Hi, Chenyang,    You don't need to delete the substructure from the molecule. 
Just check whehter the mapped atoms have been matched. For example:
m = Chem.MolFromSmiles('CC(=O)O')OH = Chem.MolFromSmarts('[OH]')COOH = 
Chem.MolFromSmarts('C(O)=O')
m.GetSubstructMatches(OH)>> ((3,),)m.GetSubstructMatchs(COOH)>> ((1, 3, 2),)
Since atom "3" has been already matched, it should be ignored. So you can 
create a "set" to record the matched atoms to avoid repetitive count.


Hongbin Yang 杨弘宾


 From: Chenyang ShiDate: 2017-03-06 14:04To: Greg LandrumCC: RDKit 
DiscussSubject: Re: [Rdkit-discuss] delete a substructureHi Greg,
Thanks for a prompt reply. I did try "GetSubstructMatches()" and it returns 
correct numbers of substructures for CH3COOH. The potential problem with this 
approach is that if the molecule is getting complicated, it will possibly 
generate duplicate numbers for certain functional groups. For example, --OH 
(alcohol) group will be likely also counted in --COOH. A safer way, in my mind, 
is to remove the substructure that has been counted. 
Greg, you mentioned "chemical reaction functionality", can you show me a demo 
script with that using CH3COOH as an example. I will definitely delve into the 
manual to learn more. But reading your code will be a good start. 
Thanks,Chenyang
 
On Sun, Mar 5, 2017 at 10:15 PM, Greg Landrum <greg.land...@gmail.com> wrote:
Hi Chenyang,
If you're really interested in counting the number of times the substructure 
appears, you can do that much quicker with `GetSubstructMatches()`:
In [2]: m = Chem.MolFromSmiles('CC(C)CCO')In [3]: 
len(m.GetSubstructMatches(Chem.MolFromSmarts('[CH3;X4]')))
Out[3]: 2
Is that sufficient, or do you actually want to sequentially remove all of the 
groups in your list?
If you actually want to remove them, you are probably better off using the 
chemical reaction functionality instead of DeleteSubstructs(), which 
recalculates the number of implicit Hs on atoms after each call.
-greg

On Mon, Mar 6, 2017 at 4:21 AM, Chenyang Shi <cs3...@columbia.edu> wrote:
I am new to rdkit but I am already impressed by its vibrant community. I have a 
question regarding deleting substructure. In the RDKIT documentation, this is a 
snippet of code describing how to delete substructure:
>>>m = Chem.MolFromSmiles("CC(=O)O")>>>patt = 
>>>Chem.MolFromSmarts("C(=O)[OH]")>>>rm = AllChem.DeleteSubstructs(m, 
>>>patt)>>>Chem.MolToSmiles(rm)'C'
This block of code first loads a molecule CH3COOH using SMILES code, then 
defines a substructure COOH using SMARTS code which is to be deleted. After 
final line of code, the program outputs 'C', in SMILES form. 
I had wanted to develop a method for detecting number of groups in a molecule. 
In CH3COOH case, I can search number of --CH3 and --COOH group by using their 
respective SMARTS code with no problem. However, when molecule becomes more 
complicated, it is preferred to delete the substructure that has been searched 
before moving to next search using SMARTS code. Well, in current case, after 
searching -COOH group and deleting it, the leftover is 'C' which is essentially 
CH4 instead of --CH3. I cannot proceed with searching with SMARTS code for 
--CH3 ([CH3;A;X4!R]). 
Is there any way to work around this?Thanks,Chenyang 
 

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