Re: [Rdkit-discuss] Problem getting valence

[Lewis M. <lew...@gm...>]

Thankyou Paolo and Chris! These hydrogens were added while editing the
molecule beforehand but I assumed sanitizing would remove them.

Cheers
Lewis

On Thu, 26 Jul 2018 at 7:59 pm, Chris Earnshaw <cge...@gm...> wrote:

> Hi
>
> It looks to me like N5 [nH:5] also has a problem. This has 3 connections
> to heavy atoms, is specified to have a hydrogen attached, but has no
> charge. This may not have triggered an error but it looks wrong, especially
> in this structure. Surely this atom should just be [n:5] ?
>
> Best regards,
> Chris
>
> On 26 July 2018 at 10:42, Paolo Tosco <pao...@gm...> wrote:
>
>> Dear Lewis,
>>
>> C #7 indeed has 5 valences:
>>
>>  *
>>  |
>> -C=O
>>  |
>>  H
>>
>>
>> If you change [CH:14] into [C:14] sanitization will succeed.
>>
>> Cheers,
>> p.
>>
>> On 07/26/18 09:42, Lewis J Martin wrote:
>>
>> Hi all,
>>
>> I have generated a molecule that I can both visualize and export as
>> SMILES, but I can't Sanitize it. Creating a new molecule from that SMILES
>> fails due to something to do with the valence. It seems to me that it has
>> the correct amount of bonds.
>>
>> Code to reproduce and 'debugging' that Ive tried:
>> --------------------------------------
>> #sanitize=False or it won't load this SMILES
>> mol =
>> Chem.MolFromSmiles('[CH3:0][CH2:1][CH2:2][CH2:3][CH2:4][nH:5]1[c:6]([CH:14](=[O:15])[*:16])[n:7][c:8]2[cH:9][cH:10][cH:11][cH:12][c:13]12',sanitize=False)
>>
>> #print atom indices and atomic number:
>> for i in mol.GetAtoms():
>>         print(i, i.GetIdx(), i.GetAtomicNum())
>>
>> #display bonds relating to index 7. Seems correct for a carbon.
>> for i in mol.GetBonds():
>>     if i.GetBeginAtomIdx()==7 or i.GetEndAtomIdx()==7:
>>         print(i.GetBeginAtomIdx(), i.GetEndAtomIdx(), i.GetBondType())
>>
>> #print valences. Fails on index 7.
>> for i in mol.GetAtoms():
>>     print(i.GetIdx(), i.GetExplicitValence())
>> --------------------------------------
>>
>>
>> Can anyone please offer some advice as to what the problem is?
>> Much appreciated!
>>
>> Lewis
>>
>>
>> PS. here is the output I get:
>>
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 0 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c60> 1 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 2 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c60> 3 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 4 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c60> 5 7
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 6 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c60> 7 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 8 8
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c60> 9 0
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 10 7
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c60> 11 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 12 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c60> 13 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 14 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c60> 15 6
>> <rdkit.Chem.rdchem.Atom object at 0x11a440c10> 16 6
>> 6 7 SINGLE
>> 7 8 DOUBLE
>> 7 9 SINGLE
>> 0 4
>> 1 4
>> 2 4
>> 3 4
>> 4 4
>> 5 3
>> 6 4
>>
>> ---------------------------------------------------------------------------RuntimeError                              Traceback (most recent call last)<ipython-input-24-62fd51819686> in <module>()      7       8 for i in mol.GetAtoms():----> 9     print(i.GetIdx(), i.GetExplicitValence())     10         #valence = oneMol.GetAtomWithIdx(7).GetExplicitValence()     11 #print(valence)
>> RuntimeError: Pre-condition Violation
>> 	getExplicitValence() called without call to calcExplicitValence()
>> 	Violation occurred on line 162 in file Code/GraphMol/Atom.cpp
>> 	Failed Expression: d_explicitValence > -1
>> 	RDKIT: 2018.03.3
>> 	BOOST: 1_65_1
>>
>>
>>
>>
>>
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