VdwContact presets (#223)

* add presets for VdWContact
* fix intersphinx_mapping

CHANGELOG.md

@@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- `VdWContact` now accepts a `preset` parameter to easily use different van der Waals radii values:
+  one of `mdanalysis` (default), `rdkit`, or `csd`.
 - `IFP.interactions()` iterator that yields all interaction data for a given frame in
   a single flat structure. This makes iterating over the `fp.ifp` results a bit
   easier / less nested.

docs/conf.py

@@ -110,12 +110,12 @@
 html_static_path = []  # ['_static']
 
 intersphinx_mapping = {
-    "https://docs.python.org/3/": None,
-    "https://numpy.org/doc/stable/": None,
-    "https://docs.mdanalysis.org/stable/": None,
-    "https://www.rdkit.org/docs/": None,
-    "https://pandas.pydata.org/docs/": None,
-    "https://multiprocess.readthedocs.io/en/latest/": None,
+    "python": ("https://docs.python.org/3/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "mdanalysis": ("https://docs.mdanalysis.org/stable/", None),
+    "rdkit": ("https://www.rdkit.org/docs/", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
+    "multiprocess": ("https://multiprocess.readthedocs.io/en/latest/", None),
 }
 
 

prolif/fingerprint.py

@@ -81,7 +81,11 @@ class Fingerprint:
         PiStacking, Anionic, Cationic, CationPi, PiCation, VdWContact.
     parameters : dict, optional
         New parameters for the interactions. Mapping between an interaction name and a
-        dict of parameters as they appear in the interaction class.
+        dict of parameters as they appear in the interaction class (see the
+        :mod:`prolif.interactions` module's documentation for all classes parameters)::
+
+            >>> fp = plf.Fingerprint(parameters={"Hydrophobic": {"distance": 3.8}})
+
     count : bool
         For a given interaction class and pair of residues, there might be multiple
         combinations of atoms that satisfy the interaction constraints. This parameter

prolif/interactions/constants.py

@@ -0,0 +1,114 @@
+"""
+Constants used by the package for interactions.
+"""
+
+from MDAnalysis.topology.tables import vdwradii
+from rdkit.Chem import GetPeriodicTable
+
+VDWRADII = {symbol.capitalize(): radius for symbol, radius in vdwradii.items()}
+
+PT = GetPeriodicTable()
+RDKIT_VDWRADII = {PT.GetElementSymbol(i): PT.GetRvdw(i) for i in range(1, 119)}
+
+# Table 1 of https://doi.org/10.1039/C3DT50599E
+CSD_VDWRADII = {
+    "H": 1.2,
+    "He": 1.43,
+    "Li": 2.12,
+    "Be": 1.98,
+    "B": 1.91,
+    "C": 1.77,
+    "N": 1.66,
+    "O": 1.5,
+    "F": 1.46,
+    "Ne": 1.58,
+    "Na": 2.5,
+    "Mg": 2.51,
+    "Al": 2.25,
+    "Si": 2.19,
+    "P": 1.9,
+    "S": 1.89,
+    "Cl": 1.82,
+    "Ar": 1.83,
+    "K": 2.73,
+    "Ca": 2.62,
+    "Sc": 2.58,
+    "Ti": 2.46,
+    "V": 2.42,
+    "Cr": 2.45,
+    "Mn": 2.45,
+    "Fe": 2.44,
+    "Co": 2.4,
+    "Ni": 2.4,
+    "Cu": 2.38,
+    "Zn": 2.39,
+    "Ga": 2.32,
+    "Ge": 2.29,
+    "As": 1.88,
+    "Se": 1.82,
+    "Br": 1.86,
+    "Kr": 2.25,
+    "Rb": 3.21,
+    "Sr": 2.84,
+    "Y": 2.75,
+    "Zr": 2.52,
+    "Nb": 2.56,
+    "Mo": 2.45,
+    "Tc": 2.44,
+    "Ru": 2.46,
+    "Rh": 2.44,
+    "Pd": 2.15,
+    "Ag": 2.53,
+    "Cd": 2.49,
+    "In": 2.43,
+    "Sn": 2.42,
+    "Sb": 2.47,
+    "Te": 1.99,
+    "I": 2.04,
+    "Xe": 2.06,
+    "Cs": 3.48,
+    "Ba": 3.03,
+    "La": 2.98,
+    "Ce": 2.88,
+    "Pr": 2.92,
+    "Nd": 2.95,
+    "Sm": 2.9,
+    "Eu": 2.87,
+    "Gd": 2.83,
+    "Tb": 2.79,
+    "Dy": 2.87,
+    "Ho": 2.81,
+    "Er": 2.83,
+    "Tm": 2.79,
+    "Yb": 2.8,
+    "Lu": 2.74,
+    "Hf": 2.63,
+    "Ta": 2.53,
+    "W": 2.57,
+    "Re": 2.49,
+    "Os": 2.48,
+    "Ir": 2.41,
+    "Pt": 2.29,
+    "Au": 2.32,
+    "Hg": 2.45,
+    "Tl": 2.47,
+    "Pb": 2.6,
+    "Bi": 2.54,
+    "Ac": 2.8,
+    "Th": 2.93,
+    "Pa": 2.88,
+    "U": 2.71,  # noqa
+    "Np": 2.82,
+    "Pu": 2.81,
+    "Am": 2.83,
+    "Cm": 3.05,
+    "Bk": 3.4,
+    "Cf": 3.05,
+    "Es": 2.7,
+}
+
+VDW_PRESETS = {
+    "mdanalysis": VDWRADII,
+    "rdkit": RDKIT_VDWRADII,
+    "csd": CSD_VDWRADII,
+}

prolif/interactions/interactions.py

@@ -12,8 +12,8 @@
 
 from itertools import product
 from math import degrees, radians
+from typing import Dict, Literal, Optional
 
