[ openbabel-Feature Requests-1373872 ] Revised "bond" class

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[ openbabel-Feature Requests-1373872 ] Revised "bond" class

Feature Requests item #1373872, was opened at 2005-12-05 15:36
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Category: API
Group: 2.1
Status: Open
Priority: 5
Submitted By: Geoff Hutchison (ghutchis)
Assigned to: Nobody/Anonymous (nobody)
Summary: Revised "bond" class

Initial Comment:
The current OBBond class is very limited. The idea of chemical bonds
includes quite a variety:

* standard covalent bonds
* ionic bonds
* hydrogen bonds
* disulfide and chalcogenide bonds (e.g., Se-S)
* agostic interactions
* metal coordinatation
* three-center bonds (e.g., diborane)

Recent papers have discussed metal-metal bonds going up to 4-fold, 5-
fold, and 6-fold M-M bonds (i.e., not just single, double, and triple).

And of course covalent bonds include "hapticity" where ferrocene is eta-5
coordinate, and the Fe atom interacts equally with all five carbon atoms in
the Cp group.

The current OBBond class has support for little of this flexibility. In
general, there are few backwards-incompatible problems (except perhaps
for bond orders, where BO = 5 currently implies aromatic). But a more
flexible hierarchy would improve support for additional chemical ontology
in future OB versions.


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