Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-12 Thread Greg Landrum
The molecule has been constructed without problems, but the jupyter
rendering code is failing.
This isn't particularly surprising, that code is really set up to render
non-query molecules, not things constructed from SMARTS.

If you want to get a rendering of a molecule build from SMARTS in the
notebook, try:

from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1'
mol =Chem.MolFromSmarts(sa)
Draw.MolToImage(mol,kekulize=False)


Best,
-greg


On Wed, Jul 12, 2017 at 5:10 PM, Chicago Ji  wrote:

> the code :
> 
> from rdkit import Chem
> from rdkit.Chem.Draw import IPythonConsole
> sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1'
> mol =Chem.MolFromSmarts(sa)
> mol
> -
>
> The error information:
>
> RDKit ERROR: [16:07:15]
> RDKit ERROR:
> RDKit ERROR: 
> RDKit ERROR: Pre-condition Violation
> RDKit ERROR: getExplicitValence() called without call to calcExplicitValence()
> RDKit ERROR: Violation occurred on line 162 in file 
> soft/rdkit/Code/GraphMol/Atom.cpp
> RDKit ERROR: Failed Expression: d_explicitValence > -1
> RDKit ERROR: 
> RDKit ERROR:
> RDKit ERROR: [16:07:15] Can't kekulize mol.  Unkekulized atoms: 4 5 6 7 8 9
> RDKit ERROR:
>
>
> ---
>
>
> On Wed, Jul 12, 2017 at 2:27 PM, Greg Landrum 
> wrote:
>
>>
>>
>> On Tue, Jul 11, 2017 at 6:53 PM, Chicago Ji  wrote:
>>
>>>  Thanks a lot for your code.
>>>
>>> I met another error. I don't know whether it's Normal.
>>>
>>> I have a correct SMILES, and read it through MolFromSmarts:
>>>
>>> 
>>> sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1'
>>> Chem.MolFromSmarts(sa)
>>> 
>>>
>>>
>>> Is there something wrong with my input?
>>>
>>
>> Looks fine to me:
>>
>> In [9]: sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1'
>>
>> In [10]: m = Chem.MolFromSmarts(sa)
>>
>> In [11]: m.GetNumAtoms()
>> Out[11]: 35
>>
>>
>> What error do you see?
>>
>> -greg
>>
>>
>
--
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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-11 Thread Chicago Ji
Hi, Greg.

 Thanks a lot for your code.

I met another error. I don't know whether it's Normal.

I have a correct SMILES, and read it through MolFromSmarts:


sa = 'CC(C)(C)c1ccc(cc1)C(O)CCCN1CCC(CC1)C(O)(c1c1)c1c1'
Chem.MolFromSmarts(sa)



Is there something wrong with my input?

Many Thanks.

Best,
Changge



On Tue, Jul 11, 2017 at 4:53 PM, Greg Landrum 
wrote:

> Here's a simple bit of code that shows how to get only pharmacophore
> features whose atoms are contained completely in the MCS:
> https://gist.github.com/greglandrum/faf47bd161d9b3af5374c358d0a0786d
>
> An interesting extension to this, which I may do for a blog post later, is
> to further filter things to get the "maximum common pharmacophore"
>
> -greg
>
>
> On Tue, Jul 11, 2017 at 1:41 PM, Greg Landrum 
> wrote:
>
>> Interesting use case.
>>
>> I can send some sample code for this later this afternoon.
>>
>>
>> On Tue, Jul 11, 2017 at 11:43 AM, Chicago Ji 
>> wrote:
>>
>>> Hi, Greg,
>>>
>>> The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only
>>> output the result as SMARTS.
>>>
>>> Maybe I can calculate atom features of the "mother molecule', and then
>>> extract those belonging to the common substructure.
>>>
>>> Or I can delete some atoms of the 'mother molecule', and output as
>>> SMILES.
>>>
>>> Many thanks for your help.
>>>
>>> Best,
>>> Changge
>>>
>>>
>>> On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrum 
>>> wrote:
>>>
 Using the pharmacophore search code on molecules constructed from
 SMARTS is, in many circumstances, unlikely to yield the results that you
 are looking for. Query-Query matching is different than Query-Atom 
 matching.

 It's more common to look for ph4 features in molecules constructed from
 SMILES or from a mol file. Is there a particular reason that you need to
 use SMARTS?

