pidibble.baseparsers module

class pidibble.baseparsers.ListParser(d=',')

Bases: object

A simple parser for lists of strings, with a customizable delimiter.

parse(string)

Parse a string into a list of strings, using the specified delimiter. If no delimiter is specified, it splits on whitespace.

Parameters:

string (str) – The string to parse.

Returns:

A list of strings parsed from the input string.

Return type:

list

class pidibble.baseparsers.NonconformanceRegistry

Bases: object

Accumulates types of PDB-format nonconformance encountered during a parse, rather than every individual instance.

Real-world PDB files routinely deviate from the fixed-column standard (for example, a charge column that holds O- instead of a bare number). A single file can contain tens of thousands of instances of the same deviation, so logging each one is useless noise. This registry collapses them by type, keyed by (record_key, field, kind) — e.g. ("ATOM", "charge", "not coercible to Float") — keeping a running count and one exemplar (the offending value and its byte range) per type so the end-of-parse summary can point at something concrete.

add(record_key, nc)

Record one nonconformance instance under its type signature.

Parameters:

• record_key (str) – The record type the instance was found in (e.g. ATOM).

• nc (dict) – A nonconformance descriptor as produced by StringParser, with keys field, kind, byte_range, and value.

report(log, label='')

Emit one INFO line per nonconformance type to the given logger.

Parameters:

• log (logging.Logger) – The logger to emit the summary to.

• label (str, optional) – A label for the source being parsed (e.g. the PDB id), included in the summary header.

types()

Return the accumulated nonconformance types.

Returns:

One (record_key, field, kind, count, byte_range, example) tuple per distinct nonconformance type.

Return type:

list of tuple

class pidibble.baseparsers.StringParser(fmtdict, typemap, allowed={})

Bases: object

A parser for fixed-width strings, with a customizable field map.

Parameters:

• fmtdict (dict) – A dictionary mapping field names to tuples of (type, byte_range).

• typemap (dict) – A dictionary mapping type names to Python types.

• allowed (dict, optional) – A dictionary mapping field values to allowed values, for validation.

parse(record)

Parse a fixed-width string record into a dictionary of fields.

Parameters:

record (str) – The fixed-width string record to parse.

Returns:

A dictionary of fields parsed from the input record.

Return type:

dict

report_field_error(record, k)

Report an error in parsing a specific field from a fixed-width string record.

Parameters:

• record (str) – The fixed-width string record that caused the error.

• k (str) – The field name that caused the error.

report_record_error(record, byte_range=[])

Report an error in parsing a fixed-width string record.

Parameters:

• record (str) – The fixed-width string record that caused the error.

• byte_range (list, optional) – A list of byte ranges to highlight in the error message. If empty, the entire record is reported.

pidibble.baseparsers.list_parse(obj, d)

A factory function to create a ListParser with a specific delimiter.

Parameters:

• obj (type) – The class to instantiate (should be ListParser).

• d (str or None) – The delimiter to use for parsing. If None, it will split on whitespace.

Returns:

A function that takes a string and returns a list of parsed strings.

Return type:

function

pidibble.baseparsers.safe_float(x)

Convert a string to a float, returning 0.0 if the string is ‘nan’.

pidibble.baseparsers.str2int_sig(arg: str)

Convert a string to an integer, returning -1 if the string is not numeric. If the string starts with a ‘-’, it is returned as an integer.