polymerist.polymers.smidgelib.smidgeread

Automata for reading SMIDGE strings into their graph representations

Attributes

LOGGER

Classes

`SMIDGEReaderRegister`	Information accessed by machine states during the SMIDGE writing process
`SMIDGEReadState`	Abstract based for reading MID graphs from SMIDGE strings
`Accumulate`	Collect characters into a buffer
`ChainNew`	Reset actions when beginning a new chain
`MonomerStart`	Begin reading in a new monomer
`MonomerEnd`	Finish reading a monomer and add it to the graph
`BondStart`	Initialize reading of a bond token
`BondEnd`	Abstract based for reading MID graphs from SMIDGE strings
`BranchStart`	Mark position of branch point in stack for backtrack
`BranchEnd`	Return to previous branch point
`SMIDGEReader`	Pushdown automaton for translating SMIDGE strings to and from monomer graphs

Module Contents

polymerist.polymers.smidgelib.smidgeread.LOGGER

class polymerist.polymers.smidgelib.smidgeread.SMIDGEReaderRegister[source]

Information accessed by machine states during the SMIDGE writing process

monograph: polymerist.polymers.monographs.MonomerGraph | None

bond_info: polymerist.polymers.smidgelib.MonomerGraphBondInfo

curr_token: str = ''

node_idx: int = 0

str_buffer: str = ''

node_stack: list[int] = []

class polymerist.polymers.smidgelib.smidgeread.SMIDGEReadState[source]

Bases: abc.ABC

Abstract based for reading MID graphs from SMIDGE strings

abstractmethod state_action(register: SMIDGEReaderRegister) → None[source]

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

class polymerist.polymers.smidgelib.smidgeread.Accumulate[source]

Bases: SMIDGEReadState

Collect characters into a buffer

state_action(register: SMIDGEReaderRegister) → None[source]

class polymerist.polymers.smidgelib.smidgeread.ChainNew[source]

Bases: SMIDGEReadState

Reset actions when beginning a new chain

state_action(register: SMIDGEReaderRegister) → None[source]

class polymerist.polymers.smidgelib.smidgeread.MonomerStart[source]

Bases: SMIDGEReadState

Begin reading in a new monomer

state_action(register: SMIDGEReaderRegister) → None[source]

class polymerist.polymers.smidgelib.smidgeread.MonomerEnd[source]

Bases: SMIDGEReadState

Finish reading a monomer and add it to the graph

state_action(register: SMIDGEReaderRegister) → None[source]

class polymerist.polymers.smidgelib.smidgeread.BondStart[source]

Bases: SMIDGEReadState

Initialize reading of a bond token

state_action(register: SMIDGEReaderRegister) → None[source]

class polymerist.polymers.smidgelib.smidgeread.BondEnd[source]

Bases: SMIDGEReadState

Abstract based for reading MID graphs from SMIDGE strings

state_action(register: SMIDGEReaderRegister) → None[source]

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

Bases: SMIDGEReadState

Mark position of branch point in stack for backtrack

state_action(register: SMIDGEReaderRegister) → None[source]

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

Bases: SMIDGEReadState

Return to previous branch point

state_action(register: SMIDGEReaderRegister) → None[source]

class polymerist.polymers.smidgelib.smidgeread.SMIDGEReader[source]

Pushdown automaton for translating SMIDGE strings to and from monomer graphs

state: SMIDGEReadState

read_smidge(smidge_string: str, start_node_idx: int = 0) → polymerist.polymers.monographs.MonomerGraph[source]: Parse a SMIDGE (“SMILES-like Monomer Interconnectivity & Degree Graph Encoding”) string and read it into a networkX Graph