 -greg


 On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji 
 wrote:

> Hi Greg,
>
> I want to get pharmacophore feature for each atom on the molecule
> using GetFeaturesForMol().
>
> It seems that sanitization is a must before running
> GetFeaturesForMol().
>
> Many Thanks.
>
> Best,
> Changge
>
> On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum 
> wrote:
>
>> Hi Changge,
>>
>> Is there any particular reason that you're calling
>> updatePropertyCache on the molecule? That's not an operation that's
>> normally necessary.
>>
>> Best,
>> -greg
>>
>>
>>
>> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji 
>> wrote:
>>
>>> Dear all,
>>>
>>> I met a problem with Aromatic N atoms.
>>>
>>> Here is the code:
>>> 
>>>
>>> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-
>>> !@[#7]-@1-@[#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[
>>> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:
>>> [#6]:[#6]:[#6]:[#6]:[#6]:1'
>>>
>>> mc = Chem.MolFromSmarts(sa,False)
>>>
>>> mc.UpdatePropertyCache()
>>>
>>> --
>>>
>>> The error info says " Explicit valence for atom # 16 N, 4, is
>>> greater than permitted"
>>>
>>> I also tried sanifix3.AdjustAromaticNs, but that doesn't work.
>>>
>>> Is there an easy way to solve this problem?
>>>
>>> Many thanks.
>>>
>>>
>>> Best Regards,
>>> Changge
>>>
>>>
>>>
>>> 
>>> --
>>> 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
>>> Rdkit-discuss@lists.sourceforge.net
>>> 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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-11 Thread Greg Landrum
Here's a simple bit of code that shows how to get only pharmacophore
features whose atoms are contained completely in the MCS:
https://gist.github.com/greglandrum/faf47bd161d9b3af5374c358d0a0786d

An interesting extension to this, which I may do for a blog post later, is
to further filter things to get the "maximum common pharmacophore"

-greg


On Tue, Jul 11, 2017 at 1:41 PM, Greg Landrum 
wrote:

> Interesting use case.
>
> I can send some sample code for this later this afternoon.
>
>
> On Tue, Jul 11, 2017 at 11:43 AM, Chicago Ji  wrote:
>
>> Hi, Greg,
>>
>> The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only
>> output the result as SMARTS.
>>
>> Maybe I can calculate atom features of the "mother molecule', and then
>> extract those belonging to the common substructure.
>>
>> Or I can delete some atoms of the 'mother molecule', and output as SMILES.
>>
>> Many thanks for your help.
>>
>> Best,
>> Changge
>>
>>
>> On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrum 
>> wrote:
>>
>>> Using the pharmacophore search code on molecules constructed from SMARTS
>>> is, in many circumstances, unlikely to yield the results that you are
>>> looking for. Query-Query matching is different than Query-Atom matching.
>>>
>>> It's more common to look for ph4 features in molecules constructed from
>>> SMILES or from a mol file. Is there a particular reason that you need to
>>> use SMARTS?
>>>
>>> -greg
>>>
>>>
>>> On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji 
>>> wrote:
>>>
 Hi Greg,

 I want to get pharmacophore feature for each atom on the molecule using
 GetFeaturesForMol().

 It seems that sanitization is a must before running GetFeaturesForMol().

 Many Thanks.

 Best,
 Changge

 On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum 
 wrote:

> Hi Changge,
>
> Is there any particular reason that you're calling updatePropertyCache
> on the molecule? That's not an operation that's normally necessary.
>
> Best,
> -greg
>
>
>
> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji 
> wrote:
>
>> Dear all,
>>
>> I met a problem with Aromatic N atoms.
>>
>> Here is the code:
>> 
>>
>> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-
>> !@[#7]-@1-@[#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[
>> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:
>> [#6]:[#6]:[#6]:[#6]:[#6]:1'
>>
>> mc = Chem.MolFromSmarts(sa,False)
>>
>> mc.UpdatePropertyCache()
>>
>> --
>>
>> The error info says " Explicit valence for atom # 16 N, 4, is
>> greater than permitted"
>>
>> I also tried sanifix3.AdjustAromaticNs, but that doesn't work.
>>
>> Is there an easy way to solve this problem?
>>
>> Many thanks.
>>
>>
>> Best Regards,
>> Changge
>>
>>
>>
>> 
>> --
>> 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
>> Rdkit-discuss@lists.sourceforge.net
>> 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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-11 Thread Greg Landrum
Interesting use case.

I can send some sample code for this later this afternoon.


