Graph plots

CHANGELOG.md

@@ -206,6 +206,8 @@
 * [Bugfix] - [#208](https://github.com/a-r-j/graphein/pull/208) explicitly installs `jupyter_contrib_nbextensions` in Docker.
 
 ### 1.5.1
+* [Feature] - [#197](https://github.com/a-r-j/graphein/pull/197/) adds support for sizing and colouring nodes in asteroid plots
+* [Feature] - [#197](https://github.com/a-r-j/graphein/pull/197/) adds utilities for retrieving a list of graph/node/edge attribute names in `graphein.utils.utils`.
 
 #### Protein
 
@@ -215,6 +217,7 @@
 * [Feature] - [#189](https://github.com/a-r-j/graphein/pull/189/) adds a `residue_id` column to PDB dfs to enable easier accounting in atom graphs.
 * [Feature] - [#189](https://github.com/a-r-j/graphein/pull/189/) refactors torch geometric datasets to use parallelised download for faster dataset preparation.
 
+
 #### Bugfixes
 
 * [Patch] - [#187](https://github.com/a-r-j/graphein/pull/187) updates sequence retrieval due to UniProt API changes.

graphein/protein/features/nodes/amino_acid.py

@@ -18,6 +18,8 @@
     BASE_AMINO_ACIDS,
     HYDROGEN_BOND_ACCEPTORS,
     HYDROGEN_BOND_DONORS,
+    HYDROPHOBICITY_SCALES,
+    HYDROPHOBICITY_TYPE,
     RESI_THREE_TO_1,
 )
 from graphein.utils.utils import onek_encoding_unk
@@ -277,3 +279,43 @@ def hydrogen_bond_acceptor(
     if not sum_features:
         features = np.array(features > 0).astype(int)
     d["hbond_acceptors"] = features
+
+
+def hydrophobicity(
+    n: str,
+    d: Dict[str, Any],
+    mapping: HYDROPHOBICITY_TYPE = "kd",
+    return_array: bool = True,
+) -> Union[np.ndarray, pd.Series]:
+    """
+    Adds hydrophobicity values for each residue to graph nodes.
+    See :const:`~graphein.protein.resi_atoms.HYDROPHOBICITY_SCALES` for
+    values and available scales.
+
+    :param n: Node ID. Unused - kept to maintain consistent function signature.
+    :type n: str
+    :param d: Dictionary of node attributes.
+    :type d: Dict[str, Any]
+    :param mapping: Which hydrophobicity scale to use. See
+        :const:`~graphein.protein.resi_atoms.HYDROPHOBICITY_TYPE` for supported types.
+    :type mapping: graphien.protein.resi_atoms.HYDROPHOBICITY_TYPE
+    :param return_array: If ``True``, returns a ``np.ndarray``, otherwise returns
+        a ``pd.Series``. Default is ``True``.
+    :type return_array: bool
+    """
+    assert (
+        mapping in HYDROPHOBICITY_SCALES.keys()
+    ), f"Unsupported mapping: {mapping}. Supported mappings: {HYDROPHOBICITY_SCALES.keys()}"
+    hydr = HYDROPHOBICITY_SCALES[mapping]
+
+    amino_acid = d["residue_name"]
+    try:
+        features = hydr[amino_acid]
+    except:
+        features = pd.Series(np.zeros(1))
+
+    if return_array:
+        features = np.array(features)
+
+    d[f"hydrophobicity_{mapping}"] = features
+    return features

graphein/protein/resi_atoms.py

@@ -19,6 +19,7 @@
 
 import numpy as np
 from sklearn.preprocessing import StandardScaler
+from typing_extensions import Literal
 
 BACKBONE_ATOMS: List[str] = ["N", "CA", "C", "O"]
 """Atoms present in Amino Acid Backbones."""
@@ -1103,6 +1104,151 @@
 https://pubs.acs.org/doi/10.1021/j100785a001
 """
 
