def boundsStringFromReaction(reaction: libsbml.Reaction,
model: libsbml.Model) -> str:
"""Render string of bounds from the reaction.
:param reaction: SBML reaction instance
:param model: SBML model instance
:return: String of bounds extracted from the reaction
"""
bounds = ""
rfbc = reaction.getPlugin("fbc")
if rfbc is not None:
# get values for bounds
lb_id, ub_id = None, None
lb_value, ub_value = None, None
if rfbc.isSetLowerFluxBound():
lb_id = rfbc.getLowerFluxBound()
lb_p = model.getParameter(lb_id)
if lb_p.isSetValue():
lb_value = lb_p.getValue()
if rfbc.isSetUpperFluxBound():
ub_id = rfbc.getUpperFluxBound()
ub_p = model.getParameter(ub_id)
if ub_p.isSetValue():
ub_value = ub_p.getValue()
if (lb_value is not None) or (ub_value is not None):
bounds = f"""
<code>[{lb_value}
<i class="fa fa-sort fa-rotate-90" aria-hidden="true"></i>
{ub_value}]
</code>
"""
return bounds
def _gene_product_association_from_reaction(
reaction: libsbml.Reaction, ) -> Optional[str]:
"""Render string representation of the GeneProductAssociation for given reaction.
:param reaction: SBML reaction instance
:return: string representation of GeneProductAssociation
"""
rfbc = reaction.getPlugin("fbc")
gpa = (str(rfbc.getGeneProductAssociation().getAssociation().toInfix())
if (rfbc and rfbc.isSetGeneProductAssociation()) else None)
return gpa
def geneProductAssociationStringFromReaction(
reaction: libsbml.Reaction) -> str:
"""Render string representation of the GeneProductAssociation for given reaction.
:param reaction: SBML reaction instance
:return: string representation of GeneProductAssociation
"""
info = ""
rfbc = reaction.getPlugin("fbc")
if rfbc and rfbc.isSetGeneProductAssociation():
gpa = rfbc.getGeneProductAssociation()
association = gpa.getAssociation()
info = association.toInfix()
return info
def _bounds_dict_from_reaction(reaction: libsbml.Reaction,
model: libsbml.Model) -> Optional[Dict]:
"""Render string of bounds from the reaction.
:param reaction: SBML reaction instance
:param model: SBML model instance
:return: String of bounds extracted from the reaction
"""
bounds: Optional[Dict]
rfbc = reaction.getPlugin("fbc")
if rfbc is not None:
# get values for bounds
lb_id: Optional[str] = None
ub_id: Optional[str] = None
lb_value: Optional[float] = None
ub_value: Optional[float] = None
if rfbc.isSetLowerFluxBound():
lb_id = rfbc.getLowerFluxBound()
lb_p: libsbml.Parameter = model.getParameter(lb_id)
if lb_p.isSetValue():
lb_value = lb_p.getValue()
if rfbc.isSetUpperFluxBound():
ub_id = rfbc.getUpperFluxBound()
ub_p: libsbml.Parameter = model.getParameter(ub_id)
if ub_p.isSetValue():
ub_value = ub_p.getValue()
bounds = {
"lowerFluxBound": {
"id": lb_id,
"value": lb_value,
},
"upperFluxBound": {
"id": ub_id,
"value": ub_value,
},
}
else:
bounds = None
return bounds
def set_flux_bounds(reaction: libsbml.Reaction, lb: float, ub: float) -> None:
"""Set flux bounds on given reaction."""
rplugin = reaction.getPlugin("fbc")
rplugin.setLowerFluxBound(lb)
rplugin.setUpperFluxBound(ub)