Vdw bonds#2706

Merged

JacksonBurns merged 27 commits into

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vdW_bonds

Jun 8, 2026

Commits on Jun 8, 2026

draw vdW bond, the same way we do H bonds

bjkreitz
authored and
JacksonBurns
committed
Adjust remove vdW bond, using new has_covalent_surface_bond function

bjkreitz
authored and
JacksonBurns
committed
Make has_covalent_surface_bond more efficient.

rwest
authored and
JacksonBurns
committed
Add test_has_covalent_surface_bond to test has_covalent_surface_bond.

rwest
authored and
JacksonBurns
committed
Simplify remove_van_der_waals_bonds

rwest
authored and
JacksonBurns
committed
Accelerate is_multidentate.

rwest
authored and
JacksonBurns
committed
change is_molecule_forbidden

bjkreitz
authored and
JacksonBurns
committed
adding find_formate_delocalization_paths to pathfinder

bjkreitz
authored and
JacksonBurns
committed
Fix some Cython declarations in pathfinder.py

rwest
authored and
JacksonBurns
committed
add resonance structure generation for formate to resonance.py

bjkreitz
authored and
JacksonBurns
committed
add label for vdW bond in get_desorbed_molecules

bjkreitz
authored and
JacksonBurns
committed
add more constraints to formate path in resonance.py

bjkreitz
authored and
JacksonBurns
committed
clean up pathfinder and add constraints

bjkreitz
authored and
JacksonBurns
committed
add features for N species

bjkreitz
authored and
JacksonBurns
committed
Consider generate_formate_resonance_structures when no features specified.

rwest
authored and
JacksonBurns
committed
Rename generate_formate_resonance_structures to generate_adsorbate_formate_resonance_structures

rwest
authored and
JacksonBurns
committed
Test the new remove_van_der_waals_bonds behaviour.

rwest
authored and
JacksonBurns
committed
Add comments describing current implementation of is_molecule_forbidden

rwest
authored and
JacksonBurns
committed
Refactor is_molecule_forbidden checks in reaction family.

rwest
authored and
JacksonBurns
committed
Add has_vdw_surface_bond method on Molecule.

rwest
authored and
JacksonBurns
committed
Fix bug and add tests: unbonded X gives True for has_vdw_surface_bond

rwest
authored and
JacksonBurns
committed
Avoid calling fails_species_constraints() twice in a row.

rwest
authored and
JacksonBurns
committed
restructure is_molecule_forbbiden

bjkreitz
authored and
JacksonBurns
committed
restructure is_molecule_forbidden to check for vdWBidentate in family name

bjkreitz
authored and
JacksonBurns
committed
TEMPORARY: set RMG_DATABASE_BRANCH: formate_families

rwest
authored and
JacksonBurns
committed
Improve diagnostics for "Family had N reactants?" kinetics test failure

authored and
JacksonBurns
committed
Revert "TEMPORARY: set RMG_DATABASE_BRANCH: formate_families"
JacksonBurns
committed

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Vdw bonds#2706

Vdw bonds#2706
JacksonBurns merged 27 commits into
mainfrom
vdW_bonds

Commits on Jun 8, 2026

draw vdW bond, the same way we do H bonds

Adjust remove vdW bond, using new has_covalent_surface_bond function

Make has_covalent_surface_bond more efficient.

Add test_has_covalent_surface_bond to test has_covalent_surface_bond.

Simplify remove_van_der_waals_bonds

Accelerate is_multidentate.

change is_molecule_forbidden

adding find_formate_delocalization_paths to pathfinder

Fix some Cython declarations in pathfinder.py

add resonance structure generation for formate to resonance.py

add label for vdW bond in get_desorbed_molecules

add more constraints to formate path in resonance.py

clean up pathfinder and add constraints

add features for N species

Consider generate_formate_resonance_structures when no features specified.

Rename generate_formate_resonance_structures to generate_adsorbate_formate_resonance_structures

Test the new remove_van_der_waals_bonds behaviour.

Add comments describing current implementation of is_molecule_forbidden

Refactor is_molecule_forbidden checks in reaction family.

Add has_vdw_surface_bond method on Molecule.

Fix bug and add tests: unbonded X gives True for has_vdw_surface_bond

Avoid calling fails_species_constraints() twice in a row.

restructure is_molecule_forbbiden

restructure is_molecule_forbidden to check for vdWBidentate in family name

TEMPORARY: set RMG_DATABASE_BRANCH: formate_families

Improve diagnostics for "Family had N reactants?" kinetics test failure

Revert "TEMPORARY: set RMG_DATABASE_BRANCH: formate_families"