On Tue, Jul 11, 2017 at 11:43 AM, Chicago Ji  wrote:

> Hi, Greg,
>
> The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only
> output the result as SMARTS.
>
> Maybe I can calculate atom features of the "mother molecule', and then
> extract those belonging to the common substructure.
>
> Or I can delete some atoms of the 'mother molecule', and output as SMILES.
>
> Many thanks for your help.
>
> Best,
> Changge
>
>
> On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrum 
> wrote:
>
>> Using the pharmacophore search code on molecules constructed from SMARTS
>> is, in many circumstances, unlikely to yield the results that you are
>> looking for. Query-Query matching is different than Query-Atom matching.
>>
>> It's more common to look for ph4 features in molecules constructed from
>> SMILES or from a mol file. Is there a particular reason that you need to
>> use SMARTS?
>>
>> -greg
>>
>>
>> On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji  wrote:
>>
>>> Hi Greg,
>>>
>>> I want to get pharmacophore feature for each atom on the molecule using
>>> GetFeaturesForMol().
>>>
>>> It seems that sanitization is a must before running GetFeaturesForMol().
>>>
>>> Many Thanks.
>>>
>>> Best,
>>> Changge
>>>
>>> On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum 
>>> wrote:
>>>
 Hi Changge,

 Is there any particular reason that you're calling updatePropertyCache
 on the molecule? That's not an operation that's normally necessary.

 Best,
 -greg



 On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji 
 wrote:

> Dear all,
>
> I met a problem with Aromatic N atoms.
>
> Here is the code:
> 
>
> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-
> !@[#7]-@1-@[#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[
> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:
> [#6]:[#6]:[#6]:[#6]:[#6]:1'
>
> mc = Chem.MolFromSmarts(sa,False)
>
> mc.UpdatePropertyCache()
>
> --
>
> The error info says " Explicit valence for atom # 16 N, 4, is greater
> than permitted"
>
> I also tried sanifix3.AdjustAromaticNs, but that doesn't work.
>
> Is there an easy way to solve this problem?
>
> Many thanks.
>
>
> Best Regards,
> Changge
>
>
>
> 
> --
> 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
> Rdkit-discuss@lists.sourceforge.net
> 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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-11 Thread Chicago Ji
Hi, Greg,

The SMARTS comes from MCS.FindMCS() analysis. It seems that MCS can only
output the result as SMARTS.

Maybe I can calculate atom features of the "mother molecule', and then
extract those belonging to the common substructure.

Or I can delete some atoms of the 'mother molecule', and output as SMILES.

Many thanks for your help.

Best,
Changge


On Tue, Jul 11, 2017 at 8:26 AM, Greg Landrum 
wrote:

> Using the pharmacophore search code on molecules constructed from SMARTS
> is, in many circumstances, unlikely to yield the results that you are
> looking for. Query-Query matching is different than Query-Atom matching.
>
> It's more common to look for ph4 features in molecules constructed from
> SMILES or from a mol file. Is there a particular reason that you need to
> use SMARTS?
>
> -greg
>
>
> On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji  wrote:
>
>> Hi Greg,
>>
>> I want to get pharmacophore feature for each atom on the molecule using
>> GetFeaturesForMol().
>>
>> It seems that sanitization is a must before running GetFeaturesForMol().
>>
>> Many Thanks.
>>
>> Best,
>> Changge
>>
>> On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum 
>> wrote:
>>
>>> Hi Changge,
>>>
>>> Is there any particular reason that you're calling updatePropertyCache
>>> on the molecule? That's not an operation that's normally necessary.
>>>
>>> Best,
>>> -greg
>>>
>>>
>>>
>>> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji 
>>> wrote:
>>>
 Dear all,

 I met a problem with Aromatic N atoms.

 Here is the code:
 

 sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@
 [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[
 #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:
 [#6]:[#6]:[#6]:[#6]:[#6]:1'

 mc = Chem.MolFromSmarts(sa,False)

 mc.UpdatePropertyCache()

 --

 The error info says " Explicit valence for atom # 16 N, 4, is greater
 than permitted"

 I also tried sanifix3.AdjustAromaticNs, but that doesn't work.

 Is there an easy way to solve this problem?

 Many thanks.


 Best Regards,
 Changge



 
 --
 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
 Rdkit-discuss@lists.sourceforge.net
 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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-11 Thread Greg Landrum
Using the pharmacophore search code on molecules constructed from SMARTS
is, in many circumstances, unlikely to yield the results that you are
looking for. Query-Query matching is different than Query-Atom matching.

It's more common to look for ph4 features in molecules constructed from
SMILES or from a mol file. Is there a particular reason that you need to
use SMARTS?

