", fixed])
# Print out the table.
print(format_table(contents=contents))