pestifer.objs.patch module

A patch is a modification to a residue or residues defined in the CHARMM force field by PRES records. It is used to apply specific modifications to residues in a molecular structure, such as adding or removing functional groups or modifying the residue’s properties.

class pestifer.objs.patch.Patch(*args, patchname: str, chainID: str, resid: ResID, residue: Residue = None, use_in_segment: str | None = None, use_after_regenerate: bool | None = False)

Bases: BaseObj

A class for handing patch residues

assign_residue(residue: Residue)

Assigns a Residue object to the patch.

chainID: str

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': False}

Configuration for pydantic.BaseModel.

model_post_init(context: Any, /) → None

This function is meant to behave like a BaseModel method to initialize private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

• self – The BaseModel instance.

• context – The context.

patchname: str

resid: ResID

residue: Residue

return_TcL()

Writes the patch command.

shortcode() → str

Convert the Adapter instance to a shortcode string.

Returns:

The shortcode string in the format patchname:chainID:resID.

Return type:

str

use_after_regenerate: bool | None

use_in_segment: str | None

class pestifer.objs.patch.PatchList(initlist: Iterable[T] = ())

Bases: BaseObjList[Patch]

A class for handling lists of Patch objects

This class inherits from BaseObjList and provides methods to manage a list of Patch objects.

assign_residues(Residues: ResidueList) → PatchList

Assigns a list of Residue objects to the patch residues.

Parameters:

Residues (list of Residue) – A list of Residue objects to be assigned to the patch residues.

Returns:

A new PatchList object containing the residues that were not assigned because no applicable residues were found

Return type:

PatchList

describe()

Returns a string description of the PatchList.

Returns:

A description of the PatchList, including the number of patches it contains.

Return type:

str