Re: [Rdkit-discuss] Question about Run Reaction
Hi Taka,
Yes, you need to sanitize every product molecule, after each step.
Best wishes,
Michal
On 7 February 2016 at 01:58, Taka Seri wrote:
> Hi Michal,
>
> Thank you for your quick and kind response.
> I tried to sanitize mol according to your advice.
> And my code worked fine !
> Thanks you. ;-)
> By the way, If I want to run several reaction steps. Do I need to
> sanitize each molecules?
>
>
> # reactiontest.py
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> mol = Chem.MolFromSmiles("c1c1")
> rxn = AllChem.ReactionFromSmarts( "[cH&$(c(c)c):2]>>[c:2][F]" )
> ps1= rxn.RunReactants( (mol,) )
> ps1
> mol2 = ps1[0][0]
> Chem.SanitizeMol( mol2 )
> ps2= rxn.RunReactants( (mol2,) )
> uniq = set( [ Chem.MolToSmiles(x[0], isomericSmiles=True ) for x in ps2 ]
> )
> print( uniq )
> ---
> from shell
>
> $ python reactiontest.py
>
> {'Fc1ccc(F)cc1', 'Fc1(F)c1', 'Fc1c1F'}
>
> -
> Best regards,
> Takayuki
>
> 2016年2月6日(土) 23:01 Michal Krompiec :
>
>> Hi Taka,
>> You have to call SanitizeMol() on the product(s) explicitely. The error
>> is caused by the reactants not being 'sanitized'.
>> Best wishes,
>> Michal
>>
>>
>> On Saturday, 6 February 2016, Taka Seri wrote:
>>
>>> Dear RDKitters,
>>>
>>> I have question about rdkit reaction function.
>>> I want to generate molecules using several reaction steps.
>>> I referred rdkit blog post, and wrote following code.
>>> But second step of reaction caused error.
>>> I could not difference about mol and mol2 object.
>>> I wonder if anyone could help me.
>>> Best regards,
>>>
>>> Takayuki
>>>
>>>
>>> In [1]: from rdkit import Chem
>>>
>>> In [2]: from rdkit.Chem import AllChem
>>>
>>> In [3]: mol = Chem.MolFromSmiles("c1ccc(F)cc1")
>>>
>>> In [6]: rxn = AllChem.ReactionFromSmarts('[cH&$(c(c)c):2]>>[c:2][F]')
>>>
>>> #first step works fine.
>>>
>>> In [7]: ps = rxn.RunReactants((mol,))
>>>
>>> #Bud second step did not work...
>>>
>>> In [9]: mol2 = ps[0][0]
>>>
>>> In [11]: ps = rxn.RunReactants((mol2,))
>>>
>>> [22:23:10]
>>>
>>>
>>>
>>>
>>> Pre-condition Violation
>>>
>>> getNumImplicitHs() called without preceding call to calcImplicitValence()
>>>
>>> Violation occurred on line 166 in file
>>> /Users/landrgr1/anaconda3/anaconda/conda-bld/work/Code/GraphMol/Atom.cpp
>>>
>>> Failed Expression: d_implicitValence>-1
>>>
>>>
>>>
>>>
>>>
>>> ---
>>>
>>> RuntimeError Traceback (most recent call
>>> last)
>>>
>>> in ()
>>>
>>> > 1 ps = rxn.RunReactants((mol2,))
>>>
>>>
>>> RuntimeError: Pre-condition Violation
>>>
>>>
>>>
--
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Re: [Rdkit-discuss] Question about Run Reaction
Hi Michal,
Thank you for your quick and kind response.
I tried to sanitize mol according to your advice.
And my code worked fine !
Thanks you. ;-)
By the way, If I want to run several reaction steps. Do I need to sanitize
each molecules?
# reactiontest.py
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles("c1c1")
rxn = AllChem.ReactionFromSmarts( "[cH&$(c(c)c):2]>>[c:2][F]" )
ps1= rxn.RunReactants( (mol,) )
ps1
mol2 = ps1[0][0]
Chem.SanitizeMol( mol2 )
ps2= rxn.RunReactants( (mol2,) )
uniq = set( [ Chem.MolToSmiles(x[0], isomericSmiles=True ) for x in ps2 ] )
print( uniq )
---
from shell
$ python reactiontest.py
{'Fc1ccc(F)cc1', 'Fc1(F)c1', 'Fc1c1F'}
-
Best regards,
Takayuki
2016年2月6日(土) 23:01 Michal Krompiec :
> Hi Taka,
> You have to call SanitizeMol() on the product(s) explicitely. The error is
> caused by the reactants not being 'sanitized'.
> Best wishes,
> Michal
>
>
> On Saturday, 6 February 2016, Taka Seri wrote:
>
>> Dear RDKitters,
>>
>> I have question about rdkit reaction function.
