Maybe this could work here too.Įdits by you hit this issue from search engines, please update all deps to v7.8.7 or above.

To help with this situation a convenience function has been added to OBAtom that sets the implicit hydrogen count to be consistent with normal valence rules.Const baseConfig = Start->SetImplicitHCount(bondorder >= hcount ? 0 : hcount - bondorder) Įnd->SetImplicitHCount(bondorder >= hcount ? 0 : hcount - bondorder) įor the particular case of creating a new atom, it is worth noting that the implicit hydrogen count defaults to zero and that users must set it themselves if necessary. Unsigned int hcount = start->GetImplicitHCount() Note that care should be taken not to set the hydrogen count to a negative value when decrementing. This also applies to deleting an atom, since this deletes any bonds connected to it. While this may seem like a major change, adapting code to handle the change should be straightforward: adding or removing a bond should be accompanied by incrementing or decrementing the implicit hydrogen count by the bond order. With OB 3.0, there were four implicit hydrogens on each carbon before we made the bond, and there still are four - they didn’t go anywhere and weren’t automatically adjusted. OB 2.x just works out the count based on standard valence rules. If we read the SMILES string C.C, create a bond between the two atoms and write out the SMILES string, we get different answers for OB 2.x ( CC) versus OB 3.0 ( ). The disadvantage was that it was difficult for the user to specify non-standard valencies, may have papered-over problems with the data, gave rise to subtle bugs which were not easily addressed and had poorer performance.Īs an example of how the behavior has changed, let’s look at creating a bond. In contrast, in OB 2.x this was a derived property worked out from valence rules and some additional flags set on an atom to indicate non-standard valency.įrom the point of view of the user, the advantage of the 2.x approach was that the user never needed to consider the implicit hydrogens their count was calculated based on the explicit atoms (a behavior known as “floating valence”).

$lyx update babel$

Modify your document and then View -> update -> DVI, View -> Update -> PostScript (you will need to reload the ps file from gv) to see updated. If you are interested in the underlying latex source, File-> Export -> Latex and read the generated latex file. This is how other mature cheminformatics toolkits handle implicit hydrogens. Lyx actually export the lyx file to latex and call latex, xdvi, postscript etc to do these. This value can be interrogated and set independently of any other property of the atom.

With OB 3.0, the number of implicit hydrogens is stored as a property of the atom.

Lyx update babel