schrodinger.protein.residue_identifier module¶

Canonical representation of a residue identifier.

class schrodinger.protein.residue_identifier.FormatCode¶

Bases: StrEnum

%-codes used in residue identifier format strings.

CHAIN = 'c'¶

RES_CODE_LONG = 'R'¶

RES_CODE_SHORT = 'r'¶

INS_CODE = 'i'¶

NUM = 'n'¶

class schrodinger.protein.residue_identifier.CaseStyle¶

Bases: StrEnum

Case transformation applied to string fields during formatting.

ORIGINAL = 'original'¶

UPPER = 'upper'¶

LOWER = 'lower'¶

TITLE = 'title'¶

schrodinger.protein.residue_identifier.COLON_SPACE_FMT = '%c:%R %n%i'¶: "A:ALA 123" or "A:ALA 123B"

schrodinger.protein.residue_identifier.COLON_UNDERSCORE_FMT = '%c:%R_%n%i'¶: "A:ALA_123" or "A:ALA_123B"

schrodinger.protein.residue_identifier.COLON_NUM_FMT = '%c:%n%i'¶: "A:123" or "A:123B"

schrodinger.protein.residue_identifier.DISPLAY_FMT = '%R%n%i'¶: "ALA123" or "ALA123B"

class schrodinger.protein.residue_identifier.ResidueIdentifier(num: int, res_code: str | None = None, chain: str | None = None, ins_code: str | None = None)¶

Bases: object

Canonical representation of a residue identifier.

Supports parsing from and formatting to multiple string representations using a strftime-style format language with %-codes.

Format codes:

%c  chain name
%R  multi-letter residue code (e.g. ALA, GLY)
%r  single-letter residue code (e.g. A, G) -- derived from res_code
%n  residue number (possibly negative)
%i  insertion code (single alpha char; placeholder if missing)
%%  literal '%'

Common format strings are provided as module-level constants: COLON_SPACE_FMT, COLON_UNDERSCORE_FMT, COLON_NUM_FMT, DISPLAY_FMT.

num: int¶

res_code: str | None = None¶

chain: str | None = None¶

ins_code: str | None = None¶

__init__(num: int, res_code: str | None = None, chain: str | None = None, ins_code: str | None = None) → None¶

format(fmt: str, *, ins_placeholder: str = '', case_style: CaseStyle = CaseStyle.ORIGINAL) → str¶

Format this identifier using a %-code format string.

Parameters:

fmt – Format string with %-codes.
ins_placeholder – String to substitute when ins_code is None.
case_style – Case transformation applied to all string field values.

Raises:

ValueError – If a required field is None or if %r is used with an unrecognised res_code.

Returns:

Formatted string.

classmethod parse(s: str, fmt: str, *, ins_placeholder: str = '') → ResidueIdentifier¶

Parse a string using a %-code format string.

Parameters:

s – The string to parse.
fmt – Format string with %-codes.
ins_placeholder – Placeholder value that should be interpreted as None for the insertion code field.

Raises:

ValueError – On format mismatch, adjacency violation, or unknown single-letter code for %r.

Returns:

Parsed ResidueIdentifier.

classmethod from_residue(residue: _Residue) → ResidueIdentifier¶

Construct from a schrodinger.structure._Residue.

Parameters:: residue – A structure residue object.
Returns:: New ResidueIdentifier.