>> I want to generate molecules using several reaction steps.
>> I referred rdkit blog post, and wrote following code.
>> But second step of reaction caused error.
>> I could not difference about mol and mol2 object.
>> I wonder if anyone could help me.
>> Best regards,
>>
>> Takayuki
>>
>>
>> In [1]: from rdkit import Chem
>>
>> In [2]: from rdkit.Chem import AllChem
>>
>> In [3]: mol = Chem.MolFromSmiles("c1ccc(F)cc1")
>>
>> In [6]: rxn = AllChem.ReactionFromSmarts('[cH&$(c(c)c):2]>>[c:2][F]')
>>
>> #first step works fine.
>>
>> In [7]: ps = rxn.RunReactants((mol,))
>>
>> #Bud second step did not work...
>>
>> In [9]: mol2 = ps[0][0]
>>
>> In [11]: ps = rxn.RunReactants((mol2,))
>>
>> [22:23:10]
>>
>>
>>
>>
>> Pre-condition Violation
>>
>> getNumImplicitHs() called without preceding call to calcImplicitValence()
>>
>> Violation occurred on line 166 in file
>> /Users/landrgr1/anaconda3/anaconda/conda-bld/work/Code/GraphMol/Atom.cpp
>>
>> Failed Expression: d_implicitValence>-1
>>
>>
>>
>>
>>
>> ---
>>
>> RuntimeError Traceback (most recent call
>> last)
>>
>> in ()
>>
>> > 1 ps = rxn.RunReactants((mol2,))
>>
>>
>> RuntimeError: Pre-condition Violation
>>
>>
>>
--
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Re: [Rdkit-discuss] Question about Run Reaction
Hi Taka,
You have to call SanitizeMol() on the product(s) explicitely. The error is
caused by the reactants not being 'sanitized'.
Best wishes,
Michal
On Saturday, 6 February 2016, Taka Seri wrote:
> Dear RDKitters,
>
> I have question about rdkit reaction function.
> I want to generate molecules using several reaction steps.
> I referred rdkit blog post, and wrote following code.
> But second step of reaction caused error.
> I could not difference about mol and mol2 object.
> I wonder if anyone could help me.
> Best regards,
>
> Takayuki
>
>
> In [1]: from rdkit import Chem
>
> In [2]: from rdkit.Chem import AllChem
>
> In [3]: mol = Chem.MolFromSmiles("c1ccc(F)cc1")
>
> In [6]: rxn = AllChem.ReactionFromSmarts('[cH&$(c(c)c):2]>>[c:2][F]')
>
> #first step works fine.
>
> In [7]: ps = rxn.RunReactants((mol,))
>
> #Bud second step did not work...
>
> In [9]: mol2 = ps[0][0]
>
> In [11]: ps = rxn.RunReactants((mol2,))
>
> [22:23:10]
>
>
>
>
> Pre-condition Violation
>
> getNumImplicitHs() called without preceding call to calcImplicitValence()
>
> Violation occurred on line 166 in file
> /Users/landrgr1/anaconda3/anaconda/conda-bld/work/Code/GraphMol/Atom.cpp
>
> Failed Expression: d_implicitValence>-1
>
>
>
>
> ---
>
> RuntimeError Traceback (most recent call
> last)
>
> in ()
>
> > 1 ps = rxn.RunReactants((mol2,))
>
>
> RuntimeError: Pre-condition Violation
>
>
>
--
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[Rdkit-discuss] Question about Run Reaction
Dear RDKitters,
I have question about rdkit reaction function.
I want to generate molecules using several reaction steps.
I referred rdkit blog post, and wrote following code.
But second step of reaction caused error.
I could not difference about mol and mol2 object.
I wonder if anyone could help me.
Best regards,
Takayuki
In [1]: from rdkit import Chem
In [2]: from rdkit.Chem import AllChem
In [3]: mol = Chem.MolFromSmiles("c1ccc(F)cc1")
In [6]: rxn = AllChem.ReactionFromSmarts('[cH&$(c(c)c):2]>>[c:2][F]')
#first step works fine.
In [7]: ps = rxn.RunReactants((mol,))
#Bud second step did not work...
In [9]: mol2 = ps[0][0]
In [11]: ps = rxn.RunReactants((mol2,))
[22:23:10]
Pre-condition Violation
getNumImplicitHs() called without preceding call to calcImplicitValence()
Violation occurred on line 166 in file
/Users/landrgr1/anaconda3/anaconda/conda-bld/work/Code/GraphMol/Atom.cpp
Failed Expression: d_implicitValence>-1
---
RuntimeError Traceback (most recent call last)
in ()
> 1 ps = rxn.RunReactants((mol2,))
RuntimeError: Pre-condition Violation
--
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