Hi guys,

I recently found that the GetBestRMS() fails to return the optimal RMS in
the following case (Glycine: O4 and O5 flips in the reference and probe
molecules).
The returned RMSD and Shape Tanimoto values are 0.81 and
0.66, respectively, not as good as expected. Is there anything that I can
try to fix it? Thank you!

*- Reference molecule:*
 reference
  ------

  5  4  0     0  0  0  0  0  0999 V2000
    1.5410   -3.2260   72.8820 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2100   -3.1110   71.5380 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7090   -1.6960   71.3190 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0850   -0.7620   71.8600 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7200   -1.5200   70.6150 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
M  END

*- Probe molecule:*
probe
  --------

  5  4  0  0  0  0  0  0  0  0999 V2000
    2.2790   -3.8306   72.1929 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6557   -2.5350   72.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4976   -1.5750   71.4929 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1497   -0.3851   71.3826 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6830   -1.9893   70.9366 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
M  END


*- Code:*
from rdkit import Chem
from rdkit.Chem import AllChem, rdMolAlign, rdShapeHelpers


def rms_st(probe, reference):
    rms = float(AllChem.GetBestRMS(probe, reference))
    st = float(1 - rdShapeHelpers.ShapeTanimotoDist(probe, reference))
    return rms, st


refSuppl = Chem.SDMolSupplier('ref.sdf')
probeSuppl = Chem.SDMolSupplier('probe.sdf')

for mol in refSuppl:
    refMol = Chem.RemoveHs(mol)
    for m in probeSuppl:
        probeMol = Chem.RemoveHs(m)
        RMS, ST = rms_st(probeMol, refMol)
        print(("{0:.3f}".format(RMS)))
        print(("{0:.3f}".format(ST)))

Best,
Leon
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