[Rdkit-discuss] How to merge reaction rules?

2019-02-27 Thread ?????? 
Hi
Recently, I have some problems with rdkit. 

Smirks of reaction-A is 
CC(C)(CO)C(O)C(=O)NCCC(=O)O.O>>CC(C)(CO)C(O)C(=O)O.NCCC(=O)O
Smirks of reaction-B is 
CC(=O)OCC1=C(C(=O)O)N2C(=O)C(NC(=O)(=O)O)C2SC1.O>>CC(=O)OCC1=C(C(=O)O)N2C(=O)C(N)C2SC1.O=C(O)(=O)O

Rule of reaction-A is 
([C:5]-[NH;+0:6]-[C;H0;+0:7](-[C:9])=[O:8]).([OH2;+0:16])>>([C:9]-[C;H0;+0:7](=[O:8])-[OH;+0:16]).([C:5]-[NH2;+0:6])
  
Rule of reaction-B is 
([C:17]-[NH;+0:18]-[C;H0;+0:19](-[C:21])=[O:20]).([OH2;+0:27])>>([C:17]-[NH2;+0:18]).([C:21]-[C;H0;+0:19](=[O:20])-[OH;+0:27])
#radius = 1

>>>  from rdkit.Chem import MolToSmiles,MolFromSmiles,AllChem
>>> rule_rxn_a = 
>>> AllChem.ReactionFromSmarts('([C:5]-[NH;+0:6]-[C;H0;+0:7](-[C:9])=[O:8]).([OH2;+0:16])>>([C:9]-[C;H0;+0:7](=[O:8])-[OH;+0:16]).
([C:5]-[NH2;+0:6])')
>>> rule_rxn_b = 
>>> AllChem.ReactionFromSmarts('([C:17]-[NH;+0:18]-[C;H0;+0:19](-[C:21])=[O:20]).([OH2;+0:27])>>([C:17]-[NH2;+0:18]).([C:21]-[C;H0
;+0:19](=[O:20])-[OH;+0:27])')
>>> result_from_rule_a = [[MolToSmiles(k) for k in j] for j in 
>>> rule_rxn_a.RunReactants([MolFromSmiles(i) for i in 
>>> ['CC(C)(CO)C(O)C(=O)NCCC(=O)O
','O']])]
>>> result_from_rule_a
[['CC(C)(CO)C(O)C(=O)O', 'NCCC(=O)O']]
>>> result_from_rule_b = [[MolToSmiles(k) for k in j] for j in 
>>> rule_rxn_b.RunReactants([MolFromSmiles(i) for i in 
>>> ['CC(C)(CO)C(O)C(=O)NCCC(=O)O
','O']])]
>>> result_from_rule_b
[['NCCC(=O)O', 'CC(C)(CO)C(O)C(=O)O']]

For the same reactants, rule_rxn_a and rule_rxn_b can produce the same 
products.  We can also see that Rule-A and Rule-B are the same, except  some 
atom labels. 
Are there some automatic methods to identify that  rule-a and rule-b are the 
same . 
I am looking forward your reply.

Best Wishes
Shaozhen___
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[Rdkit-discuss] test cases

2019-02-27 Thread tech tech 
Hi,

Does rdkit have a test database with a large number of mol files? Or a
large number of RXN files?


Thanks,

Tom


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Re: [Rdkit-discuss] rotate a conformer around an axis?

2019-02-27 Thread Michal Krompiec 
Thanks Taka, this is just what I needed!
Michal

On Wed, 27 Feb 2019 at 03:19, Taka Seri  wrote:

> Hi Mchal,
>
> TransformConformer can rotate molecule with given rotation matrix I think.
>
> I rotate mol by using the method.
> Following code rotates molecule around x, y, z axis.
>
> https://nbviewer.jupyter.org/github/iwatobipen/playground/blob/master/rotation_mol.ipynb
>
> Unfortunately molecule will not render on github but you can view molecule
> if you run the code on your PC.
> I hope this would be some of help.
>
> Best regards,
> Taka
>
>
> 2019年2月26日(火) 17:55 Michal Krompiec :
>
>> Hello,
>> I'd like to check if a particular axis is a C2 symmetry axis of a
>> conformer. How do I rotate my conformer around an axis? (apart from
>> extracting the coordinates into numpy, multiplying by a rotation matrix and
>> updating the coordinates)
>> Can TransformConformer function be used for this?
>> Thanks,
>> Michal
>>
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