-from MDAnalysis.topology.tables import vdwradii
 from rdkit import Geometry
 from rdkit.Chem import MolFromSmarts
 
@@ -24,6 +24,7 @@
     Interaction,
     SingleAngle,
 )
+from prolif.interactions.constants import VDW_PRESETS, VDWRADII  # noqa
 from prolif.utils import angle_between_limits, get_centroid, get_ring_normal_vector
 
 __all__ = [
@@ -43,7 +44,6 @@
     "XBAcceptor",
     "XBDonor",
 ]
-VDWRADII = {symbol.capitalize(): radius for symbol, radius in vdwradii.items()}
 
 
 class Hydrophobic(Distance):
@@ -438,13 +438,19 @@ class VdWContact(Interaction):
 
     Parameters
     ----------
-    tolerance : float
+    tolerance : float, optional
         Tolerance added to the sum of vdW radii of atoms before comparing to
         the interatomic distance. If ``distance <= sum_vdw + tolerance`` the
-        atoms are identified as a contact
+        atoms are identified as a contact.
     vdwradii : dict, optional
         Updates to the vdW radii dictionary, with elements (first letter uppercase) as a
         key and the radius as a value.
+    preset : str, optional
+        Which preset of vdW radii to use. ``mdanalysis`` and ``rdkit`` correspond to the
+        values used by the corresponding package, ``csd`` uses values calculated from
+        the Cambridge Structural Database in doi.org/10.1039/C3DT50599E. ``rdkit`` and
+        ``csd`` should contain almost all elements, as opposed to ``mdanalysis`` which
+        only defines a limited subset.
 
     Raises
     ------
@@ -455,15 +461,41 @@ class VdWContact(Interaction):
     .. versionchanged:: 2.0.0
         Added the ``vdwradii`` parameter.
 
+    .. versionchanged:: 2.1.0
+        Added the ``preset`` parameter.
+
     """
 
-    def __init__(self, tolerance=0.0, vdwradii=None):
+    def __init__(
+        self,
+        tolerance: float = 0.0,
+        vdwradii: Optional[Dict[str, float]] = None,
+        preset: Literal["mdanalysis", "rdkit", "csd"] = "mdanalysis",
+    ) -> None:
         if tolerance >= 0:
             self.tolerance = tolerance
         else:
             raise ValueError("`tolerance` must be 0 or positive")
         self._vdw_cache = {}
-        self.vdwradii = {**VDWRADII, **vdwradii} if vdwradii else VDWRADII
+        self.preset = preset.lower()
+        preset_vdw = VDW_PRESETS[self.preset]
+        self.vdwradii = {**preset_vdw, **vdwradii} if vdwradii else preset_vdw
+
+    def _get_radii_sum(self, atom1: str, atom2: str) -> float:
+        try:
+            return self.vdwradii[atom1] + self.vdwradii[atom2]
+        except KeyError:
+            missing = []
+            if atom1 not in self.vdwradii:
+                missing.append(f"{atom1!r}")
+            if atom2 not in self.vdwradii:
+                missing.append(f"{atom2!r}")
+            raise ValueError(
+                f"van der Waals radius for atom {' and '.join(missing)} not found."
+                " Either specify the missing radii in the `vdwradii` parameter for the"
+                " VdWContact interaction, or use a preset different from the current"
+                f" {self.preset!r}."
+            ) from None
 
     def detect(self, ligand, residue):
         lxyz = ligand.GetConformer()
@@ -475,7 +507,7 @@ def detect(self, ligand, residue):
             try:
                 vdw = self._vdw_cache[elements]
             except KeyError:
-                vdw = self.vdwradii[lig] + self.vdwradii[res] + self.tolerance
+                vdw = self._get_radii_sum(lig, res) + self.tolerance
                 self._vdw_cache[elements] = vdw
             dist = lxyz.GetAtomPosition(la.GetIdx()).Distance(
                 rxyz.GetAtomPosition(ra.GetIdx()),

tests/test_interactions.py

@@ -8,6 +8,7 @@
 from prolif.fingerprint import Fingerprint
 from prolif.interactions import VdWContact
 from prolif.interactions.base import _INTERACTIONS, Interaction, get_mapindex
+from prolif.interactions.constants import VDW_PRESETS
 
 # disable rdkit warnings
 lg = RDLogger.logger()
@@ -183,6 +184,25 @@ def test_vdwcontact_vdwradii_update(self, any_mol, any_other_mol):
         metadata = vdw.detect(any_mol[0], any_other_mol[0])
         assert next(metadata, None) is None
 
+    @pytest.mark.parametrize(
+        ("any_mol", "any_other_mol"),
+        [("benzene", "cation")],
+        indirect=["any_mol", "any_other_mol"],
+    )
+    @pytest.mark.parametrize("preset", ["mdanalysis", "rdkit", "csd"])
+    def test_vdwcontact_preset(self, any_mol, any_other_mol, preset):
+        vdw = VdWContact(preset=preset)
+        metadata = vdw.detect(any_mol[0], any_other_mol[0])
+        assert next(metadata, None) is not None
+        assert vdw.vdwradii == VDW_PRESETS[preset]
+
+    def test_vdwcontact_radii_missing(self):
+        vdw = VdWContact(preset="mdanalysis")
+        with pytest.raises(
+            ValueError, match=r"van der Waals radius for atom .+ not found"
+        ):
+            vdw._get_radii_sum("X", "Y")
+
     @pytest.mark.parametrize(
         ("interaction_qmol", "smiles", "expected"),
         [