Source code for graphein.protein.config

"""Base Config object for use with Protein Graph Construction."""
# Graphein
# Author: Arian Jamasb <>
# License: MIT
# Project Website:
# Code Repository:
from __future__ import annotations

from functools import partial
from pathlib import Path
from typing import Any, Callable, List, Optional, Union

from deepdiff import DeepDiff
from pydantic import BaseModel
from typing_extensions import Literal

from graphein.protein.edges.distance import add_peptide_bonds
from graphein.protein.features.nodes.amino_acid import meiler_embedding
from graphein.utils.config import PartialMatchOperator, PathMatchOperator

class DSSPConfig(BaseModel):
    executable: str = "mkdssp"

[docs]class GetContactsConfig(BaseModel): """ Config object for parameters relating to running ``GetContacts``. ``GetContacts`` is an optional dependency from which intramolecular interactions can be computed and used as edges in the graph. More information about ``GetContacts`` can be found at :param get_contacts_path: Path to ``GetContacts`` installation :type get_contacts_path: pathlib.Path :param contacts_dir: Path to store output of ``GetContacts`` :type contacts_dir: pathlib.Path :param pdb_dir: Path to PDB files to be used to compute intramolecular interactions. :type pdb_dir: pathlib.Path :param granularity: Specifies the node types of the graph, defaults to ``"CA"`` for alpha-carbons as nodes. Other options are ``"CB"`` (beta-carbon), ``"atom"`` for all-atom graphs, and ``"centroid"`` for nodes positioned as residue centroids. :type granularity: str """ get_contacts_path: Path = Path( "/Users/arianjamasb/github/getcontacts/" ).resolve() contacts_dir: Path = Path("../examples/contacts/").resolve() pdb_dir: Path = Path("../examples/pdbs/").resolve() granularity: str = "CA"
GraphAtoms = Literal[ "N", "CA", "C", "O", "CB", "OG", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "OD1", "ND2", "CG1", "CG2", "CD", "CE", "NZ", "OD2", "OE1", "NE2", "OE2", "OH", "NE", "NH1", "NH2", "OG1", "SD", "ND1", "SG", "NE1", "CE3", "CZ2", "CZ3", "CH2", "OXT", ] """Allowable atom types for nodes in the graph.""" GranularityOpts = Literal["atom", "centroids"] """Allowable granularity options for nodes in the graph."""
[docs]class ProteinGraphConfig(BaseModel): """ Config Object for Protein Structure Graph Construction. If you encounter a problematic structure, perusing may provide some additional insight. PDBs are notoriously troublesome and this is an excellent overview. :param granularity: Controls the granularity of the graph construction. ``"atom"`` builds an atomic-scale graph where nodes are constituent atoms. Residue-level graphs can be build by specifying which constituent atom should represent node positions (see :const:`~graphein.protein.config.GraphAtoms`). Additionally, ``"centroids"`` can be specified to compute the centre of gravity for a given atom (Specified in :const:`~graphein.protein.config.GranularityOpts`). Defaults to ``"CA"`` (alpha-Carbon). :type granularity: str (Union[graphein.protein.config.GraphAtoms, graphein.protein.config.GranularityOpts]) :param keep_hets: Controls whether or not heteroatoms are removed from the PDB file. These are typically modified residues, bound ligands, crystallographic adjuvants, ions or water molecules. For more information, see: :type keep_hets: bool :param insertions: Controls whether or not insertions are allowed. :type insertions: bool :param pdb_dir: Specifies path to download protein structures into. :type pdb_dir: pathlib.Path :param verbose: Specifies verbosity of graph creation process. :type verbose: bool :param exclude_waters: Specifies whether or not water molecules are excluded from the structure :type excluded_waters: bool :param deprotonate: Specifies whether or not to remove ``H`` atoms from the graph. :type deprotonate: bool :param protein_df_processing_functions: List of functions that take a ``pd.DataFrame`` and return a ``pd.DataFrame``. This allows users to define their own series of processing functions for the protein structure DataFrame and override the default sequencing of processing steps provided by Graphein. We refer users to our low-level API tutorial for more details. :type protein_df_processing_functions: Optional[List[Callable]] :param edge_construction_functions: List of functions that take an ``nx.Graph`` and return an ``nx.Graph`` with desired edges added. Prepared edge constructions can be found in :ref:`graphein.protein.edges` :type edge_construction_functions: List[Callable] :param node_metadata_functions: List of functions that take an ``nx.Graph`` :type node_metadata_functions: List[Callable], optional :param edge_metadata_functions: List of functions that take an :type edge_metadata_functions: List[Callable], optional :param graph_metadata_functions: List of functions that take an ``nx.Graph`` and return an ``nx.Graph`` with added graph-level features and metadata. :type graph_metadata_functions: List[Callable], optional :param get_contacts_config: Config object containing parameters for running ``GetContacts`` for computing intramolecular contact-based edges. Defaults to None. :type get_contacts_config: GetContactsConfig, optional :param dssp_config: Config Object containing reference to ``DSSP`` executable. Defaults to None. **NB** DSSP must be installed. See installation instructions: :type dssp_config: DSSPConfig, optional """ granularity: Union[GraphAtoms, GranularityOpts] = "CA" keep_hets: bool = False insertions: bool = False pdb_dir: Path = Path( "../examples/pdbs/" ) # Also suggest to avoid hard-coding paths if possible! verbose: bool = False exclude_waters: bool = True deprotonate: bool = False # Graph construction functions protein_df_processing_functions: Optional[List[Callable]] = None edge_construction_functions: List[Union[Callable, str]] = [ add_peptide_bonds ] node_metadata_functions: Optional[List[Union[Callable, str]]] = [ meiler_embedding ] edge_metadata_functions: Optional[List[Union[Callable, str]]] = None graph_metadata_functions: Optional[List[Callable]] = None # External Dependency configs get_contacts_config: Optional[GetContactsConfig] = None dssp_config: Optional[DSSPConfig] = None def __eq__(self, other: Any) -> bool: """Overwrites the BaseModel __eq__ function in order to check more specific cases (like partial functions).""" if isinstance(other, ProteinGraphConfig): return ( DeepDiff( self, other, custom_operators=[ PartialMatchOperator(types=[partial]), PathMatchOperator(types=[Path]), ], ) == {} ) return self.dict() == other
[docs]class ProteinMeshConfig(BaseModel): """ Config object for parameters relating to Protein Mesh construction with ``PyMol`` **NB** PyMol must be installed. See: :param pymol_command_line_options: List of CLI args for running PyMol. See: Defaults to ``"-cKq"`` () :type pymol_command_line_options: str, optional :param pymol_commands: List of Commands passed to PyMol in surface construction. :type pymol_commands: List[str], optional """ pymol_command_line_options: Optional[str] = "-cKq" pymol_commands: Optional[List[str]] = ["show surface"]