def test_is_valid_formula_1(self):
input = '(NH3)2'
result = cf.is_valid_formula(input)
expected = True
self.assertEqual(result, expected)
def test_is_valid_formula_14(self):
input = '(3)Na+'
result = cf.is_valid_formula(input)
expected = False
self.assertEqual(result, expected)
def test_is_valid_formula_16(self):
input = 'CH3C(O)CH3'
result = cf.is_valid_formula(input)
expected = True
self.assertEqual(result, expected)
def isValidate_molecular_formula(value):
from pyEQL.chemical_formula import is_valid_formula
if not is_valid_formula(value):
return False
return True
def test_is_valid_formula_12(self):
input = 'Mg)(OH)2'
result = cf.is_valid_formula(input)
expected = False
self.assertEqual(result, expected)
def validate_molecular_formula(value):
if not is_valid_formula(value):
raise ValidationError(_('%(value)s is not a valid molecular formula'),
params={'value': value})
def search_parameters(self,formula):
'''Each time a new solute species is created in a solution, this function:
1) searches to see whether a list of parameters for the species has already been
compiled from the database
2) searches all files in the specified database directory(ies) for the species
3) creates a Parameter object for each value found
4) compiles these objects into a set
5) adds the set to a dictionary indexed by species name (formula)
6) points the new solute object to the dictionary
formula : str
String representing the chemical formula of the species.
'''
# get the hill_order() and is_valid_formula() methods from the chemistry module
import pyEQL.chemical_formula as chem
# if the formula is already in the database, then we've already searched
# and compiled parameters, so there is no need to do it again.
if formula in self.parameters_database:
pass
else:
# add an entry to the parameters database
self.parameters_database[formula] = set()
# search all the files in each database directory
for directory in self.database_dir:
for file in os.listdir(directory):
# reset the line number count
line_num = 0
# ignore the template file
if file == 'template.tsv':
continue
# look at only .csv files
if ".tsv" in file:
# open each file
current_file = open(directory+'/'+file,'r')
# read each line of the file, looking for the formula
try:
for line in current_file:
line_num += 1
try:
# look for keywords in the first column of each file. If found,
# store the entry from the 2nd column
if 'Name' in line:
param_name = _parse_line(line)[1]
elif 'Description' in line:
param_desc = _parse_line(line)[1]
elif 'Unit' in line:
param_unit = _parse_line(line)[1]
elif 'Reference' in line:
param_ref = _parse_line(line)[1]
elif 'Temperature' in line:
param_temp = _parse_line(line)[1]
elif 'Pressure' in line:
param_press = _parse_line(line)[1]
elif 'Ionic Strength' in line:
param_ionic = _parse_line(line)[1]
elif 'Comment' in line:
param_comment = _parse_line(line)[1]
# use the hill_order() function to standardize the
# supplied formula. Then standardize teh formulas in the
# database and see if they match.
# this allows a database entry for 'MgCl2' to be matched
# even if the user enters 'Mg(Cl)2', for example
elif chem.is_valid_formula(_parse_line(line)[0]):
if chem.hill_order(formula) == chem.hill_order(_parse_line(line)[0]):
