units¶
Conversion of CellML units to SBML unit definitions.
The standard units of CellML (second, metre, kilogram, gram, mole,
litre, dimensionless, ampere, kelvin, ...) are all unit kinds of SBML
level 3 and are used by name. A custom Units becomes a UnitDefinition
whose units reference base kinds only: a reference to another custom Units
is expanded recursively.
Bases: ValueError
CellML units cannot be converted to SBML.
dataclass
¶
One unit of an SBML unit definition: (multiplier * 10^scale * kind)^exponent.
Scale of a CellML unit prefix.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
prefix
|
str
|
SI prefix name ( |
required |
Returns:
| Type | Description |
|---|---|
int
|
The power of ten. |
Raises:
| Type | Description |
|---|---|
UnitsConversionError
|
if the prefix is unknown. |
Expand CellML units into SBML base units.
A CellML unit stands for multiplier * (10^prefix * reference)^exponent,
an SBML unit for (multiplier * 10^scale * kind)^exponent: the prefix
becomes the scale and the multiplier its root multiplier^(1/exponent).
A unit referencing custom units is expanded recursively, every
resulting exponent multiplied by the outer exponent and the outer factor
multiplier * 10^(prefix * exponent) folded into the first resulting
unit. A factor which is left, e.g. of a unit with the exponent 0, becomes
a dimensionless unit with that multiplier.
New base units (custom units without any unit) have no SBML
counterpart and are dropped with a warning, except for item.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
units
|
Any
|
libcellml units. |
required |
model
|
Model
|
model the units belong to, resolves references to custom units. |
required |
Returns:
| Type | Description |
|---|---|
list[BaseUnit]
|
The base units, empty for units without any |
Raises:
| Type | Description |
|---|---|
UnitsConversionError
|
for an unknown reference or prefix. |
Add a unit definition for every custom units of a CellML model.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
model_cellml
|
Model
|
CellML model. |
required |
model_sbml
|
Model
|
SBML model the definitions are added to. |
required |
Returns:
| Type | Description |
|---|---|
dict[str, str]
|
The SBML unit id by CellML units name, for |
SBML unit id of a CellML units name.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
units_name
|
str
|
name of the units of a variable. |
required |
unit_ids
|
dict[str, str]
|
result of |
required |
Returns:
| Type | Description |
|---|---|
str
|
The unit definition id for custom units, the name itself for standard units. |