Distance between two compounds is obtained using the euclidean distance
between the two fingerprint vectors of the two compounds.
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0268-9
On Sat, 14 Mar 2020 at 16:24, Chris Swain via OpenBabel-discuss <
openbabel-discuss@lists.sourcefo
On 14/03/2020 23:24, Chris Swain via OpenBabel-discuss wrote:
One of the tools is to calculate spectrophores
Described in details here.
https://open-babel.readthedocs.io/en/latest/Fingerprints/spectrophore.html
I’ve tried this and this gives the following output
ID_02 1.49538 2.12033 1.75
Hi,
in principle there should be no restriction on the under limit for the number
of atoms, so I can’t recall exactly why we did put this 'atoms < 3’ restriction
in the code in first instance. So I guess you can safely remove this check and
replace it with a lower limit like 1 or so.
Hans
On
I know nothing about what spectrophores are, but I can tell you all the
molecules you provided have 2 atoms.
The code for spectrophores checks if your molecule has at least 3 atoms.
And gives you the error you've listed if your molecule has less than 3
atoms:
https://github.com/openbabel/openbabel
