Feat/update vdw radii

doc/examples/scripts/structure/modeling/rotamer_library.py

@@ -64,7 +64,7 @@
         support = coord[atom_i]
 
         # Only atoms at one side of the rotatable bond should be moved
-        # So the original Bondist is taken...
+        # So the original Bondlist is taken...
         bond_list_without_axis = residue.bonds.copy()
         # ...the rotatable bond is removed...
         bond_list_without_axis.remove_bond(atom_i, atom_j)

doc/references.bib

@@ -542,6 +542,19 @@ @article{Ma2002
   doi = {10.1093/bioinformatics/18.3.440}
 }
 
+@article{Mantina2009,
+  author = {Mantina, Manjeera and Chamberlin, Adam C. and Valero, Rosendo and Cramer, Christopher J. and Truhlar, Donald G.},
+  title = {Consistent van der Waals Radii for the Whole Main Group},
+  journal = {The Journal of Physical Chemistry A},
+  volume = {113},
+  number = {19},
+  pages = {5806-5812},
+  year = {2009},
+  doi = {10.1021/jp8111556},
+  note = {PMID: 19382751},
+  url = {https://doi.org/10.1021/jp8111556}
+}
+
 @article{Mariani2013,
   title = {{{lDDT}}: A Local Superposition-Free Score for Comparing Protein Structures and Models Using Distance Difference Tests},
   shorttitle = {{{lDDT}}},

src/biotite/structure/info/radii.py

@@ -26,37 +26,106 @@
     ("S",  1, 0) : 1.77,
     ("S",  2, 0) : 1.77, # Not official, added for completeness (MET)
     ("S",  2, 1) : 1.77,
-    ("F",  1, 0) : 1.47, # Taken from _SINGLE_RADII
-    ("CL", 1, 0) : 1.75, # Taken from _SINGLE_RADII
-    ("BR", 1, 0) : 1.85, # Taken from _SINGLE_RADII
+    ("F",  1, 0) : 1.47, # Taken from _SINGLE_ELEMENT_VDW_RADII
+    ("CL", 1, 0) : 1.75, # Taken from _SINGLE_ELEMENT_VDW_RADII
+    ("BR", 1, 0) : 1.85, # Taken from _SINGLE_ELEMENT_VDW_RADII
     ("I",  1, 0) : 1.98, # Taken from _SINGLE_RADII
 }
 
-_SINGLE_RADII = {
-    "H":  1.20,
+_SINGLE_ELEMENT_VDW_RADII = {
+    # Main group
+    # Row 1 (Period 1)
+    "H":  1.10,
     "HE": 1.40,
 
+    # Row 2 (Period 2)
+    "LI": 1.81,
+    "BE": 1.53,
+    "B":  1.92,
     "C":  1.70,
     "N":  1.55,
     "O":  1.52,
     "F":  1.47,
     "NE": 1.54,
 
+    # Row 3 (Period 3)
+    "NA": 2.27,
+    "MG": 1.73,
+    "AL": 1.84,
     "SI": 2.10,
     "P":  1.80,
     "S":  1.80,
     "CL": 1.75,
     "AR": 1.88,
 
+    # Row 4 (Period 4)
+    "K":  2.75,
+    "CA": 2.31,
+    "GA": 1.87,
+    "GE": 2.11,
     "AS": 1.85,
     "SE": 1.90,
-    "BR": 1.85,
+    "BR": 1.83,
     "KR": 2.02,
 
+    # Row 5 (Period 5)
+    "RB": 3.03,
+    "SR": 2.49,
+    "IN": 1.93,
+    "SN": 2.17,
+    "SB": 2.06,
     "TE": 2.06,
     "I":  1.98,
     "XE": 2.16,
+
+    # Row 6 (Period 6)
+    "CS": 3.43,
+    "BA": 2.68,
+    "TL": 1.96,
+    "PB": 2.02,
+    "BI": 2.07,
+    "PO": 1.97,
+    "AT": 2.02,
+    "RN": 2.20,
+
+    # Row 7 (Period 7)
+    "FR": 3.48,
+    "RA": 2.83,
+
+    # Transition metals (relevant ones only)
+    # Row 1
+    "FE": 2.05,
+    "CU": 2.00,
+    "ZN": 2.10,
+    "MN": 2.05,
+    "CO": 2.00,
+    "NI": 2.00,
+
+    # Row 2
+    'MO': 2.10,
+    'RU': 2.05,
+
+    # Row 3
+    'W': 2.10,
+    'PT': 2.05,
+    'AU': 2.10,
 }
+"""
+Van der Waals radii for main group and transition elements.
+
+Main group:
+Source: https://pubs.acs.org/doi/10.1021/jp8111556, Table 12 (Mantina et al. 2009)
+
+Transition metals:
+Source: RDKit, 2024.9.4 Release
+https://github.com/rdkit/rdkit/blob/af6347963f25cfe8fe4db0638410b2f3a8e8bd89/Code/GraphMol/atomic_data.cpp#L51
+
+Where available, these values were cross-checked vs the CRC Handbook of
+Chemistry and Physics (105th edition) and verified that they are closely
+in line (barring very minor discrepancies, usually < 0.05 Å).
+We cannot use the CRC values directly as they are not permissively licensed.
+"""
+
 # fmt: on
 
 # A dictionary that caches radii for each residue
@@ -167,7 +236,7 @@ def _calculate_protor_radii(res_name):
 def vdw_radius_single(element):
     """
     Get the Van-der-Waals radius of an atom from the given element.
-    :footcite:`Bondi1964`
+    :footcite:`Mantina2009`
 
     Parameters
     ----------
@@ -194,4 +263,4 @@ def vdw_radius_single(element):
     >>> print(vdw_radius_single("C"))
     1.7
     """
-    return _SINGLE_RADII.get(element.upper())
+    return _SINGLE_ELEMENT_VDW_RADII.get(element.upper())

src/biotite/structure/sasa.pyx

@@ -83,7 +83,8 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
             - **Single** - A set, which uses a defined VdW radius for
               every single atom, therefore hydrogen atoms are required
               in the model (e.g. NMR elucidated structures).
-              :footcite:`Bondi1964`
+              Values for main group elements are taken from :footcite:`Mantina2009`,
+              and for relevant transition metals from the RDKit.
 
         By default *ProtOr* is used.
 

tests/structure/data/misc/sasa.py

@@ -2,7 +2,7 @@
 import warnings
 from pathlib import Path
 import mdtraj
-from biotite.structure.info.radii import _SINGLE_RADII as SINGLE_RADII
+from biotite.structure.info.radii import _SINGLE_ELEMENT_VDW_RADII as SINGLE_RADII
 
 PDB_IDS = ["1l2y", "1gya"]
 STRUCTURE_DIR = Path(__file__).parents[1]