def get_all_reactions(rxns_file):
'''
Given a .rxns input file, returns a list of reaction entries.
The return data structure is pretty complex. It's a list of tuples of lists
of dictionaries which values being tuples. Example return:
[
(15, {'reactants': [(1, 'H'), (2, 'O')], 'products': [(3, 'H2O')]}),
(15, {'reactants': ..., 'products': ...}),
(30, {'reactants': [(10, 'H'), (12, 'O')], 'products': [(13, 'H2O')]}),
(30, {'reactants': ..., 'products': ...}),
etc.,
]
'''
reactions = Reactions_Wrapper()
reactions.load(rxns_file)
all_reactions = []
for each_iteration_reactions in reactions:
if each_iteration_reactions != []:
for each_reaction in each_iteration_reactions:
all_reactions.append(
(reactions.iteration, each_reaction)
)
return all_reactions
def get_all_reactions(rxns_file):
"""
Given a .rxns input file, returns a list of reaction entries.
The return data structure is pretty complex. It's a list of tuples of lists
of dictionaries which values being tuples. Example return:
[
(15, {'reactants': [(1, 'H'), (2, 'O')], 'products': [(3, 'H2O')]}),
(15, {'reactants': ..., 'products': ...}),
(30, {'reactants': [(10, 'H'), (12, 'O')], 'products': [(13, 'H2O')]}),
(30, {'reactants': ..., 'products': ...}),
etc.,
]
"""
reactions = Reactions_Wrapper()
reactions.load(rxns_file)
all_reactions = []
for each_iteration_reactions in reactions:
if each_iteration_reactions != []:
for each_reaction in each_iteration_reactions:
all_reactions.append((reactions.iteration, each_reaction))
return all_reactions
def __init__(self):
self.reactions_wrapper = Reactions_Wrapper()
pass
class Grouped_Reactions_Wrapper:
#Define some class variables:
f = None #File handle for rxns file
reactions_list = []
grouped_reaction_number = 0
reactions_wrapper = None
def __init__(self):
self.reactions_wrapper = Reactions_Wrapper()
pass
def __iter__(self):
'''We want this to be iterable.'''
return self
def load(self, input_file):
self.f = file(input_file)
self.reset()
def reset(self):
'''
Resets the iterator to the beginning. This is NOT a standard function
for an iterator. It's one I made up.
'''
self.f.seek(0)
#Discard the first two informative lines
self.f.next()
self.f.next()
#Discard the next two blank lines
self.f.next()
self.f.next()
def next(self):
'''
Loads the next iteration of reactions and returns it.
Returns a list of tuples. The first element of the tuple is the
iteration. The second element of the tuple is the reaction (as a
dictionary). The dictionary has keys 'reactants'
and 'products'. The values are tuples with first element being molecule
number, second element being molecule formula.
Sample return:
[
(15, {'reactants': [(1, 'H'), (2, 'O')], 'products': [(3, 'H2O')]}),
(30, {'reactants': ..., 'products': ...}),
etc.
]
'''
f = self.f #Just to simplify things
reactions = []
#Process the grouped reaction number line. Sample line:
#Begin grouped reaction: 0
grouped_reaction_number_regex = re.compile(r'^Begin grouped reaction: (\d+)')
grouped_reaction_number_match = grouped_reaction_number_regex.match(f.next())
if grouped_reaction_number_match:
self.grouped_reaction_number = int(grouped_reaction_number_match.group(1))
#Skip the next line which is just the divider line:
#-------------------------------------------------
f.next()
else:
print 'ERROR: Grouped reaction number line could not be found!'
sys.exit(1)
#Okay, now process all the reactions within this grouped reaction. We
#detect the end of this grouped reaction through the separator:
#----------------------------------
end_grouped_reaction_regex = re.compile(r'^-+')
for line in f:
#Check for end of grouped reaction:
if end_grouped_reaction_regex.match(line):
#Throw out next two lines
f.next()
f.next()
break
#A sample line is like:
#60: HO20Ti10(3) -> HO19Ti10(4) + O(5)
#So we'll split by : first.
split_by_colon = line.split(':')
iteration = split_by_colon[0]
reaction_line = split_by_colon[1]
#Now parse the reaction line
parsed_reaction_line = self.reactions_wrapper.parse_reaction_line(reaction_line)
#Now place this parsed reaction in our mapping data structure:
reactions.append(
(iteration, parsed_reaction_line)
)
return reactions
def __init__(self):
self.reactions_wrapper = Reactions_Wrapper()
pass
class Grouped_Reactions_Wrapper:
#Define some class variables:
f = None #File handle for rxns file
reactions_list = []
grouped_reaction_number = 0
reactions_wrapper = None
def __init__(self):
self.reactions_wrapper = Reactions_Wrapper()
pass
def __iter__(self):
'''We want this to be iterable.'''
return self
def load(self, input_file):
self.f = file(input_file)
self.reset()
def reset(self):
'''
Resets the iterator to the beginning. This is NOT a standard function
for an iterator. It's one I made up.
'''
self.f.seek(0)
#Discard the first two informative lines
self.f.next()
self.f.next()
#Discard the next two blank lines
self.f.next()
self.f.next()
def next(self):
'''
Loads the next iteration of reactions and returns it.
Returns a list of tuples. The first element of the tuple is the
iteration. The second element of the tuple is the reaction (as a
dictionary). The dictionary has keys 'reactants'
and 'products'. The values are tuples with first element being molecule
number, second element being molecule formula.
Sample return:
[
(15, {'reactants': [(1, 'H'), (2, 'O')], 'products': [(3, 'H2O')]}),
(30, {'reactants': ..., 'products': ...}),
etc.
]
'''
f = self.f #Just to simplify things
reactions = []
#Process the grouped reaction number line. Sample line:
#Begin grouped reaction: 0
grouped_reaction_number_regex = re.compile(
r'^Begin grouped reaction: (\d+)')
grouped_reaction_number_match = grouped_reaction_number_regex.match(
f.next())
if grouped_reaction_number_match:
self.grouped_reaction_number = int(
grouped_reaction_number_match.group(1))
#Skip the next line which is just the divider line:
#-------------------------------------------------
f.next()
else:
print 'ERROR: Grouped reaction number line could not be found!'
sys.exit(1)
#Okay, now process all the reactions within this grouped reaction. We
#detect the end of this grouped reaction through the separator:
#----------------------------------
end_grouped_reaction_regex = re.compile(r'^-+')
for line in f:
#Check for end of grouped reaction:
if end_grouped_reaction_regex.match(line):
#Throw out next two lines
f.next()
f.next()
break
#A sample line is like:
#60: HO20Ti10(3) -> HO19Ti10(4) + O(5)
#So we'll split by : first.
split_by_colon = line.split(':')
iteration = split_by_colon[0]
reaction_line = split_by_colon[1]
#Now parse the reaction line
parsed_reaction_line = self.reactions_wrapper.parse_reaction_line(
reaction_line)
#Now place this parsed reaction in our mapping data structure:
reactions.append((iteration, parsed_reaction_line))
return reactions
