# Find reactions with different names.
if firstReactions[rxnId]['name'] != secondReactions[rxnId]['name']:
diffNames.add(rxnId)
different.add(rxnId)
# Find reactions with different status.
if firstReactions[rxnId]['status'] != secondReactions[rxnId]['status']:
diffStatus.add(rxnId)
different.add(rxnId)
# Find reactions with different stoichiometry. Convert the dictionaries to a tuple
# so we can use set operations to compare.
firstReactants = set()
firstProducts = set()
reactants, products = helper.parseEquation(firstReactions[rxnId]['equation'])
for index in range(len(reactants)):
cpd = helper.parseCompoundIdStoich(reactants[index])
firstReactants.add( ( cpd['stoich'], cpd['compound'] ) )
for index in range(len(products)):
cpd = helper.parseCompoundIdStoich(products[index])
firstProducts.add( ( cpd['stoich'], cpd['compound'] ) )
secondReactants = set()
secondProducts = set()
reactants, products = helper.parseEquation(secondReactions[rxnId]['equation'])
for index in range(len(reactants)):
cpd = helper.parseCompoundIdStoich(reactants[index])
secondReactants.add( ( cpd['stoich'], cpd['compound'] ) )
for index in range(len(products)):
cpd = helper.parseCompoundIdStoich(products[index])
secondProducts.add( ( cpd['stoich'], cpd['compound'] ) )
# name, abbreviation, formula, defaultCharge, isCofactor
helper = BiochemHelper()
compounds = helper.readCompoundsFile(args.compoundfile,
includeLinenum=False)
for index in range(len(compounds)):
biochem['compounds'].append(compounds[index])
# Add the reactions from the reactions file. Required fields: id, name,
# abbreviation, direction, thermoReversibility, status, defaultProtons, reagents.
reactions = helper.readReactionsFile(args.reactionfile,
includeLinenum=False)
for index in range(len(reactions)):
rxn = reactions[index]
reactants, products = helper.parseEquation(rxn['equation'])
if reactants is None and products is None: # @todo Need to confirm this
continue
rxn['reagents'] = list()
for rindex in range(len(reactants)):
cpd = helper.parseCompoundIdStoich(reactants[rindex])
reagent = dict()
reagent['compound_ref'] = '~/compounds/id/' + cpd['compound']
reagent['compartment_ref'] = '~/compartments/id/' + cpd[
'compartmentId']
reagent['coefficient'] = cpd['stoich'] * -1.0
reagent[
'isCofactor'] = 0 # @todo Is this set separately from value in compound?
rxn['reagents'].append(reagent)
for pindex in range(len(products)):
cpd = helper.parseCompoundIdStoich(products[pindex])
# Check for invalid direction.
if rxn['direction'] != '<' and rxn['direction'] != '>' and rxn['direction'] != '=':
badDirection.append(index)
# Check for unknown or invalid reversibility.
if rxn['reversibility'] == '?':
unknownReversibility.append(index)
elif rxn['reversibility'] != '<' and rxn['reversibility'] != '>' and rxn['reversibility'] != '=':
badReversibility.append(index)
# Check for different equation and code fields.
if rxn['equation'] != rxn['code']:
diffEquationCode.append(index)
# Check for missing reactants and/or products.
reactants, products = helper.parseEquation(rxn['equation'])
if reactants is None and products is None:
noEquation.append(index)
else:
if len(reactants) == 0:
noReactants.append(index)
if len(products) == 0:
noProducts.append(index)
# reactants, products = helper.parseEquation(rxn['definition'])
# if reactants is None and products is None:
# noDefinition.append(index)
# Check reaction status.
if rxn['status'] == 'OK':
okStatus += 1
