Modification

Module

viennaptm.modification.modification_library

class Modification(*, residue_original_abbreviation: str, residue_modified_abbreviation: str, atom_mapping: Tuple[str | None, str | None]]=<factory>, add_branches: List[AddBranch] = <factory>, metadata: ModificationMetadata = <factory>)

Bases: BaseModel

Definition of a residue application.

A Modification specifies how an original residue is transformed into a modified residue. It includes atom mappings between the two residue states and one or more application branches that describe how atoms are added and aligned.

Variables:

• residue_original_abbreviation (str) – Abbreviation of the original residue.

• residue_modified_abbreviation (str) – Abbreviation of the modified residue.

• atom_mapping (list[tuple[str | None, str | None]]) – Mapping between original and modified atom names. Each entry is a tuple (original, modified) where either element may be None to indicate deletion or addition.

• add_branches (list[AddBranch]) – Branches defining how atoms are geometrically added.

Note

Atom deletions and renaming are handled exclusively via atom_mapping; branches only describe atom additions.

add_branches: List[AddBranch]

atom_mapping: List[Tuple[str | None, str | None]]

metadata: ModificationMetadata

model_config = {'extra': 'forbid'}

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

residue_modified_abbreviation: str

residue_original_abbreviation: str

Methods

__init__(**data)	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, ...])
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)