I had a similar problem to this when removing atoms from a molecule. When you
remove an atom, the atoms IDs change, therefore resulting in a seg fault, or
your atoms not being in the correct range.
The way I got around this was to sort the IDs of the atoms I want to remove
from highest to lowest, so the atoms with higher IDs are removed first, this
will not affect the IDs of the atoms with lower IDs.
Here is the relevant discussion
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01937.html
Thanks,
Sarah
On 22 Mar 2012, at 15:56, JP wrote:
> And as a follow up - running this:
>
> #!/usr/bin/env python
>
> from rdkit import Chem
>
> mol = Chem.MolFromSmiles("CCC1CNCC1CC")
> edit_mol = Chem.EditableMol(mol)
> edit_mol.RemoveAtom(0)
>
> for atom in edit_mol.GetMol().GetAtoms():
> print atom.GetIdx()
>
> gives seg fault...
>
> jp@xxx:~/tmp$ test.py
> Segmentation fault
>
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
>
> On 22 March 2012 15:52, JP <jeanpaul.ebe...@inhibox.com> wrote:
>
> Hi there at RDKit,
>
> I have a set of atom indices from a molecule I want to keep, and any atom
> which is not in this list I want to discard.
>
> I thought of implementing this as follows:
>
> #!/usr/bin/env python
>
> from rdkit import Chem
>
> mol = Chem.MolFromSmiles("CCC1CNCC1CC")
>
> keep_atoms = [2,3,4] # assume these exist in the above as an example, you can
> print the atom ids to check
>
> edit_mol = Chem.EditableMol(mol)
> for atom in mol.GetAtoms():
> if atom.GetIdx() not in keep_atoms:
> edit_mol.RemoveAtom(atom.GetIdx())
>
> I am not sure this is the best implementation (also because it does not
> work), but it's a try.
>
> The end result should be an sdf file with only atoms 2,3,4 from the original
> molecule.
>
> When I run the above I get:
>
> [15:45:50]
>
> ****
> Range Error
> idx
> Violation occurred on line 143 in file
> /opt/RDKit_2011_12_1/Code/GraphMol/ROMol.cpp
> Failed Expression: 0 <= 6 <= 5
> ****
>
> Traceback (most recent call last):
> File "./test.py", line 12, in <module>
> edit_mol.RemoveAtom(atom.GetIdx())
> RuntimeError: Range Error
>
> I cannot quite understand this error. Can anyone shed some light?
> I mean this is related to me deleting 3 atoms from the molecule, so it
> somehow expects the range to be from 0 <= x <= 5 instead of 0 <= x <= 8...
> but why is there this check in place?
>
> Many Thanks
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
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