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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