def extend_S_from_gams_inputfile(self, filename=None):
"""Extend S matrix using the gams S matrix format.
Args:
filename (None, optional): The name of the inputfile.
"""
self.S = gams_parser.convert_parameter_table_to_dict(os.path.join(
self.data_filepath, filename),
Sdict=self.S)
self.refresh_database(previous_operations_on='S')
def load(self):
# Method 1: JSON approach
if self.dbdict_json is not None:
self.logger.debug('Reading S matrix from JSON...')
self.Sji = json.load(
open(
os.path.join(
self.data_filepath,
self.dbdict_json['Sji']),
'r+'))
self.S = self.transpose_S(self.Sji)
self.reactions = sorted(self.Sji.keys())
self.internal_rxns = copy.deepcopy(self.reactions)
self.metabolites = sorted(self.S.keys())
self.logger.debug('Reading reaction type file...')
self.rxntype = json.load(
open(
os.path.join(
self.data_filepath,
self.dbdict_json['reactiontype']),
'r+'))
# Method 2: Standard GAMS input file
else:
self.logger.debug('Reading S matrix from txt...')
self.S = gams_parser.convert_parameter_table_to_dict(
os.path.join(self.data_filepath,
self.dbdict_gams['Sji'])
)
self.Sji = self.transpose_S(self.S)
# Load reactions
self.logger.debug('Reading reaction file...')
self.reactions = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath, self.dbdict_gams['reaction'])
)
# Create internal reactions list
self.internal_rxns = copy.deepcopy(self.reactions)
self.logger.debug('Reading metabolite file...')
self.metabolites = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath, self.dbdict_gams['metabolite'])
)
self.logger.debug('Reading reaction type file...')
self.rxntype = gams_parser.convert_parameter_list_to_dict(
os.path.join(self.data_filepath, self.dbdict_gams['reactiontype']),
datadict=None
)
self.validate()
def load_toy_model(self):
# Method 1: JSON approach
if self.dbdict_json is not None:
self.logger.debug('Reading S matrix from JSON...')
self.Sji = json.load(
open(os.path.join(self.data_filepath, self.dbdict_json['Sji']),
'r+'))
self.S = self.transpose_S(self.Sji)
self.reactions = sorted(self.Sji.keys())
self.internal_rxns = copy.deepcopy(self.reactions)
self.metabolites = sorted(self.S.keys())
self.logger.debug('Reading reaction type file...')
self.rxntype = json.load(
open(
os.path.join(self.data_filepath,
self.dbdict_json['reactiontype']), 'r+'))
self.logger.debug('Reading Nint(loop, j) from JSON...')
#no hay loops en el toy_model
#self.Ninternal = json.load(
# open(
# os.path.join(
# self.data_filepath,
# self.dbdict_json['Nint']),
# 'r+'))
#self.loops = sorted(self.Ninternal.keys())
# Method 2: Standard GAMS input file
else:
self.logger.debug('Reading S matrix from txt...')
self.S = gams_parser.convert_parameter_table_to_dict(
os.path.join(self.data_filepath, self.dbdict_gams['Sji']))
self.Sji = self.transpose_S(self.S)
self.logger.debug('Reading metabolite file...')
self.metabolites = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath,
self.dbdict_gams['metabolite']))
# Load reactions
self.logger.debug('Reading reaction file...')
self.reactions = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath, self.dbdict_gams['reaction']))
self.internal_rxns = copy.deepcopy(self.reactions)
self.logger.debug('Reading reaction type file...')
self.rxntype = gams_parser.convert_parameter_list_to_dict(
os.path.join(self.data_filepath,
self.dbdict_gams['reactiontype']),
datadict=None)
self.logger.debug('Reading Nint(loop, j) from txt...')
self.Ninternal = gams_parser.convert_parameter_table_to_dict(
os.path.join(self.data_filepath, self.dbdict_gams['Nint']))
self.logger.debug('Reading loop file...')
self.loops = gams_parser.convert_set_to_list(
os.path.join(self.data_filepath, self.dbdict_gams['loops']))
if self.excluded_reactions is not None:
self.all_excluded_reactions = list(
set(self.excluded_reactions + self.blocked_rxns))
else:
self.all_excluded_reactions = self.blocked_rxns
#self.validate()
if self.reduce_model_size:
self.remove_blocked_reactions()
self.validate()