Hi Leon,
check the documentation for Chem.AddHs():
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=addhs#rdkit.Chem.rdmolops.AddHs
ARGUMENTS:
[...]
addCoords: (optional) if this toggle is set, The Hs will have 3D
coordinates set. Default value is 0 (no 3D coords).
So if you wish hydrogen coordinates to be nonzero, you need to add the
addCoords parameter:
mol2 = Chem.AddHs(mol, addCoords=True)
Cheers,
p.
On 10/12/2019 19:19, topgunhaides . wrote:
Hi guys,
Can anyone help me with the RemoveHs() and AddHs()? Please see
example below.
from rdkit import Chem
from rdkit.Chem import AllChem
suppl = Chem.SDMolSupplier('123.sdf')
# 123.sdf has 3D structure with Hs coordinates
# By default, Hs are removed by SDMolSupplier (see mol1.sdf)
for mol in suppl:
print(mol.GetNumAtoms())
w1 = Chem.SDWriter('./mol1.sdf')
w1.write(mol)
mol2 = Chem.AddHs(mol)
print(mol2.GetNumAtoms())
w2 = Chem.SDWriter('./mol2.sdf')
w2.write(mol2)
AllChem.EmbedMultipleConfs(mol2, numConfs=1000, maxAttempts=1000,
pruneRmsThresh=1.0)
cids = [conf.GetId() for conf in mol2.GetConformers()]
It is strange that the Hs coordinates after calling Chem.AddHs(mol)
are all zeros (see below for part of the mol2.sdf):
......
5.1350 -0.0950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7331 0.4050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4030 -0.0950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
......
As you can see I am using mol2 for embedding, but its Hs coordinates
are apparently problematic.
Can anyone help me with this?
I am planning to add Hs for embedding and optimization, then remove Hs
for RMSD, and finally add Hs back for writing into output file. Thank you!
Best,
Leon
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