Hi Geoff,
On 3 Feb 2014, at 05:23, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote:
to be molecules with nonsense formal charges on aromatic atoms, which then
fail to
be Kekulized given the mismatched valence states.
OK, I have an interesting test case from Noel's python
Hi all,
Here's the metal-organic framework
MIL-100https://gist.github.com/patrickfuller/8569792.
It has a 12,000-atom unit cell, and it crashes openbabel when it's loaded.
Looking through the source, it seems that the crash is due to automatic
O(N^2) bond inference on crystals. I was able to
The presence of the hydrogen on the pyridinium nitrogen is critical for
aromaticity.
Yes, except there are decidedly users who feel that with SMILES, explicit
hydrogens only need to be used in cases of stereochemistry.
I remember a thread with Andrew Dalke (now CC'ed) where he argued IIRC,
So you can use -ab or -aB if you want to ignore ConnectTheDots.
Good to know, thanks!
The biggest talk has largely centered on PerceiveBondOrders and Kekule /
aromatic detection, which are usually slower than ConnectTheDots. If you'd
like to take a stab at an improved implementation of
FYI, Roger added a connect the dots to RDKit a few months back for a
PDB parser. You can see his discussion of various algorithms at the
end of http://www.slideshare.net/NextMoveSoftware/rdkit-gems. We could
repurpose this code considering the licence.
- Noel
On 3 February 2014 19:58, Patrick
On Mon, Feb 3, 2014 at 8:12 AM, Geoffrey Hutchison
geoff.hutchi...@gmail.com wrote:
The presence of the hydrogen on the pyridinium nitrogen is critical for
aromaticity.
Yes, except there are decidedly users who feel that with SMILES, explicit
hydrogens only need to be used in cases of