-greg


On Tue, Jul 11, 2017 at 8:54 AM, Chicago Ji  wrote:

> Hi Greg,
>
> I want to get pharmacophore feature for each atom on the molecule using
> GetFeaturesForMol().
>
> It seems that sanitization is a must before running GetFeaturesForMol().
>
> Many Thanks.
>
> Best,
> Changge
>
> On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum 
> wrote:
>
>> Hi Changge,
>>
>> Is there any particular reason that you're calling updatePropertyCache on
>> the molecule? That's not an operation that's normally necessary.
>>
>> Best,
>> -greg
>>
>>
>>
>> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji  wrote:
>>
>>> Dear all,
>>>
>>> I met a problem with Aromatic N atoms.
>>>
>>> Here is the code:
>>> 
>>>
>>> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@
>>> [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[
>>> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:
>>> [#6]:[#6]:[#6]:[#6]:[#6]:1'
>>>
>>> mc = Chem.MolFromSmarts(sa,False)
>>>
>>> mc.UpdatePropertyCache()
>>>
>>> --
>>>
>>> The error info says " Explicit valence for atom # 16 N, 4, is greater
>>> than permitted"
>>>
>>> I also tried sanifix3.AdjustAromaticNs, but that doesn't work.
>>>
>>> Is there an easy way to solve this problem?
>>>
>>> Many thanks.
>>>
>>>
>>> Best Regards,
>>> Changge
>>>
>>>
>>>
>>> 
>>> --
>>> 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
>>> Rdkit-discuss@lists.sourceforge.net
>>> 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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-11 Thread Chicago Ji
Hi Greg,

I want to get pharmacophore feature for each atom on the molecule using
GetFeaturesForMol().

It seems that sanitization is a must before running GetFeaturesForMol().

Many Thanks.

Best,
Changge

On Tue, Jul 11, 2017 at 7:31 AM, Greg Landrum 
wrote:

> Hi Changge,
>
> Is there any particular reason that you're calling updatePropertyCache on
> the molecule? That's not an operation that's normally necessary.
>
> Best,
> -greg
>
>
>
> On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji  wrote:
>
>> Dear all,
>>
>> I met a problem with Aromatic N atoms.
>>
>> Here is the code:
>> 
>>
>> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@
>> [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[
>> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:
>> [#6]:[#6]:[#6]:[#6]:[#6]:1'
>>
>> mc = Chem.MolFromSmarts(sa,False)
>>
>> mc.UpdatePropertyCache()
>>
>> --
>>
>> The error info says " Explicit valence for atom # 16 N, 4, is greater
>> than permitted"
>>
>> I also tried sanifix3.AdjustAromaticNs, but that doesn't work.
>>
>> Is there an easy way to solve this problem?
>>
>> Many thanks.
>>
>>
>> Best Regards,
>> Changge
>>
>>
>>
>> 
>> --
>> 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
>> Rdkit-discuss@lists.sourceforge.net
>> 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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


Re: [Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-11 Thread Greg Landrum
Hi Changge,

Is there any particular reason that you're calling updatePropertyCache on
the molecule? That's not an operation that's normally necessary.

Best,
-greg



On Mon, Jul 10, 2017 at 8:37 PM, Chicago Ji  wrote:

> Dear all,
>
> I met a problem with Aromatic N atoms.
>
> Here is the code:
> 
>
> sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@
> [#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[
> #7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:
> [#6]:[#6]:[#6]:[#6]:[#6]:1'
>
> mc = Chem.MolFromSmarts(sa,False)
>
> mc.UpdatePropertyCache()
>
> --
>
> The error info says " Explicit valence for atom # 16 N, 4, is greater
> than permitted"
>
> I also tried sanifix3.AdjustAromaticNs, but that doesn't work.
>
> Is there an easy way to solve this problem?
>
> Many thanks.
>
>
> Best Regards,
> Changge
>
>
>
> 
> --
> 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
> Rdkit-discuss@lists.sourceforge.net
> 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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


[Rdkit-discuss] Valance Error on Aromatic N atoms.

2017-07-10 Thread Chicago Ji
Dear all,

I met a problem with Aromatic N atoms.

Here is the code:


sa='[#8]=!@[#6]-@1-@[#7]-@[#6]-@[#6]-@[#7]-@1-!@[#6]-!@[#6]-!@[#7]-@1-@
[#6]-@[#6]-@[#6](-@[#6]-@[#6]-@1)-!@[#6]:1:[#6]:[#7](:[#6]:2:[#6]:[#6]:[#6](:[#6]:[#6]:1:2)-!@[Cl])-!@[#6]:1:[#6]:[#6]:[#6]:[#6]:[#6]:1'

mc = Chem.MolFromSmarts(sa,False)

mc.UpdatePropertyCache()

--

The error info says " Explicit valence for atom # 16 N, 4, is greater than
permitted"

I also tried sanifix3.AdjustAromaticNs, but that doesn't work.

Is there an easy way to solve this problem?

Many thanks.


Best Regards,
Changge
--
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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss