Hi Paolo, Thank you....! I missed it.
Best, Leon On Tue, Dec 10, 2019 at 5:31 PM Paolo Tosco <paolo.tosco.m...@gmail.com> wrote: > 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 > > > > > _______________________________________________ > Rdkit-discuss mailing > listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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