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Include bond order in TopologyGraph #461

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Include bond order in TopologyGraph #461

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22517f7
Include bond order in TopologyGraph
justinGilmer Sep 17, 2021
9b5400f
If bond is not in dictionary, set to unknown
justinGilmer Sep 17, 2021
de633d5
Merge remote-tracking branch 'upstream/master' into feat/add_bond_types
justinGilmer Oct 27, 2021
48c8fc5
Convert bond orders to an Enum
justinGilmer Oct 27, 2021
dfb9825
Merge branch 'main' into feat/add_bond_types
daico007 Oct 23, 2023
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47 changes: 40 additions & 7 deletions foyer/topology_graph.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ def add_atom(self, index, name, atomic_number=None, element=None, **kwargs):
atom_data = AtomData(index, name, atomic_number, element, **kwargs)
self.add_node(index, atom_data=atom_data)

def add_bond(self, atom_1_index, atom_2_index):
def add_bond(self, atom_1_index, atom_2_index, bond_type="1"):
"""Add a bond(edge) between two atoms in this TopologyGraph.

Parameters
Expand All @@ -88,8 +88,18 @@ def add_bond(self, atom_1_index, atom_2_index):
The index of the first atom that forms this bond
atom_2_index: int
The index of the second atom that forms this bond
bond_type: str, default = "1"
The type of bond being added, can be:
"1": single,
"2": double,
"3": triple,
"am": amide,
"ar": aromatic,
"un": unknown,
"du": dummy
"nc": not connected
"""
self.add_edge(atom_1_index, atom_2_index)
self.add_edge(atom_1_index, atom_2_index, {"bond_type": bond_type})

def atoms(self, data=False):
"""Iterate through atoms in the TopologyGraph."""
Expand Down Expand Up @@ -140,9 +150,19 @@ def from_parmed(cls, structure: Structure):
atomic_number=atomic_number,
element=element,
)

bond_type_dict = {
round(1, 2): "1",
round(2, 2): "2",
round(3, 2): "3",
round(1.5, 2): "ar",
round(1.25, 2): "am",
}
for bond in structure.bonds:
topology_graph.add_bond(bond.atom1.idx, bond.atom2.idx)
topology_graph.add_bond(
bond.atom1.idx,
bond.atom2.idx,
bond_type=bond_type_dict.get(round(bond.order, 2), "un"),
)

return topology_graph

Expand Down Expand Up @@ -183,11 +203,22 @@ def from_openff_topology(cls, openff_topology):
element=element,
)

bond_type_dict = {
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This might be better implemented as an Enum.

"Single": "1",
"Double": "2",
"Triple": "3",
"Aromatic": "ar",
"Amide": "am",
}
for top_bond in openff_topology.topology_bonds:
atoms_indices = [
atom.topology_atom_index for atom in top_bond.atoms
]
top_graph.add_bond(atoms_indices[0], atoms_indices[1])
top_graph.add_bond(
atoms_indices[0],
atoms_indices[1],
bond_type=bond_type_dict.get(top_bond.bond_order, "un"),
)

return top_graph

Expand Down Expand Up @@ -233,12 +264,14 @@ def from_gmso_topology(cls, gmso_topology):
atomic_number=atom.element.atomic_number,
element=atom.element.symbol,
)

# until gmso has bond orders, assume single bonds
for top_bond in gmso_topology.bonds:
atoms_indices = [
gmso_topology.get_index(atom)
for atom in top_bond.connection_members
]
top_graph.add_bond(atoms_indices[0], atoms_indices[1])
top_graph.add_bond(
atoms_indices[0], atoms_indices[1], bond_type="1"
)

return top_graph