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Vdw bonds #2706

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32c6af2
draw vdW bond
bjkreitz Jul 12, 2024
c4fea25
adjust remove vdW bond
bjkreitz Jul 15, 2024
e6ef712
change is_molecule_forbidden
bjkreitz Jul 17, 2024
f143e9e
remove comments
bjkreitz Jul 17, 2024
4fa53c7
Merge branch 'main' into vdW_bonds
bjkreitz May 12, 2026
495c893
adding find_formate_delocalization_paths to pathfinder
bjkreitz May 13, 2026
2076aeb
add resonance structure generation for formate to resonance.py
bjkreitz May 13, 2026
3153f51
new has_covalent_surface_bond function
bjkreitz May 13, 2026
61e05e6
add label for vdW bond in get_desorbed_molecules
bjkreitz May 13, 2026
5c4d2e6
combine drawing of vdW and H bonds
bjkreitz May 13, 2026
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14 changes: 10 additions & 4 deletions rmgpy/data/kinetics/family.py
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Expand Up @@ -1670,11 +1670,17 @@ def is_molecule_forbidden(self, molecule):
return True

# forbid vdw multi-dentate molecules for surface families
surface_sites = []
if "surface" in self.label.lower():
if molecule.get_num_atoms('X') > 1:
for atom in molecule.atoms:
if atom.atomtype.label == 'Xv':
return True
if "surface_monodentate_to_vdw_bidentate" in self.label.lower() and molecule.get_num_atoms('X') > 1:
surface_sites = [atom.atomtype.label for atom in molecule.atoms if 'X' in atom.atomtype.label]
if all(site == 'Xv' for site in surface_sites):
return True
else:
if molecule.get_num_atoms('X') > 1:
for atom in molecule.atoms:
if atom.atomtype.label == 'Xv':
return True
Comment on lines 1680 to +1689
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Copilot AI Apr 1, 2026

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This introduces a behavior switch based on a hard-coded substring match of self.label, which makes the forbidden-structure logic depend on naming conventions rather than an explicit family attribute/configuration. This is fragile (label changes become behavior changes). Prefer exposing an explicit flag/attribute on the family (or configuring this in the family definition/data) to control whether mixed covalent+vdW multidentate surface bindings are allowed.

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return False

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2 changes: 1 addition & 1 deletion rmgpy/molecule/converter.py
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Expand Up @@ -97,7 +97,7 @@ def to_rdkit_mol(mol, remove_h=True, return_mapping=False, sanitize=True, save_o
label_dict[label] = [saved_index]
rd_bonds = Chem.rdchem.BondType
orders = {'S': rd_bonds.SINGLE, 'D': rd_bonds.DOUBLE, 'T': rd_bonds.TRIPLE, 'B': rd_bonds.AROMATIC,
'Q': rd_bonds.QUADRUPLE}
'Q': rd_bonds.QUADRUPLE, 'vdW': rd_bonds.UNSPECIFIED}
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Mapping vdW to BondType.UNSPECIFIED may interact poorly with RDKit sanitization and downstream chemistry perception (some RDKit operations treat UNSPECIFIED as query/unknown and can fail or behave unexpectedly on “normal” molecules). Consider either (a) skipping creation of vdW bonds in RDKit and encoding connectivity via properties/atom maps, or (b) conditionally disabling sanitization (or clearly documenting expected sanitizer behavior) when vdW bonds are present.

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# Add the bonds
for atom1 in mol.vertices:
for atom2, bond in atom1.edges.items():
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3 changes: 3 additions & 0 deletions rmgpy/molecule/draw.py
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Expand Up @@ -1214,6 +1214,9 @@ def _render_bond(self, atom1, atom2, bond, cr):
elif bond.is_hydrogen_bond():
# Draw a dashed line
self._draw_line(cr, x1, y1, x2, y2, dashed=True, dash_sizes=[0.5, 3.5])
elif bond.is_van_der_waals():
# Draw a dashed line
self._draw_line(cr, x1, y1, x2, y2, dashed=True, dash_sizes=[0.5, 3.5])
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The hydrogen_bond and van_der_waals rendering blocks are identical. Combine these branches (e.g., one condition for “draw dashed bond”) to reduce duplication and keep styling consistent if dash parameters change later.

Suggested change
elif bond.is_hydrogen_bond():
# Draw a dashed line
self._draw_line(cr, x1, y1, x2, y2, dashed=True, dash_sizes=[0.5, 3.5])
elif bond.is_van_der_waals():
# Draw a dashed line
self._draw_line(cr, x1, y1, x2, y2, dashed=True, dash_sizes=[0.5, 3.5])
elif bond.is_hydrogen_bond() or bond.is_van_der_waals():
# Draw a dashed line for hydrogen bonds and van der Waals interactions
self._draw_line(cr, x1, y1, x2, y2, dashed=True, dash_sizes=[0.5, 3.5])

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else:
self._draw_line(cr, x1, y1, x2, y2)
else:
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20 changes: 16 additions & 4 deletions rmgpy/molecule/molecule.py
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Expand Up @@ -62,7 +62,7 @@

################################################################################

bond_orders = {'S': 1, 'D': 2, 'T': 3, 'B': 1.5}
bond_orders = {'S': 1, 'D': 2, 'T': 3, 'B': 1.5, 'vdW': 0}

globals().update({
'bond_orders': bond_orders,
Expand Down Expand Up @@ -1258,9 +1258,19 @@ def remove_van_der_waals_bonds(self):
Remove all van der Waals bonds.
"""
cython.declare(bond=Bond)
for bond in self.get_all_edges():
if bond.is_van_der_waals():
self.remove_bond(bond)
if self.is_multidentate():
#bond_types =
#possible_bonds_with_resonance = #TODO: Include possible nitrogen bonds
if any([k in ['O-X', 'C#X', 'C=X', 'C-X'] for k in self.enumerate_bonds()]):
pass
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This logic is hard to reason about and brittle due to (1) reliance on hard-coded bond “signature” strings, (2) order-dependence (e.g., if enumeration yields X-O instead of O-X), (3) the placeholder pass, and (4) commented-out partial lines. Consider refactoring to a clearly named boolean like has_covalent_surface_bond, avoid constructing a list inside any(...), and make the surface-bond detection order-independent (or use atom/bond properties rather than string signatures).

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else:
for bond in self.get_all_edges():
if bond.is_van_der_waals():
self.remove_bond(bond)
else:
for bond in self.get_all_edges():
if bond.is_van_der_waals():
self.remove_bond(bond)
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The docstring says this method “Remove[s] all van der Waals bonds”, but the new multidentate branch intentionally preserves vdW bonds for certain structures. Update the docstring (or rename/parameterize the method) so callers and future maintainers don’t rely on outdated semantics.

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def sort_atoms(self):
"""
Expand Down Expand Up @@ -2942,6 +2952,8 @@ def get_desorbed_molecules(self):
bonded_atom.increment_radical()
bonded_atom.increment_lone_pairs()
bonded_atom.label = '*4'
elif bond.is_van_der_waals():
bonded_atom.label = '*5'
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The new '*5' label is a magic value with no explanation in this method. If *1–*4 have established meanings elsewhere, please document what *5 represents (and why it’s safe), or define/centralize these labels as named constants to prevent drift and collisions.

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else:
raise NotImplementedError("Can't remove surface bond of type {}".format(bond.order))
desorbed_molecule.remove_atom(site)
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