since atoms seem to get repurposed on copy constructor/+= etc, I think a
better tracking system would be very useful.
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Here at NM, various tricks are sometimes used to store the identity
for these sorts of things; e.g. setting the isotope number, adding
atom classes or atom data. We could make an API addition to return the
identity of the new atoms after calling .Add functions if you pass in
a suitable vector.
- N
It's a pity OpenBabel is so unfriendly in modifications which atoms are
deleted.
Maybe this would work. Identify the bonds that need breaking in the the
two input molecules, but don't break them. Combine the two molecules
with the += operator. I think the idx s of the atoms from the second
mol
Indeed, however, you lose the index of the atom in the original molecule you
want to create a bond to, due to the index/id reordering that happens upon
the fragment::Separate.
I am doing two fragment::separate calls. The first is to remove the
sidechain from the protein to create a protein /w vaca
Aren't the atoms added in the same order in which they appear in the
sidechain fragment? So the first new atom will have an atomidx one
greater than the number of atoms in the original molecule, etc.
- Noel
On 16 December 2013 09:53, Nicholas.Browning wrote:
> still in need of a solution.
>
>
>
still in need of a solution.
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Dear All,
I have run into a problem with regards to the way in which OBMol deals with
atom ids.
My code structure is as follows:
//Preparing the fragments
-load an amino acid library into separate OBMol objects.
-Delete (by index) the C(alpha)-C(beta) in each molecule to create two
fragments.
