addImplicitsHydrogens

[lpatiny]

@rufenerc

In the code:

openchemlib/src/main/java/com/actelion/research/chem/contrib/HydrogenHandler.java

Line 266 in 61d98e7

}

Before returning from the function please could you add:

molecule.ensureHelperArrays(Molecule.cHelperNeighbours);

Like that we get a molecule with right connectivity helper arrays after expanding the hydrogens.

[thsa]

Dear Luc,

this would be colliding with the general concept that one always calls
ensureHelperArrays() just before(!) they are needed and after a function
just in case somebody could need them. There are various reasons:

• at the end of a method one cannot foresee, which state will be needed
  (neighbours, rings or even stereostuff)
• after the method creating helpers one might do some other molecule
  changes, which would destroy the helper state again

Finally, this is your code, but I would advise against it and call
ensureHelperArrays() just before where you need it.

Best wishes,

Thomas

On Mon, Sep 26, 2016 at 1:13 PM, Luc Patiny notifications@github.com
wrote:

@rufenerc https://github.com/rufenerc

In the code:

https://github.com/Actelion/openchemlib/blob/
61d98e7/src/main/java/com/
actelion/research/chem/contrib/HydrogenHandler.java#L266

Before returning from the function please could you add:

molecule.ensureHelperArrays(Molecule.cHelperNeighbours);

Like that we get a molecule with right connectivity helper arrays after
expanding the hydrogens.

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[lpatiny]

OK it will be a habit to take ... Thanks