jLM.ParticleSizeSupport.ParticleSizeMixin Class Reference

Inheritance diagram for jLM.ParticleSizeSupport.ParticleSizeMixin:

Public Member Functions
	__init__ (self, *args, **kwargs)
ParticleSizeValidator	size_validator (self)
	enable_particle_sizes (self, bool enable=True)
	set_particle_size (self, species, int size)
int	get_particle_size (self, species)
dict	get_all_particle_sizes (self)
	distribute_concentration_safe (self, species, region, float concentration)
	distribute_number_safe (self, species, region, int count)
Dict	get_capacity_summary (self)
	validate_all_species (self)
	print_capacity_summary (self)

Public Attributes
	lattice
	siteLattice = self.lattice.getSiteLatticeView()
	particleLattice = self.lattice.getParticleLatticeView()
	speciesList

Protected Member Functions
	_upgrade_to_extended_lattice (self)
	_copy_lattice_data (self, source, dest)

Protected Attributes
	_size_validator = None
dict	_particle_sizes = {}

Detailed Description

Mixin class to add particle size support to RDME classes.

Constructor & Destructor Documentation

__init__()

jLM.ParticleSizeSupport.ParticleSizeMixin.__init__	(		self,
		*	args,
		**	kwargs )

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Member Function Documentation

_copy_lattice_data()

jLM.ParticleSizeSupport.ParticleSizeMixin._copy_lattice_data ( self, source, dest )

protected

Copy lattice data from source to destination.

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_upgrade_to_extended_lattice()

jLM.ParticleSizeSupport.ParticleSizeMixin._upgrade_to_extended_lattice ( self )

protected

Upgrade to ByteLatticeExtended for size support.

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distribute_concentration_safe()

jLM.ParticleSizeSupport.ParticleSizeMixin.distribute_concentration_safe	(		self,
			species,
			region,
		float	concentration )

Distribute concentration with size validation.

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

Raises:
    ParticleSizeError: If concentration exceeds capacity

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distribute_number_safe()

jLM.ParticleSizeSupport.ParticleSizeMixin.distribute_number_safe	(		self,
			species,
			region,
		int	count )

Distribute particle count with size validation.

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

Raises:
    ParticleSizeError: If count exceeds capacity

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enable_particle_sizes()

jLM.ParticleSizeSupport.ParticleSizeMixin.enable_particle_sizes	(		self,
		bool	enable = True )

Enable or disable particle size checking.

Args:
    enable: Whether to enable size checking

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get_all_particle_sizes()

dict jLM.ParticleSizeSupport.ParticleSizeMixin.get_all_particle_sizes

(

self

)

Get all particle sizes as a dictionary mapping species ID to size.

Returns:
    dict: Dictionary mapping species ID (int) to particle size (int)

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get_capacity_summary()

Dict jLM.ParticleSizeSupport.ParticleSizeMixin.get_capacity_summary

(

self

)

Get a summary of capacity information for all species.

Returns:
    Dictionary with capacity information for each species

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get_particle_size()

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

Get the size for a species.

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print_capacity_summary()

jLM.ParticleSizeSupport.ParticleSizeMixin.print_capacity_summary

(

self

)

Print a formatted capacity summary.

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set_particle_size()

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

Set the size for a species.

Args:
    species: Species object or name
    size: Size of the particle

Example:
    sim.set_particle_size(sim.sp.Protein, 2)
    sim.set_particle_size("LargeComplex", 4)

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size_validator()

ParticleSizeValidator jLM.ParticleSizeSupport.ParticleSizeMixin.size_validator

(

self

)

Get the particle size validator.

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validate_all_species()

jLM.ParticleSizeSupport.ParticleSizeMixin.validate_all_species

(

self

)

Validate all species against size constraints.

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Member Data Documentation

_particle_sizes

dict jLM.ParticleSizeSupport.ParticleSizeMixin._particle_sizes = {}

protected

_size_validator

jLM.ParticleSizeSupport.ParticleSizeMixin._size_validator = None

protected

lattice

jLM.ParticleSizeSupport.ParticleSizeMixin.lattice

particleLattice

jLM.ParticleSizeSupport.ParticleSizeMixin.particleLattice = self.lattice.getParticleLatticeView()

siteLattice

jLM.ParticleSizeSupport.ParticleSizeMixin.siteLattice = self.lattice.getSiteLatticeView()

speciesList

jLM.ParticleSizeSupport.ParticleSizeMixin.speciesList

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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