[Rdkit-discuss] About RemoveHs and AddHs

[topgunhaides . <sun...@gm...>]

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