Graph plots

CHANGELOG.md

@@ -1,4 +1,6 @@
 ### 1.5.1
+* [Feature] - [#197](https://github.com/a-r-j/graphein/pull/197/) adds support for sizing and colouring nodes in asteroid plots
+
 
 #### Protein
 
@@ -8,6 +10,7 @@
 * [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 +18,7 @@
     HYDROGEN_BOND_ACCEPTORS,
     HYDROGEN_BOND_DONORS,
     RESI_THREE_TO_1,
+    HYDROPHOBICITY_SCALES
 )
 from graphein.utils.utils import onek_encoding_unk
 
@@ -248,3 +249,46 @@ def hydrogen_bond_acceptor(
     if not sum_features:
         features = np.array(features > 0).astype(int)
     d["hbond_acceptors"] = features
+
+
+
+"""
+TODO: add a similar 'load in' function from .csv as above?
+or stick to hydrophobicity as dict?
+
+TODO: make vector of all hydrophobicity scales instead of one chosen scale?
+
+TODO: sum features bool?
+"""
+def hydrophobicity(
+    n: str, 
+    d: Dict[str, any],
+    mapping: str = "kd",
+    return_array: bool = True,
+
+) -> None:
+    """
+    :param n: node ID
+    :type n: str
+    :param d: dict of node attributes
+    :type d: Dict[str, any]
+
+    :param mapping: which hydrophobicity scale to use.
+    :type mapping: str
+    :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()
+    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["hydrophobicity"] = features
+    return features

graphein/protein/resi_atoms.py

@@ -836,6 +836,148 @@
 https://pubs.acs.org/doi/10.1021/j100785a001
 """
 
+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,