prolint.core.groups¶

Atom group extensions for ProLint.

This module provides extended atom group classes with additional functionality for biomolecular interaction analysis.

Classes¶

`PLAtomGroupBase`	Abstract base class for ProLint atom group operations.
`ExtendedAtomGroup`	Extended MDAnalysis AtomGroup with additional ProLint functionality.

Module Contents¶

class prolint.core.groups.PLAtomGroupBase[source]¶

Bases: abc.ABC

Abstract base class for ProLint atom group operations.

Defines the interface for atom group manipulation methods used throughout ProLint.

Add atoms to the atom group.

Parameters:

resname (str or list of str, optional) – Residue name(s) to add.
atomname (str or list of str, optional) – Atom name(s) to add.
resnum (int or list of int, optional) – Residue number(s) to add.
atomids (int or list of int, optional) – Atom ID(s) to add.

Returns:

New atom group with added atoms.

Return type:

ExtendedAtomGroup

Remove atoms from the atom group.

Parameters:

resname (str or list of str, optional) – Residue name(s) to remove.
atomname (str or list of str, optional) – Atom name(s) to remove.
resnum (int or list of int, optional) – Residue number(s) to remove.
atomids (int or list of int, optional) – Atom ID(s) to remove.

Returns:

New atom group with specified atoms removed.

Return type:

ExtendedAtomGroup

abstractmethod get_resnames(resids: Iterable[int], out: type[list] | type[dict] = list) → list[str] | Dict[int, str][source]¶

Get residue names for given residue IDs.

Parameters:

resids (Iterable of int) – Residue IDs to look up.
out (type, default=list) – Output format: list or dict.

Returns:

Residue names as list or as {resid: resname} mapping.

Return type:

list of str or dict

abstractmethod get_resids(resname: str) → numpy.ndarray[source]¶

Get residue IDs for a given residue name.

Parameters:: resname (str) – Residue name to look up.
Returns:: Array of residue IDs matching the residue name.
Return type:: ndarray

abstractmethod get_all_resids(resnames: Iterable[str], out: type[list] | type[dict] = list) → list[numpy.ndarray] | Dict[str, numpy.ndarray][source]¶

Get residue IDs for multiple residue names.

Parameters:

resnames (Iterable of str) – Residue names to look up.
out (type, default=list) – Output format: list or dict.

Returns:

Residue IDs as list of arrays or as {resname: resids} mapping.

Return type:

list or dict

abstractmethod filter_resids_by_resname(resids: Iterable[int], resname: str) → numpy.ndarray[source]¶

Filter residue IDs to keep only those matching a residue name.

Parameters:

resids (Iterable of int) – Residue IDs to filter.
resname (str) – Residue name to match.

Returns:

Subset of input resids that match the residue name.

Return type:

ndarray

property unique_resnames: numpy.ndarray[source]¶

Abstractmethod:

Unique residue names in the atom group.

Returns:: Array of unique residue names.
Return type:: ndarray

property resname_counts: collections.Counter[source]¶

Abstractmethod:

Count of residues for each residue name.

Returns:: Mapping of residue name to count.
Return type:: Counter

class prolint.core.groups.ExtendedAtomGroup(*args: Any, **kwargs: Any)[source]¶

Bases: MDAnalysis.AtomGroup, PLAtomGroupBase

Extended MDAnalysis AtomGroup with additional ProLint functionality.

Provides enhanced methods for manipulating and querying atom selections, with cached properties for efficient repeated access.

Parameters:

*args (tuple) – Arguments passed to MDAnalysis AtomGroup.
**kwargs (dict) – Keyword arguments passed to MDAnalysis AtomGroup.

Examples

>>> from prolint import Universe
>>> u = Universe("topology.gro", "trajectory.xtc")
>>> u.database.unique_resnames
array(['POPC', 'POPE', 'CHOL'], dtype='<U4')
>>> u.database.resname_counts
Counter({'POPC': 128, 'POPE': 64, 'CHOL': 32})

Add atoms:

>>> extended = u.database.add(resname="DPPC")

Remove atoms:

>>> filtered = u.database.remove(resname="CHOL")