Library

This is the pydoc code for the library module.

# molli.chem.library Defines two essential classes: MoleculeLibrary and ConformerLibrary that are used for efficient binary storage of chemical data

molli.chem.library.library_type(path: Path | str)

Returns the type (ConformerLibrary or MoleculeLibrary) corresponding to the

This is intended to be a much faster way of determining the appropriate library class corresponding to a file than trial-and-error

Relies on

Parameters:

path (Path | str) – Path to library file

Returns:

Library class that fits the data in the file

Return type:

type

Raises:

SyntaxError – Raised if the UKV file contains unsupported object. This is an unexpected error in most cases.

class molli.chem.library.MoleculeLibrary(path: Path | str, *, overwrite: bool = False, readonly: bool = True, encoding: str = 'utf8', bufsize: int = -1, comment: str = None, **kwargs)

Bases: Collection[Molecule]

This class is an overarching storage system for molecules for that allows for both serialization and deserialization. Reading and writing takes place using keys as placeholders for retrieval

Examples

A MoleculeLibrary can be serialized from existing Molecules

>>> dendrobine = ml.Molecule.load_mol2(ml.files.dendrobine_mol2)
>>> mlib = ml.MoleculeLibrary('test.mlib', readonly=False)
>>> with mlib.writing():
>>>     lib[dendrobine.name] = dendrobine
>>> mlib
MoleculeLibrary(backend=UkvCollectionBackend('test.mlib'), n_items=1)

A MoleculeLibrary can be deserialized and iterated over

>>> mlib = ml.MoleculeLibrary('test.mlib')
>>> with mlib.reading():
>>>     for key in mlib:
>>>         mol = mlib[key]
>>> mol
Molecule(name='dendrobine', formula='C16 H25 N1 O2')
>>> mlib
MoleculeLibrary(backend=UkvCollectionBackend('test.mlib'), n_items=1)

These actions can be done at the same time to transfer structures

>>> mlib1 = ml.MoleculeLibrary('test1.mlib')
>>> mlib2 = ml.MoleculeLibrary('test2.mlib', readonly=False)
>>> with mlib1.reading(), mlib2.writing():
>>>     for key in mlib1:
>>>         mol = mlib1[key]
>>>         mlib2[mol.name] = mol

Notes

The default behavior with writing will be appending structures, which can be changed with the use of overwrite

class molli.chem.library.ConformerLibrary(path: Path | str, *, overwrite: bool = False, readonly: bool = True, encoding: str = 'utf8', bufsize: int = -1, comment: str = None, **kwargs)

Bases: Collection[ConformerEnsemble]

This class is an overarching storage system for ConformerEnsembles for that allows for both serialization and deserialization. Reading and writing takes place using keys as placeholders for retrieval

Examples

A ConformerLibrary can be serialized from existing Molecules

>>> ens = ml.Molecule.load_mol2(ml.files.ens_mol2)
>>> clib = ml.ConformerLibrary('test.clib', readonly=False)
>>> with clib.writing():
>>>     lib[ens.name] = ens
>>> clib
ConformerLibrary(backend=UkvCollectionBackend('test.clib'), n_items=1)

A ConformerLibrary can be deserialized and iterated over

>>> clib = ml.ConformerLibrary('test.clib')
>>> with clib.reading():
>>>     for key in clib:
>>>         ens = clib[key]
>>> ens
ConformerEnsemble(name='pentane', formula='C5 H12')
>>> clib
ConformerLibrary(backend=UkvCollectionBackend('test.clib'), n_items=1)

These actions can be done at the same time to transfer structures

>>> clib1 = ml.ConformerLibrary('test1.clib')
>>> clib2 = ml.ConformerLibrary('test2.clib', readonly=False)
>>> with clib1.reading(), clib2.writing():
>>>     for key in clib1:
>>>         ens = clib1[key]
>>>         clib2[ens.name] = ens

Notes

The default behavior with writing will be appending structures, which can be changed with the use of overwrite