Hi Rasmus,
the problem is that, as stated in the |rdmolfiles.||MolFromMolFile|()
docs, the removeHs option is only honored when sanitize is True.
So to obtain sensible results without sanitizing you should rather do
something like:
m1 = Chem.MolFromMolFile('Ran1.sdf', sanitize=False)
m1 = Chem.RemoveHs(m1, sanitize=False)
print( Chem.MolToSmiles(set_correct_Chiral_flags(m1), isomericSmiles=True) )
m2 = Chem.MolFromMolFile('Ran2.sdf', sanitize=False)
m2 = Chem.RemoveHs(m2, sanitize=False)
print( Chem.MolToSmiles(set_correct_Chiral_flags(m2), isomericSmiles=True) )
You may check the individual sanitization operations here:
https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=rdmolops%20sanitizeflags#rdkit.Chem.rdmolops.SanitizeFlags
Cheers,
p.
On 03/12/2019 12:46, Rasmus "Termo" Lundsgaard wrote:
Hi all
I would like to avoid sanitizing the sdf files, as information in
these files should be seen as the ground truth.
I however have some problems in figuring out how to read and set
chiral information from the file and also have RDkit behave the same
always. Attached are two sdf files with no 3d information and only
stereo information in the atoms section for R-Aniline. The only
difference as I see it is the order of the lines of the bond information.
Even so I get two different smiles back with isomeric information when
not sanitizing.
Attached is also the minimal python code: which for me at least outputs:
not setting chiral flags
CC(N)C(=O)O
CC(N)C(=O)O
setting chiral flags
[H]OC(=O)[C@]([H])(N([H])[H])C([H])([H])[H]
[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])[H]
setting chiral flags and sanitize
C[C@@H](N)C(=O)O
C[C@@H](N)C(=O)O
Any ideas to why this happens and how I can handle it strictly. Also
what does the sanitizing exactly do?
Regards Rasmus
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