# if there are multiple columns, pass the values as a list.
# If a single column, then just pass the value
if len(_parse_line(line)) >2:
param_value = _parse_line(line)[1:]
else:
param_value = _parse_line(line)[1]
# Create a new parameter object
parameter = pm.Parameter(param_name,param_value,param_unit, \
reference=param_ref,pressure=param_press,temperature=param_temp,ionic_strength=param_ionic,description=param_desc,comment=param_comment)
# Add the parameter to the set for this species
self.parameters_database[formula].add(parameter)
except ValueError:
logger.warning('Error encountered when reading line %s in %s' % (line_num,file))
continue
# log a warning if an invalid character prevents reading a line
except UnicodeDecodeError:
logger.warning('Invalid character found when reading %s. File skipped.' % file)
current_file.close()
def test_is_valid_formula_9(self):
input = "NaOH"
result = cf.is_valid_formula(input)
expected = True
self.assertEqual(result, expected)
def test_is_valid_formula_15(self):
input = "()"
result = cf.is_valid_formula(input)
expected = False
self.assertEqual(result, expected)
def test_is_valid_formula_3(self):
input = 'Na^+'
result = cf.is_valid_formula(input)
expected = False
self.assertEqual(result,expected)
def isValidate_molecular_formula(value):
if not is_valid_formula(value):
return False
return True
def test_is_valid_formula_1(self):
input = '(NH3)2'
result = cf.is_valid_formula(input)
expected = True
self.assertEqual(result,expected)
def test_is_valid_formula_16(self):
input = 'CH3C(O)CH3'
result = cf.is_valid_formula(input)
expected = True
self.assertEqual(result,expected)
def test_is_valid_formula_12(self):
input = 'Mg)(OH)2'
result = cf.is_valid_formula(input)
expected = False
self.assertEqual(result,expected)
def test_is_valid_formula_2(self):
input = '3CO3-'
result = cf.is_valid_formula(input)
expected = False
self.assertEqual(result, expected)
def test_is_valid_formula_17(self):
input = "CH3(CH)2(CH)2"
result = cf.is_valid_formula(input)
expected = True
self.assertEqual(result, expected)
def search_parameters(self, formula):
'''Each time a new solute species is created in a solution, this function:
1) searches to see whether a list of parameters for the species has already been
compiled from the database
2) searches all files in the specified database directory(ies) for the species
3) creates a Parameter object for each value found
4) compiles these objects into a set
5) adds the set to a dictionary indexed by species name (formula)
6) points the new solute object to the dictionary
formula : str
String representing the chemical formula of the species.
'''
# get the hill_order() and is_valid_formula() methods from the chemistry module
import pyEQL.chemical_formula as chem
# if the formula is already in the database, then we've already searched
# and compiled parameters, so there is no need to do it again.
if formula in self.parameters_database:
pass
else:
# add an entry to the parameters database
self.parameters_database[formula] = set()
# search all the files in each database directory
for directory in self.database_dir:
for file in os.listdir(directory):
# reset the line number count
line_num = 0
# ignore the template file
if file == 'template.tsv':
continue
# look at only .csv files
if ".tsv" in file:
# open each file
current_file = open(directory + '/' + file, 'r')
# read each line of the file, looking for the formula
try:
for line in current_file:
line_num += 1
try:
# look for keywords in the first column of each file. If found,
# store the entry from the 2nd column
if 'Name' in line:
param_name = _parse_line(line)[1]
elif 'Description' in line:
param_desc = _parse_line(line)[1]
elif 'Unit' in line:
param_unit = _parse_line(line)[1]
elif 'Reference' in line:
param_ref = _parse_line(line)[1]
elif 'Temperature' in line:
param_temp = _parse_line(line)[1]
elif 'Pressure' in line:
param_press = _parse_line(line)[1]
elif 'Ionic Strength' in line:
param_ionic = _parse_line(line)[1]
elif 'Comment' in line:
param_comment = _parse_line(line)[1]
# use the hill_order() function to standardize the
# supplied formula. Then standardize teh formulas in the
# database and see if they match.
# this allows a database entry for 'MgCl2' to be matched
# even if the user enters 'Mg(Cl)2', for example
elif chem.is_valid_formula(
_parse_line(line)[0]):
if chem.hill_order(
formula) == chem.hill_order(
_parse_line(line)[0]):
# if there are multiple columns, pass the values as a list.
# If a single column, then just pass the value
if len(_parse_line(line)) > 2:
param_value = _parse_line(
line)[1:]
else:
param_value = _parse_line(
line)[1]
# Create a new parameter object
parameter = pm.Parameter(param_name,param_value,param_unit, \
reference=param_ref,pressure=param_press,temperature=param_temp,ionic_strength=param_ionic,description=param_desc,comment=param_comment)
# Add the parameter to the set for this species
self.parameters_database[
formula].add(parameter)
except ValueError:
logger.warning(
'Error encountered when reading line %s in %s'
% (line_num, file))
continue
# log a warning if an invalid character prevents reading a line
except UnicodeDecodeError:
logger.warning(
'Invalid character found when reading %s. File skipped.'
% file)
current_file.close()
def isValidate_molecular_formula(value):
if not is_valid_formula(value):
return False
return True;
