def __init__(self,
db,
html_writer=None,
dissociation=None,
anchor_all=False):
PsuedoisomerTableThermodynamics.__init__(
self, name="Unified Group Contribution")
self.db = db
self.html_writer = html_writer or NullHtmlWriter()
self.dissociation = dissociation
self.transformed = False
self.CollapseReactions = False
self.epsilon = 1e-10
self.kegg = Kegg.getInstance()
self.STOICHIOMETRIC_TABLE_NAME = 'ugc_S'
self.GROUP_TABLE_NAME = 'ugc_G'
self.GIBBS_ENERGY_TABLE_NAME = 'ugc_b'
self.ANCHORED_TABLE_NAME = 'ugc_anchored'
self.COMPOUND_TABLE_NAME = 'ugc_compounds'
self.OBSERVATION_TABLE_NAME = 'ugc_observations'
self.GROUPVEC_TABLE_NAME = 'ugc_groupvectors'
self.UNIQUE_OBSERVATION_TABLE_NAME = 'ugc_unique_observations'
self.THERMODYNAMICS_TABLE_NAME = 'ugc_pseudoisomers'
self.ERRORS_TABLE_NAME = 'ugc_errors'
self.CONSERVATIONS_TABLE_NAME = 'ugc_conservations'
if anchor_all:
self.FORMATION_ENERGY_FILENAME = '../data/thermodynamics/formation_energies_anchor_all.csv'
else:
self.FORMATION_ENERGY_FILENAME = '../data/thermodynamics/formation_energies.csv'
def __init__(self, db, html_writer=None, dissociation=None, anchor_all=False):
PsuedoisomerTableThermodynamics.__init__(self, name="Unified Group Contribution")
self.db = db
self.html_writer = html_writer or NullHtmlWriter()
self.dissociation = dissociation
self.transformed = False
self.CollapseReactions = False
self.epsilon = 1e-10
self.kegg = Kegg.getInstance()
self.STOICHIOMETRIC_TABLE_NAME = 'ugc_S'
self.GROUP_TABLE_NAME = 'ugc_G'
self.GIBBS_ENERGY_TABLE_NAME = 'ugc_b'
self.ANCHORED_TABLE_NAME = 'ugc_anchored'
self.COMPOUND_TABLE_NAME = 'ugc_compounds'
self.OBSERVATION_TABLE_NAME = 'ugc_observations'
self.GROUPVEC_TABLE_NAME = 'ugc_groupvectors'
self.UNIQUE_OBSERVATION_TABLE_NAME = 'ugc_unique_observations'
self.THERMODYNAMICS_TABLE_NAME = 'ugc_pseudoisomers'
self.ERRORS_TABLE_NAME = 'ugc_errors'
self.CONSERVATIONS_TABLE_NAME = 'ugc_conservations'
if anchor_all:
self.FORMATION_ENERGY_FILENAME = '../data/thermodynamics/formation_energies_anchor_all.csv'
else:
self.FORMATION_ENERGY_FILENAME = '../data/thermodynamics/formation_energies.csv'
def __init__(self, db, dissociation=None,
html_writer=None, nist=None):
PsuedoisomerTableThermodynamics.__init__(self)
self.db = db
self.html_writer = html_writer or NullHtmlWriter()
self.nist = nist or Nist()
self.dissociation = None
self.cid2pmap_dict = {}
self.assume_no_pKa_by_default = False
self.std_diff_threshold = np.inf
def __init__(self, db, html_writer=None, transformed=False):
"""Construct a GroupContribution instance.
Args:
db: the database handle to read from.
html_writer: the HtmlWriter to write to.
kegg: a Kegg instance if you don't want to use the default one.
"""
PsuedoisomerTableThermodynamics.__init__(self,
name="Group Contribution")
self.db = db
self.html_writer = html_writer or NullHtmlWriter()
self.dissociation = None
self.transformed = transformed
self.epsilon = 1e-10
self.kegg = Kegg.getInstance()
self.bounds = deepcopy(self.kegg.cid2bounds)
self.group_nullspace = None
self.group_contributions = None
self.obs_collection = None
self.cid2error = {}
self.cid2groupvec = None
if transformed:
prefix = 'bgc'
else:
prefix = 'pgc'
self.OBSERVATION_TABLE_NAME = prefix + '_observations'
self.GROUPVEC_TABLE_NAME = prefix + '_groupvector'
self.NULLSPACE_TABLE_NAME = prefix + '_nullspace'
self.CONTRIBUTION_TABLE_NAME = prefix + '_contribution'
self.REGRESSION_TABLE_NAME = prefix + '_regression'
self.THERMODYNAMICS_TABLE_NAME = prefix + '_pseudoisomers'
self.STOICHIOMETRIC_MATRIX_TABLE_NAME = prefix + '_stoichiometry'
self.ANCHORED_CONTRIBUTIONS_TALBE_NAME = prefix + '_anchored_g'
self.ANCHORED_CIDS_TABLE_NAME = prefix + '_anchored_cids'
self.ANCHORED_P_L_TALBE_NAME = prefix + '_anchored_P_L'
def __init__(self, db, html_writer=None, transformed=False):
"""Construct a GroupContribution instance.
Args:
db: the database handle to read from.
html_writer: the HtmlWriter to write to.
kegg: a Kegg instance if you don't want to use the default one.
"""
PsuedoisomerTableThermodynamics.__init__(self, name="Group Contribution")
self.db = db
self.html_writer = html_writer or NullHtmlWriter()
self.dissociation = None
self.transformed = transformed
self.epsilon = 1e-10
self.kegg = Kegg.getInstance()
self.bounds = deepcopy(self.kegg.cid2bounds)
self.group_nullspace = None
self.group_contributions = None
self.obs_collection = None
self.cid2error = {}
self.cid2groupvec = None
if transformed:
prefix = 'bgc'
else:
prefix = 'pgc'
self.OBSERVATION_TABLE_NAME = prefix + '_observations'
self.GROUPVEC_TABLE_NAME = prefix + '_groupvector'
self.NULLSPACE_TABLE_NAME = prefix + '_nullspace'
self.CONTRIBUTION_TABLE_NAME = prefix + '_contribution'
self.REGRESSION_TABLE_NAME = prefix + '_regression'
self.THERMODYNAMICS_TABLE_NAME = prefix + '_pseudoisomers'
self.STOICHIOMETRIC_MATRIX_TABLE_NAME = prefix + '_stoichiometry'
self.ANCHORED_CONTRIBUTIONS_TALBE_NAME = prefix + '_anchored_g'
self.ANCHORED_CIDS_TABLE_NAME = prefix + '_anchored_cids'
self.ANCHORED_P_L_TALBE_NAME = prefix + '_anchored_P_L'
