Hi JP,
Sarah was right on the trick of deleting atoms in the descending order of atom
index. Regarding the segment fault, this is very likely to be a memory
management issue. Make sure you assign the result of the GetMol() call to a
temporary variable to avoid the underlying object being released prematurely.
>>> from rdkit import Chem
>>>
>>> mol = Chem.MolFromSmiles("CCC1CNCC1CC")
>>> edit_mol = Chem.EditableMol(mol)
>>> edit_mol.RemoveAtom(0)
>>> m = edit_mol.GetMol()
>>> for atom in m.GetAtoms():
... print atom.GetIdx()
...
0
1
2
3
4
5
6
7
Regards,
Eddie
On Mar 22, 2012, at 9:07 AM, Sarah Langdon wrote:
> 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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