biocrnpyler.core.polymer

The classes OrderedPolymer and OrderedMonomer are datastructures used to represent Polymers and their associatd components.

These classes are used by Chemical Reaction Network Species as well as certain Components such as DNA_construct.

Classes

MonomerCollection(monomers)	A class used to represent a collection of OrderedMonomers without any particular structure
NamedPolymer(parts, name[, ...])	The same as an OrderedPolymer but it has a name
OrderedMonomer([direction, position, parent])	a unit that belongs to an OrderedPolymer.
OrderedPolymer(parts[, default_direction])	a polymer made up of OrderedMonomers that has a specific order

class biocrnpyler.core.polymer.MonomerCollection(monomers)

A class used to represent a collection of OrderedMonomers without any particular structure

class biocrnpyler.core.polymer.NamedPolymer(parts, name, default_direction=None, circular=False)

The same as an OrderedPolymer but it has a name

parts can be a list of lists containing [[OrderedMonomer,direction],[OrderedMonomer,direction],…] alternatively, you can have a regular list, and the direcitons will end up being None

class biocrnpyler.core.polymer.OrderedMonomer(direction=None, position=None, parent=None)

a unit that belongs to an OrderedPolymer. Each unit has a direction, a location, and a link back to its parent

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

get_orphan()

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

class biocrnpyler.core.polymer.OrderedPolymer(parts, default_direction=None)

a polymer made up of OrderedMonomers that has a specific order

parts can be a list of lists containing [[OrderedMonomer,direction],[OrderedMonomer,direction],…] alternatively, you can have a regular list, and the direcitons will end up being None