biocrnpyler.Species

class biocrnpyler.Species(name: str, material_type='', attributes: List | None = None, compartment=None, **keywords)

A formal species object for a chemical reaction network (CRN).

A Species must have a name. They may also have a material_type (such as DNA, RNA, Protein), and a list of attributes.

the default is that the monomer is not part of a polymer

__init__(name: str, material_type='', attributes: List | None = None, compartment=None, **keywords)

the default is that the monomer is not part of a polymer

Methods

__init__(name[, material_type, attributes, ...])	the default is that the monomer is not part of a polymer
add_attribute(attribute)	Adds attributes to a Species
contains_species_monomer(s)	Checks if the Species has a monomer (Species) inside of it, but without checking Species.parent, Species.position, or direction.
find_polymer_component()
flatten_list(in_list)	Helper function to flatten lists
get_orphan()	returns a copy of this monomer, except with no parent.
get_removed()
get_species(**kwargs)	Used in some recursive calls where ComplexSpecies returns a list and Species will return just themselves (in a list)
monomer_eq(other)	Same as normal equality, but does not check for parents or positions.
monomer_insert(parent, position[, direction])
pretty_print([show_material, ...])	#A more powerful printing function.
remove()	Added functionality to remove direction as an attribute.
remove_attribute(attribute)	removes an attribute from a Species
replace_species(species, new_species)
set_dir(direction)
subhash()

Attributes

attributes
compartment
direction
material_type
name
parent
position

add_attribute(attribute: str)

Adds attributes to a Species

contains_species_monomer(s)

Checks if the Species has a monomer (Species) inside of it, but without checking Species.parent, Species.position, or direction. In effect, a less stringent version of __contains__.

static flatten_list(in_list) → List

Helper function to flatten lists

get_orphan()

returns a copy of this monomer, except with no parent. But it still has a position and direction

get_species(**kwargs)

Used in some recursive calls where ComplexSpecies returns a list and Species will return just themselves (in a list)

monomer_eq(other)

Same as normal equality, but does not check for parents or positions.

pretty_print(show_material=True, show_compartment=False, show_attributes=True, show_initial_condition=False, **kwargs)

#A more powerful printing function. Useful for understanding CRNs but does not return string identifiers. show_material toggles whether species.material is printed. show_attributes toggles whether species.attributes is printed

remove()

Added functionality to remove direction as an attribute.

remove_attribute(attribute: str)

removes an attribute from a Species