+HYDROPHOBICITY_TYPE = Literal["kd", "ww", "hh", "mf", "tt"]
+"""Supported hydrophobicity types. See :const:`~graphein.protein.resi_atoms.HYDROPHOBICITY_SCALES` for further details."""
+
+HYDROPHOBICITY_SCALES: Dict[str, Dict[str, float]] = {
+    "kd": {  # kdHydrophobicity (a)
+        "ILE": 4.5,
+        "VAL": 4.2,
+        "LEU": 3.8,
+        "PHE": 2.8,
+        "CYS": 2.5,
+        "MET": 1.9,
+        "ALA": 1.8,
+        "GLY": -0.4,
+        "THR": -0.7,
+        "SER": -0.8,
+        "TRP": -0.9,
+        "TYR": -1.3,
+        "PRO": -1.6,
+        "HIS": -3.2,
+        "GLU": -3.5,
+        "GLN": -3.5,
+        "ASP": -3.5,
+        "ASN": -3.5,
+        "LYS": -3.9,
+        "ARG": -4.5,
+    },
+    "ww": {  # wwHydrophobicity (b)
+        "ILE": 0.31,
+        "VAL": -0.07,
+        "LEU": 0.56,
+        "PHE": 1.13,
+        "CYS": 0.24,
+        "MET": 0.23,
+        "ALA": -0.17,
+        "GLY": -0.01,
+        "THR": -0.14,
+        "SER": -0.13,
+        "TRP": 1.85,
+        "TYR": 0.94,
+        "PRO": -0.45,
+        "HIS": -0.96,
+        "GLU": -2.02,
+        "GLN": -0.58,
+        "ASP": -1.23,
+        "ASN": -0.42,
+        "LYS": -0.99,
+        "ARG": -0.81,
+    },
+    "hh": {  # hhHydrophobicity (c)
+        "ILE": -0.60,
+        "VAL": -0.31,
+        "LEU": -0.55,
+        "PHE": -0.32,
+        "CYS": -0.13,
+        "MET": -0.10,
+        "ALA": 0.11,
+        "GLY": 0.74,
+        "THR": 0.52,
+        "SER": 0.84,
+        "TRP": 0.30,
+        "TYR": 0.68,
+        "PRO": 2.23,
+        "HIS": 2.06,
+        "GLU": 2.68,
+        "GLN": 2.36,
+        "ASP": 3.49,
+        "ASN": 2.05,
+        "LYS": 2.71,
+        "ARG": 2.58,
+    },
+    "mf": {  # mfHydrophobicity (d)
+        "ILE": -1.56,
+        "VAL": -0.78,
+        "LEU": -1.81,
+        "PHE": -2.20,
+        "CYS": 0.49,
+        "MET": -0.76,
+        "ALA": 0.0,
+        "GLY": 1.72,
+        "THR": 1.78,
+        "SER": 1.83,
+        "TRP": -0.38,
+        "TYR": -1.09,
+        "PRO": -1.52,
+        "HIS": 4.76,
+        "GLU": 1.64,
+        "GLN": 3.01,
+        "ASP": 2.95,
+        "ASN": 3.47,
+        "LYS": 5.39,
+        "ARG": 3.71,
+    },
+    "tt": {  # ttHydrophobicity (e)
+        "ILE": 1.97,
+        "VAL": 1.46,
+        "LEU": 1.82,
+        "PHE": 1.98,
+        "CYS": -0.30,
+        "MET": 1.40,
+        "ALA": 0.38,
+        "GLY": -0.19,
+        "THR": -0.32,
+        "SER": -0.53,
+        "TRP": 1.53,
+        "TYR": 0.49,
+        "PRO": -1.44,
+        "HIS": -1.44,
+        "GLU": -2.90,
+        "GLN": -1.84,
+        "ASP": -3.27,
+        "ASN": -1.62,
+        "LYS": -3.46,
+        "ARG": -2.57,
+    },
+}
+"""
+Set of (5) dictionaries that map amino acid 3-letter codes to their hydrophobicity.
+
+The scales included are from Chimera (UCSF) https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html
+and are as follows:
+
+    * kdHydrophobicity
+        (a) A simple method for displaying the hydropathic character of a protein. Kyte J, Doolittle RF. J Mol Biol. 1982 May 5;157(1):105-32.
+        https://www.ncbi.nlm.nih.gov/pubmed/7108955
+
+    * wwHydrophobicity
+        (b) Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Wimley WC, White SH. Nat Struct Biol. 1996 Oct;3(10):842-8.
+        https://www.ncbi.nlm.nih.gov/pubmed/8836100
+
+    * hhHydrophobicity
+        (c) Recognition of transmembrane helices by the endoplasmic reticulum translocon. Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, von Heijne G. Nature. 2005 Jan 27;433(7024):377-81, supplementary data.
+        https://www.ncbi.nlm.nih.gov/pubmed/15674282
+
+        In this scale, negative values indicate greater hydrophobicity.
+
+    * mfHydrophobicity
+        (d)  Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Moon CP, Fleming KG. Proc Natl Acad Sci USA. 2011 Jun 21;108(25):10174-7, supplementary data.
+        https://www.ncbi.nlm.nih.gov/pubmed/21606332
+
+        In this scale, negative values indicate greater hydrophobicity.
+
+    * ttHydrophobicity
+        (e) An amino acid “transmembrane tendency” scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity. Zhao G, London E. Protein Sci. 2006 Aug;15(8):1987-2001.
+        https://www.ncbi.nlm.nih.gov/pubmed/16877712
+"""
 
 ISOELECTRIC_POINTS: Dict[str, float] = {
     "ALA": 6.11,