Hi Leon,
While I don’t recommend this because of how “hacky” it is, on Linux it's
possible to use the headers and library files that come with the Anaconda
distribution. To do so you could point the compiler and linker to the files
within your RDKit Anaconda environment. If you use GCC this
Hi Navid,
I think you have a few options. One is to loop over your molecule’s atoms and
delete those hydrogens without any neighbors (degree = 0). In Python this would
look something like the following:
import rdkit
from rdkit import Chem
from rdkit.Chem import rdmolops
# mol =
Hello Rasmus,
I too had this problem a while ago while trying to build the RDKit on Windows,
but since I was only interested in the C++ API I gave up on the Python wrappers
altogether.
Since this is somewhat related, I’m seizing the opportunity for a suggestion:
given how convenient it is to
Hi Gustavo,
I haven’t looked into the RDKit source code for this but I assume this has to
do with the lack of CONECT records in the PDB file you attached (i.e. you are
only storing atom coordinates, not connectivity).
>From what I could gather from the RDKit documentation, the default
Hi Ganesh,
To delve a bit deeper into this, if I recall correctly, SA score is calculated
based on both:
1. The prevalence of your molecule’s chemical motifs in a virtual library of
synthesizable compounds.
2. A set of logarithmic formulas that take as parameters molecular features
Hi all,
I would like to add that you can also find the atom type definitions (perhaps
in a more human-readable format) in the original MMFF paper:
Halgren, T. Merck Molecular Force Field. I. Basis, Form, Scope,
Parameterization and Performance of MMFF94. Journal of Computational Chemistry.
Hello Francesco,
To quote your email: “But now, I'm not in Python. So I type py”
Is this a typo? I’m not aware of the Python interpreter launching when you type
“py”. If it does you may have defined an alias and you may be launching a
different Python executable. If you’re using the Anaconda3
Hello,
I'm trying to "recreate" a template ROMol compound by editing a RWMol using a
stochastic algorithm. To guide the algorithm I would like to use Morgan
fingerprints, with the goal being to reach a Tanimoto coefficient of 1 between
the current molecule's fingerprint and a reference
8 matches
Mail list logo
