Hi All,
I've been having some problems with indexes following conversion from an
EditableMol. I can create the molecule, delete a specific group of atoms, and
extract a regular molecule without issue. The Debug method indicates that I
have the intended 15-atom fragment.
smiles = "CCN1CCN(c2cc3[nH]c(C(=O)[C@@]4(CC)CC[C@](C)(O)CC4)nc3cc2Cl)CC1"mol =
Chem.MolFromSmiles(smiles)tmp = Chem.EditableMol(mol)for atom in [29, 28, 27,
26, 25, 24, 8, 7, 6, 5, 4, 3, 2, 1, 0]: tmp.RemoveAtom(atom)mol =
tmp.GetMol()mol.Debug()
Unfortunately when I try to create a SMILES for the fragment it seems to be
trying to access an atom indexed 18. Does anyone have any ideas why? It works
perfectly for other example, including deletion of the equivalent atoms from
very similar structures.
Chem.MolToSmiles(mol)
****Range ErroridxViolation occurred on line 153 in file
/home/dan/RDKit_2012_12_1/Code/GraphMol/ROMol.cppFailed Expression: 0 <= 18 <=
14****
Any help would be much appreciated.
Kind regards,
Dan Warner.
------------------------------------------------------------------------------
Get 100% visibility into Java/.NET code with AppDynamics Lite
It's a free troubleshooting tool designed for production
Get down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap2
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
