Thread: [Rdkit-discuss] Problem getting valence
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From: Lewis J M. <lew...@gm...> - 2018-07-26 08:42:59
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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 iin mol.GetAtoms():
----> 9print(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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From: Paolo T. <pao...@gm...> - 2018-07-26 09:42:13
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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 iin mol.GetAtoms():
> ----> 9print(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
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
|
|
From: Chris E. <cge...@gm...> - 2018-07-26 09:59:47
|
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
>
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> Rdkit-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
|
|
From: Lewis M. <lew...@gm...> - 2018-07-26 11:17:52
|
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
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
> --
Sent from Gmail Mobile
|
|
From: Greg L. <gre...@gm...> - 2018-07-27 17:19:26
|
On Thu, Jul 26, 2018 at 1:18 PM Lewis Martin <lew...@gm...> wrote: > Thankyou Paolo and Chris! These hydrogens were added while editing the > molecule beforehand but I assumed sanitizing would remove them. > Nope. Sanitizing doesn't do anything to modify the valence of atoms in the molecule. The idea is that sanitization should catch obvious chemistry mistakes, so that you can fix them. So if the input specifies that there is an H on an atom, the sanitization step will not change that. -greg |
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