def loadEntry(self,
index,
group1=None,
group2=None,
group3=None,
group4=None,
kinetics=None,
degeneracy=1,
label='',
duplicate=False,
reversible=True,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
rank=None,
history=None
):
reactants = []
if group1[0:3].upper() == 'OR{' or group1[0:4].upper() == 'AND{' or group1[0:7].upper() == 'NOT OR{' or group1[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group1))
else:
reactants.append(Group().fromAdjacencyList(group1))
if group2 is not None:
if group2[0:3].upper() == 'OR{' or group2[0:4].upper() == 'AND{' or group2[0:7].upper() == 'NOT OR{' or group2[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group2))
else:
reactants.append(Group().fromAdjacencyList(group2))
if group3 is not None:
if group3[0:3].upper() == 'OR{' or group3[0:4].upper() == 'AND{' or group3[0:7].upper() == 'NOT OR{' or group3[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group3))
else:
reactants.append(Group().fromAdjacencyList(group3))
if group4 is not None:
if group4[0:3].upper() == 'OR{' or group4[0:4].upper() == 'AND{' or group4[0:7].upper() == 'NOT OR{' or group4[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group4))
else:
reactants.append(Group().fromAdjacencyList(group4))
reaction = Reaction(reactants=reactants, products=[])
entry = Entry(
index = index,
label = label,
item = reaction,
data = kinetics,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
rank = rank,
history = history or [],
)
try:
self.entries[label].append(entry)
except KeyError:
self.entries[label] = [entry]
return entry
def loadEntry(self,
index,
label,
group,
kinetics,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
nodalDistance=None):
"""
nodalDistance is the distance between a given entry and its parent specified by a float
"""
if group[0:3].upper() == 'OR{' or group[0:4].upper(
) == 'AND{' or group[0:7].upper() == 'NOT OR{' or group[0:8].upper(
) == 'NOT AND{':
item = makeLogicNode(group)
else:
item = Group().fromAdjacencyList(group)
if label in self.entries:
raise DatabaseError(
"Duplicate group name {label} found in kinetics groups for {family} family."
.format(label=label, family=self.label))
self.entries[label] = Entry(index=index,
label=label,
item=item,
data=kinetics,
reference=reference,
referenceType=referenceType,
shortDesc=shortDesc,
longDesc=longDesc.strip(),
nodalDistance=nodalDistance)
def loadEntry(self,
index,
label,
group,
distances,
reference=None,
referenceType='',
shortDesc='',
longDesc=''):
if group[0:3].upper() == 'OR{' or group[0:4].upper(
) == 'AND{' or group[0:7].upper() == 'NOT OR{' or group[0:8].upper(
) == 'NOT AND{':
item = makeLogicNode(group)
else:
item = Group().fromAdjacencyList(group)
self.entries[label] = Entry(
index=index,
label=label,
item=item,
data=distances,
reference=reference,
referenceType=referenceType,
shortDesc=shortDesc,
longDesc=longDesc.strip(),
)
def loadEntry(self, index, label, group, kinetics, reference=None, referenceType='', shortDesc='', longDesc=''):
if group[0:3].upper() == 'OR{' or group[0:4].upper() == 'AND{' or group[0:7].upper() == 'NOT OR{' or group[0:8].upper() == 'NOT AND{':
item = makeLogicNode(group)
else:
item = Group().fromAdjacencyList(group)
if label in self.entries:
raise DatabaseError("Duplicate group name {label} found in kinetics groups for {family} family.".format(label=label,family=self.label))
self.entries[label] = Entry(
index = index,
label = label,
item = item,
data = kinetics,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
def loadGroup(index, label, group, kinetics, reference=None, referenceType='', shortDesc='', longDesc=''):
if group[0:3].upper() == 'OR{' or group[0:4].upper() == 'AND{' or group[0:7].upper() == 'NOT OR{' or group[0:8].upper() == 'NOT AND{':
item = makeLogicNode(group)
else:
item = Group().fromAdjacencyList(group)
entry = Entry(
index = index,
label = label,
item = item,
data = kinetics,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
entries.append(entry)
def loadEntry(
self,
index,
group1=None,
group2=None,
group3=None,
group4=None,
kinetics=None,
degeneracy=1,
label='',
duplicate=False,
reversible=True,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
rank=None,
):
reactants = []
if group1[0:3].upper() == 'OR{' or group1[0:4].upper(
) == 'AND{' or group1[0:7].upper() == 'NOT OR{' or group1[0:8].upper(
) == 'NOT AND{':
reactants.append(makeLogicNode(group1))
else:
reactants.append(Group().fromAdjacencyList(group1))
if group2 is not None:
if group2[0:3].upper() == 'OR{' or group2[0:4].upper(
) == 'AND{' or group2[0:7].upper(
) == 'NOT OR{' or group2[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group2))
else:
reactants.append(Group().fromAdjacencyList(group2))
if group3 is not None:
if group3[0:3].upper() == 'OR{' or group3[0:4].upper(
) == 'AND{' or group3[0:7].upper(
) == 'NOT OR{' or group3[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group3))
else:
reactants.append(Group().fromAdjacencyList(group3))
if group4 is not None:
if group4[0:3].upper() == 'OR{' or group4[0:4].upper(
) == 'AND{' or group4[0:7].upper(
) == 'NOT OR{' or group4[0:8].upper() == 'NOT AND{':
reactants.append(makeLogicNode(group4))
else:
reactants.append(Group().fromAdjacencyList(group4))
reaction = Reaction(reactants=reactants, products=[])
entry = Entry(
index=index,
label=label,
item=reaction,
data=kinetics,
reference=reference,
referenceType=referenceType,
shortDesc=shortDesc,
longDesc=longDesc.strip(),
rank=rank,
)
try:
self.entries[label].append(entry)
except KeyError:
self.entries[label] = [entry]
return entry