pyplate.Substance

class Substance(name: str, mol_type: int, molecule=None)

Bases: object

An abstract chemical or biological entity (e.g., reagent, enzyme, solvent, etc.). Immutable. Enzymes are assumed to require zero volume.

name

Name of substance.

mol_weight

Molecular weight (g/mol).

specific_activity

Activity units per mass if Substance is an enzyme (U/g).

density

Density if Substance is a liquid (g/mL).

concentration

Calculated concentration if Substance is a liquid (mol/mL).

molecule

cctk.Molecule if provided.

__init__(name: str, mol_type: int, molecule=None)

Create a new substance.

Parameters:

• name – Name of substance.

• mol_type – Substance.LIQUID, Substance.SOLID, or Substance.ENZYME.

• molecule – (optional) A cctk.Molecule.

If cctk.Molecule is provided, molecular weight will automatically populate. Note: Support for isotopologues will be added in the future.

Methods

__init__(name, mol_type[, molecule])	Create a new substance.
enzyme(name, specific_activity[, molecule])	Creates an enzyme.
is_enzyme()	Return true if Substance is an enzyme.
is_liquid()	Return true if Substance is a liquid.
is_solid()	Return true if Substance is a solid.
liquid(name, mol_weight, density[, molecule])	Creates a liquid substance.
solid(name, mol_weight[, molecule])	Creates a solid substance.

Attributes

ENZYME
LIQUID
SOLID
classes

ENZYME = 3

LIQUID = 2

SOLID = 1

classes = {1: 'Solids', 2: 'Liquids', 3: 'Enzymes'}

static enzyme(name: str, specific_activity: str, molecule=None) → Substance

Creates an enzyme.

Parameters:

• name – Name of enzyme.

• specific_activity – A ratio of activity units to mass (‘10 U/g’, ‘10 U/mg’, ‘0.1 mg/U’)

• molecule – (optional) A cctk.Molecule

Returns: New substance.

is_enzyme() → bool

Return true if Substance is an enzyme.

is_liquid() → bool

Return true if Substance is a liquid.

is_solid() → bool

Return true if Substance is a solid.

static liquid(name: str, mol_weight: float, density: float, molecule=None) → Substance

Creates a liquid substance.

Parameters:

• name – Name of substance.

• mol_weight – Molecular weight in g/mol

• density – Density in g/mL

• molecule – (optional) A cctk.Molecule

Returns: New substance.

static solid(name: str, mol_weight: float, molecule=None) → Substance

Creates a solid substance.

Parameters:

• name – Name of substance.

• mol_weight – Molecular weight in g/mol

• molecule – (optional) A cctk.Molecule

Returns: New substance.