ModificationLibrary

Module

viennaptm.modification.modification_library

class ModificationLibrary(library_path: str | Path = None, metadata_path: str | Path = None, pdbs_minimized: str | Path = None)

Bases: BaseModel

Container and loader for residue modifications and template structures.

The ModificationLibrary loads application definitions from a JSON library file and associates them with minimized Biopython PDB template structure. It provides indexed access to modifications and utilities for loading template residues.

Variables:

• modifications (list[Modification]) – List of available residue modifications.

• metadata (ModificationLibraryMetadata) – Metadata of the library.

• target_templates (dict[str, str]) – Mapping of residue abbreviations to PDB file paths.

load_residue_from_pdb(target_abbreviation: str) → Residue

Load a template residue from a minimized PDB file.

The PDB file must contain exactly one residue whose name matches the requested target abbreviation.

Parameters:

target_abbreviation (str) – Residue abbreviation to load.

Returns:

Template residue.

Return type:

Residue

Raises:

ValueError – If the PDB file does not contain exactly one matching residue.

metadata: ModificationLibraryMetadata

model_config = {'extra': 'forbid'}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

modifications: List[Modification]

target_templates: Dict[str, str]

Methods

__init__([library_path, metadata_path, ...])	Create a new model by parsing and validating input data from keyword arguments.
construct([_fields_set])
copy(*[, include, exclude, update, deep])	Returns a copy of the model.
dict(*[, include, exclude, by_alias, ...])
from_orm(obj)
json(*[, include, exclude, by_alias, ...])
load_residue_from_pdb(target_abbreviation)	Load a template residue from a minimized PDB file.
model_construct([_fields_set])	Creates a new instance of the Model class with validated data.
model_copy(*[, update, deep])	!!! abstract "Usage Documentation"
model_dump(*[, mode, include, exclude, ...])	!!! abstract "Usage Documentation"
model_dump_json(*[, indent, ensure_ascii, ...])	!!! abstract "Usage Documentation"
model_json_schema(by_alias, ref_template, ...)	Generates a JSON schema for a model class.
model_parametrized_name(params)	Compute the class name for parametrizations of generic classes.
model_post_init(context, /)	Override this method to perform additional initialization after __init__ and model_construct.
model_rebuild(*[, force, raise_errors, ...])	Try to rebuild the pydantic-core schema for the model.
model_validate(obj, *[, strict, extra, ...])	Validate a pydantic model instance.
model_validate_json(json_data, *[, strict, ...])	!!! abstract "Usage Documentation"
model_validate_strings(obj, *[, strict, ...])	Validate the given object with string data against the Pydantic model.
parse_file(path, *[, content_type, ...])
parse_obj(obj)
parse_raw(b, *[, content_type, encoding, ...])
schema([by_alias, ref_template])
schema_json(*[, by_alias, ref_template])
update_forward_refs(**localns)
validate(value)