TRAINED_CATIONS | \
rdchem.ResonanceFlags.UNCONSTRAINED_ANIONS)
with some post-filtering for e.g. carbocations, but feel that it may be more
efficient to put user defined constraints on each atom during the backtracking
loops, as Roger suggests.
Looking forward to hearing your thoughts on this.
Best regard
Dear Ian,
print(Chem.MolToMolBlock(ps[0][0]))
produces:
RDKit 2D
6 5 0 0 0 0 0 0 0 0999 V2000
6.49520.75000. O 0 0 0 0 0 0 0 0 0 0 0 0
5.1962 -0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
3.89710.75000. C 0 0
Dear Ian,
print(Chem.MolToMolBlock(ps[0][0]))
produces:
RDKit 2D
6 5 0 0 0 0 0 0 0 0999 V2000
6.49520.75000. O 0 0 0 0 0 0 0 0 0 0 0 0
5.1962 -0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
3.89710.75000. C 0 0
as long as your coordinates
are not too distorted.
Hope this helps,Best wishes
Maria BrandlOn Thursday, 4 October 2018, 15:49:10 BST, Eric Jonas
wrote:
Hello! I have a large database of molecules where I have, for each molecule:
1. A geometry (element, x, y, z) 2. a SMILES string
and I
Dear all,
I have installed rdkit on Windows 10 under Anaconda 3.
Everything runs smoothly, but depictions on jupyter notebooks return the warning
Warning: unable to load font metrics from dir
C:\Users\MB\Anaconda3\lib\site-packages\rdkit\sping\PIL\pilfonts
and are quite low in resolution.
Is ther
Hi Lukas,
according to the source
code:https://github.com/rdkit/rdkit/blob/master/External/CoordGen/CoordGen.h
double coordgenScaling = 50.0;
the default scaling factor, actually more like a "shrinking factor" seems to be
50, producing bond lengths of 1A.
For 1.5A bond lengths, you would need
Dear all,
this seems trivial, but it may also be worth checking the sanity of original
melting point data, crystallographers sometimes enter the melting point in
degree Celsius, when degree Fahrenheit is expected, so cross checking with the
crystallization temperature etc. can be quite useful.
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