Re: [Rdkit-discuss] RMSD value between two non-covalent molecular complexes

2017-06-22 Thread Francois BERENGER
On 06/22/2017 11:20 PM, gosia olejniczak wrote: Hi again, i found where the problem was (it seems): as i was reading in molecules from sdf file through "SDMolSupplier" by doing: suppl = Chem.SDMolSupplier(filename) the hydrogen atoms were removed (what was not obvious since e.g.

Re: [Rdkit-discuss] RMSD value between two non-covalent molecular complexes

2017-06-22 Thread gosia olejniczak
Hi again, i found where the problem was (it seems): as i was reading in molecules from sdf file through "SDMolSupplier" by doing: suppl = Chem.SDMolSupplier(filename) the hydrogen atoms were removed (what was not obvious since e.g. GetNumAtoms with "heavy" flag was returning the total number

Re: [Rdkit-discuss] RMSD value between two non-covalent molecular complexes

2017-06-21 Thread Paolo Tosco
Hi Gosia, you may want to look at the CombineMols() function in the rdmolops module. If you make a single molecule out of the two fragments, then you should manage to get what you are looking for. Cheers, p. On 06/21/17 14:47, gosia olejniczak wrote: dear RDKit experts, is it possible to

[Rdkit-discuss] RMSD value between two non-covalent molecular complexes

2017-06-21 Thread gosia olejniczak
dear RDKit experts, is it possible to calculate RMSD value between two non-covalent molecular complexes? For instance: complex1: X(conformer1) + H2O complex2: X(conformer2) + H2O i tried GetBestRMS and GetO3A.Align but the program clearly neglects H2O and calculates the RMSD only between