jLM.ParticleSizeSupport.ParticleSizeValidator Class Reference

Public Member Functions
	__init__ (self, simulation)
	set_particle_size (self, species, int size)
int	get_particle_size (self, species)
	validate_concentration (self, species, region, float concentration)
	validate_particle_count (self, species, region, int count)
Dict	get_capacity_info (self, species)
Dict	analyze_lattice_occupancy (self)
	validate_all_species (self)

Public Attributes
	sim = simulation
dict	particle_sizes = {}

Detailed Description

Validates particle concentrations and numbers against size constraints.

Constructor & Destructor Documentation

__init__()

jLM.ParticleSizeSupport.ParticleSizeValidator.__init__	(		self,
			simulation )

Initialize validator for a simulation.

Args:
    simulation: RDME simulation object

Member Function Documentation

analyze_lattice_occupancy()

Dict jLM.ParticleSizeSupport.ParticleSizeValidator.analyze_lattice_occupancy

(

self

)

Analyze current lattice occupancy considering particle sizes.

Returns:
    Dictionary with occupancy statistics

get_capacity_info()

Dict jLM.ParticleSizeSupport.ParticleSizeValidator.get_capacity_info	(		self,
			species )

Get capacity information for a species.

Args:
    species: Species object

Returns:
    Dictionary with capacity information

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get_particle_size()

int jLM.ParticleSizeSupport.ParticleSizeValidator.get_particle_size	(		self,
			species )

Get the size for a species.

Args:
    species: Species object or species ID

Returns:
    Size of the particle (default: 1)

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set_particle_size()

jLM.ParticleSizeSupport.ParticleSizeValidator.set_particle_size	(		self,
			species,
		int	size )

Set the size for a species.

Args:
    species: Species object or species ID
    size: Size of the particle (must be > 0)

Raises:
    ParticleSizeError: If size is invalid

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validate_all_species()

jLM.ParticleSizeSupport.ParticleSizeValidator.validate_all_species

(

self

)

Validate all currently configured species against size constraints.

Raises:
    ParticleSizeError: If any species violates constraints

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validate_concentration()

jLM.ParticleSizeSupport.ParticleSizeValidator.validate_concentration	(		self,
			species,
			region,
		float	concentration )

Validate that a concentration doesn't exceed site capacity.

Args:
    species: Species object
    region: Region object
    concentration: Concentration in M

Raises:
    ParticleSizeError: If concentration would exceed capacity

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validate_particle_count()

jLM.ParticleSizeSupport.ParticleSizeValidator.validate_particle_count	(		self,
			species,
			region,
		int	count )

Validate that a particle count doesn't exceed site capacity.

Args:
    species: Species object
    region: Region object
    count: Number of particles

Raises:
    ParticleSizeError: If count would exceed capacity

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Member Data Documentation

particle_sizes

dict jLM.ParticleSizeSupport.ParticleSizeValidator.particle_sizes = {}

sim

jLM.ParticleSizeSupport.ParticleSizeValidator.sim = simulation

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The documentation for this class was generated from the following file:

• /data2/LM_zls_github/Lattice-Microbes/src/jlm/jLM/ParticleSizeSupport.py