MOD Parser

class dendrotweaks.biophys.io.parser.MODFileParser

Bases: object

A parser for MOD files that uses a Pyparsing grammar to parse the content of the file.

info()

Print information about the parser.

get_ast() → Dict

Get the abstract syntax tree of the parsed content. Available after parsing the content of the file.

parse_block(block_name: str, block_content: List[str]) → List[Dict]

Parse a block of the MOD file. Ensures that parsing is independent for each block.

parse(blocks: Dict[str, List[str]], verbose: bool = True) → None

Parse the entire content of the file.

Parameters:

blocks (Dict[str, List[str]]) – A dictionary with the blocks of the MOD file.

postprocess(restore_expressions=True)

Postprocess the parsed AST.

Parameters:

restore_expressions (bool) – Whether to restore the expressions in the AST to their original form after parsing.

split_comment_block()

restore_expressions()

Restore the expressions in the AST to their original form.

find_in_blocks(pattern, block_types=['ASSIGNED', 'PROCEDURE', 'PARAMETER'])

Find a pattern in the specified block types.

Parameters:

• pattern (str) – The regex pattern to search for in the blocks.

• block_types (list) – A list of block types to search for the pattern.

Returns:

A list of matching strings if found, a single matching string if there’s only one, or None if no matches are found.

Return type:

str or list or None

Examples

Find the name of the variable representing time constant of a state variable: >>> pattern = re.compile(‘tau’, re.IGNORECASE) >>> parser.find_in_blocks(‘tau’) [‘m_tau’, ‘hTau’, ‘ntau’]

replace_in_blocks(replacements, block_types=['FUNCTION', 'PROCEDURE'])

Replace the variable names with their values or another variable name in the specified block types.

Parameters:

• replacements (dict) – A dictionary with the constants as keys and their replacement values.

• block_types (list) – A list of block types to apply the replacements to.

Examples

Replace the Faraday constant with its value in every FUNCTION block: >>> parser.replace({‘FARADAY’: 96485.309}, block_types=[‘FUNCTION’])

standardize_state_var_names()

Standardize the names of the variables representing the inf and tau of the state variables in the MOD file.

update_state_vars_with_power()

Update the state variables in the AST with the corresponding power from the equation in the BREAKPOINT block.