polymerist.polymers.smidgelib.smidgewrite

Automata for reading SMIDGE strings into their graph representations

Attributes

LOGGER

Classes

`SMIDGEWriterRegister`	Information accessed by machine states during the SMIDGE writing process
`SMIDGEWriterState`	Abstract base for automaton states used in writing MID graphs to SMIDGE strings
`CheckIsVisitedNode`	Read a node index off the stack and check if it has already been visited
`VisitNode`	Visit a node, check if it has predecessors, and mark it as visited
`WriteNode`	Add an entry for the current node to the output tokens
`WriteEdge`	Add an entry for the current edge to the output tokens
`DetermineNodeSuccessors`	Determine branching and next-node behavior
`PushNodeSuccessor`	Add a nodes DFS successor to the traversal stack
`UpdateNodeSuccessors`	Remove any node with no successors from the DFS traversal map
`BranchStart`	Mark position of branch point in stack for backtrack
`BranchEnd`	Mark the end of a branch
`SMIDGEWriter`	Register machine for translating SMIDGE strings to and from monomer graphs

Module Contents

polymerist.polymers.smidgelib.smidgewrite.LOGGER

class polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister[source]

Information accessed by machine states during the SMIDGE writing process

monograph: polymerist.polymers.monographs.MonomerGraph

bond_info: polymerist.polymers.smidgelib.smidgebonds.MonomerGraphBondInfo

tokens: list[int] = []

curr_idx: int = 0

visited: set

node_stack: list[int] = []

successors: dict[int, list[int]]

predecessors: dict[int, int]

finished: bool = False

property prev_idx: int | None: The index of the precursor to the currently active node

property node_successors: list[int]: The nodes which follow the current node in the DFS traversal (could be empty)

class polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterState[source]

Bases: abc.ABC

Abstract base for automaton states used in writing MID graphs to SMIDGE strings

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

abstractmethod transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.CheckIsVisitedNode[source]

Bases: SMIDGEWriterState

Read a node index off the stack and check if it has already been visited

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.VisitNode[source]

Bases: SMIDGEWriterState

Visit a node, check if it has predecessors, and mark it as visited

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.WriteNode[source]

Bases: SMIDGEWriterState

Add an entry for the current node to the output tokens

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.WriteEdge[source]

Bases: SMIDGEWriterState

Add an entry for the current edge to the output tokens

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.DetermineNodeSuccessors[source]

Bases: SMIDGEWriterState

Determine branching and next-node behavior

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.PushNodeSuccessor[source]

Bases: SMIDGEWriterState

Add a nodes DFS successor to the traversal stack

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.UpdateNodeSuccessors[source]

Bases: SMIDGEWriterState

Remove any node with no successors from the DFS traversal map

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.BranchStart[source]

Bases: SMIDGEWriterState

Mark position of branch point in stack for backtrack

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.BranchEnd[source]

Bases: SMIDGEWriterState

Mark the end of a branch

state_action(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]

transition(register: SMIDGEWriterRegister) → SMIDGEWriterState[source]: Define which states should follow the current one based on input

class polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriter[source]

Register machine for translating SMIDGE strings to and from monomer graphs

state: SMIDGEWriterState

write_smidge_connected_component(monograph: polymerist.polymers.monographs.MonomerGraph, start_node_idx: int | None = None) → polymerist.polymers.monographs.MonomerGraph[source]: Parse a single connected component of a monomer graph into a SMIDGE string

write_smidge(monograph: polymerist.polymers.monographs.MonomerGraph, start_node_idxs: int | Sequence[int] | None = None) → str[source]: Parse all connected components of a monograph into a complete SMIDGE string