pyKVFinder.constitutional

pyKVFinder.constitutional(cavities: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Dict[str, List[List[str]]][source]

Constitutional characterization (interface residues) of the detected cavities.

Parameters:

  • cavities (numpy.ndarray) –

    Cavity points in the 3D grid (cavities[nx][ny][nz]). Cavities array has integer labels in each position, that are:

    • -1: bulk points;

    • 0: biomolecule points;

    • 1: empty space points;

    • >=2: cavity points.

    The empty space points are regions that do not meet the chosen volume cutoff to be considered a cavity.

  • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.

  • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).

  • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.

  • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.

  • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface residues, by default False.

  • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selectedA list of integer labels of each cavity to be selected, by default None.

  • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.

  • verbose (bool, optional) – Print extra information to standard output, by default False.

Returns:

residues – A dictionary with a list of interface residues for each detected cavity.

Return type:

Dict[str, List[List[str]]]

Raises:

  • TypeError – cavities must be a numpy.ndarray.

  • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).

  • TypeError – atomic must be a list or a numpy.ndarray.

  • ValueError – atomic has incorrect shape. It must be (n, 8).

  • TypeError – vertices must be a list or a numpy.ndarray.

  • ValueError – vertices has incorrect shape. It must be (4, 3).

  • TypeError – step must be a positive real number.

  • ValueError – step must be a positive real number.

  • TypeError – probe_in must be a non-negative real number.

  • ValueError – probe_in must be a non-negative real number.

  • TypeError – ignore_backbone must be a boolean.

  • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).

  • ValueError – Invalid selection: {selection}.

  • TypeError – nthreads must be a positive integer.

  • ValueError – nthreads must be a positive integer.

  • TypeError – verbose must be a boolean.

Note

The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.

Note

The classes of residues are:

  • Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.

  • Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.

  • Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.

  • Negatively charged (R4): Aspartate, Glutamate.

  • Positively charged (R5): Arginine, Histidine, Lysine.

  • Non-standard (RX): Non-standard residues.

See also

read_pdb, read_xyz, detect, calculate_frequencies, write_results

Example

With the cavity points identified with detect, atomic data read with read_pdb or read_xyz, we can perform a constitutional characterization, that identifies the interface residues surrounding the cavities:

>>> from pyKVFinder import constitutional
>>> residues = constitutional(cavities, atomic, vertices)
>>> residues
{'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}

However, users may opt to ignore backbones contacts (C, CA, N, O) with the cavity when defining interface residues. Then, users must set ignore_backbone flag to True.

>>> residues = constitutional(cavities, atomic, vertices, ignore_backbone=True)
>>> residues
{'KAA': [['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE']], 'KAE': [['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['103', 'E', 'LEU'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['175', 'E', 'ASP'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['277', 'E', 'LEU']], 'KAR': [['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}