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. GetNumAtoms with "heavy" flag was returning the total number of atoms - including hydrogens, but none of the functions like "GetAtomIdx" etc. was seeing hydrogens - i looked in the code, maybe it is because in the "Code/GraphMol/ROMol.cpp" in all such functions the "GetNumAtoms" and not "GetNumHeavyAtoms" is called?)

then i guess that it must have messed up something somewhere, so that instead of seeing "x+h2o" the code did as if there was only "x" on a file

but if i read in the molecules as:
suppl = Chem.SDMolSupplier(filename, removeHs=False)

I was also surprised recently by this quite unfortunate default parameter value, when reading some carefully prepared 3D conformers, with hydrogens and partial charges ...

then all seems to be ok (rmsd values seem to include h2o; also h2o are drawn with py3Dmol);

best regards,
gosia



2017-06-21 16:37 GMT+02:00 gosia olejniczak <gosia.olejnic...@gmail.com <mailto:gosia.olejnic...@gmail.com>>:

    Hi Paolo,

    Thank you for the prompt answer!

    i'll try it out, but:
    - the whole complex "X+h2o" is read from one sdf file
    - Chem.Mol.GetNumAtoms gives the correct number of atoms (= it
    includes h2o) [*]

    so i'm wondering what is the best way to specify two fragments "x"
    and "h2o", so that i could use them as arguments to CombineMols()?
    does it make sense to:
    1. search for h2o pattern in "x+h2o" (GetSubstructMatch)
    2. remove h2o from the "x+h2o" complex (DeleteSubstruct) and get
    only "x" -> save it
    3. remove x from the "x+h2o" complex (DeleteSubstruct) and get only
    "h2o" -> save it
    4. then finally use CombineMols() with separate fragments from 2.
    and 3.?
    that seems a bit silly, maybe there is a simpler way?

    thank you!
    all the best,
    gosia

    [*] still, the plot of its 3D structure drawn with py3Dmol only
    shows "x" and not "x+h2o"...

    2017-06-21 16:01 GMT+02:00 Paolo Tosco <paolo.to...@unito.it
    <mailto:paolo.to...@unito.it>>:

        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 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
        X(conformer1) and X(conformer2)

        thank you!
        best regards,
        gosia


        
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