Re: [Rdkit-discuss] About RemoveHs and AddHs

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

[Rdkit-discuss] About RemoveHs and AddHs

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

Re: [Rdkit-discuss] Turn off warning in Huckel calculations.

Dear Jan, That warning is printed straight to stderr by the YAeHMOP code, so disabling Boost logging won't help. If you are using the YAeHMOP code from Python, your best option is probably to catch stderr as I described here: https://sourceforge.net/p/rdkit/mailman/message/36781695/ f =

[Rdkit-discuss] Turn off warning in Huckel calculations.

I am using the new Huckel feature to find bonded atoms using bond orders (https://github.com/jensengroup/xyz2mol : xyz2AC_huckel). This means I am doing a calculation in a mol object with no bonds based xyz coordinates I read in, including hydrogens. A calculation on water gives the following