Include bond order in TopologyGraph #461
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`Foyer` currently does not understand bond order in its `TopologyGraph`
representation and in its SMARTS grammar aside from number of connected
neighbors [C;X4], for example.
This PR adds bond order as an attribute when adding bonds in the
`TopologyGraph`, accepted options currently are:
"1" : single bonds
"2" : double bonds
"3" : triple bonds
"ar" : aromatic bonds
"am" : amide bonds
"un": unknown,
"du": dummy
"nc": not connected
The last 3 bond types ("un", "du", and "nc") are subject to change and
may not be here in the final iteration of this PR.
Support has been added when converting parmed structures, openff
topologies, as well as GMSO topologies.
| @@ -183,11 +203,22 @@ def from_openff_topology(cls, openff_topology): | |||
| element=element, | |||
| ) | |||
|
|
|||
| bond_type_dict = { | |||
There was a problem hiding this comment.
This might be better implemented as an Enum.
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #461 +/- ##
===========================================
- Coverage 69.55% 48.47% -21.09%
===========================================
Files 16 17 +1
Lines 1662 1863 +201
===========================================
- Hits 1156 903 -253
- Misses 506 960 +454 |
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PR Summary:
Foyercurrently does not understand bond order in itsTopologyGraphrepresentation and in its SMARTS grammar aside from number of connected
neighbors [C;X4], for example.
This PR adds bond order as an attribute when adding bonds in the
TopologyGraph, accepted options currently are:"1" : single bonds
"2" : double bonds
"3" : triple bonds
"ar" : aromatic bonds
"am" : amide bonds
"un": unknown,
"du": dummy
"nc": not connected
The last 3 bond types ("un", "du", and "nc") are subject to change and
may not be here in the final iteration of this PR.
Support has been added when converting parmed structures, openff
topologies, as well as GMSO topologies.
PR Checklist