Re: [Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as expected
Thanks, it works! I appreciate that Rdkit is so strict in representation of
the the molecules and the substructures. I learned a lot in the mail list.
Hongbin Yang
From: Paolo ToscoDate: 2016-10-27 17:19To: 杨弘宾; rdkit-discussSubject: Re:
[Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as
expected
Dear Hongbin,
I am afraid The SMARTS you are using is not valid, as no SSSR can
have less than 3 terms, or it wouldn't be a ring. If you
change[a!r0] into, for instance, [a!r3], then you'll find the
match you are looking for.
Cheers,
p.
On 27/10/2016 09:36, 杨弘宾 wrote:
Hi,
I
tryied using rdkit to match fragments with compounds only to
find that rdkit performed not well in SMARTS. The following is
the notebook I worked.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FragmentMatcher
from rdkit.Chem.Draw import IPythonConsole
In [49]:
p = FragmentMatcher.FragmentMatcher()
p.Init('[a!r0][NX3+](=[OX1])([O-])')
In [50]:
mol = Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
mol
Out[50]:
In [51]:
p.HasMatch(mol)
Out[51]:
0
In [52]:
print Chem.MolFromSmarts('[a!r0][NX3+](=[OX1])([O-])')
None
However, openbabel worked well in matching the substrcutre.
Even "or operator" was avaiable such as
"[a!r0][$([NX3+](=[OX1])([O-])),$([NX3](=O)=O)]".
>>>
s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
>>> a=pybel.readstring('smi','c1c1[N+](=O)[O-]')
>>> s.findall(a)
[(6, 7, 8, 9)]
It is a pity that rdkit can calculate the topological
distance between two atoms while it cannot match the
fragments... Is there any better API which I didn't find?
Hongbin
Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology
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Re: [Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as expected
Dear Hongbin,
I am afraid The SMARTS you are using is not valid, as no SSSR can have
less than 3 terms, or it wouldn't be a ring. If you change[a!r0] into,
for instance, [a!r3], then you'll find the match you are looking for.
Cheers,
p.
On 27/10/2016 09:36, 杨弘宾 wrote:
Hi,
I tryied using rdkit to match fragments with compounds only to
find that rdkit performed not well in SMARTS. The following is the
notebook I worked.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FragmentMatcher
from rdkit.Chem.Draw import IPythonConsole
In [49]:
p = FragmentMatcher.FragmentMatcher()
p.Init('[a!r0][NX3+](=[OX1])([O-])')
In [50]:
mol = Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
mol
Out[50]:
In [51]:
p.HasMatch(mol)
Out[51]:
0
In [52]:
print Chem.MolFromSmarts('[a!r0][NX3+](=[OX1])([O-])')
None
However, openbabel worked well in matching the substrcutre. Even "or
operator" was avaiable such as
"[a!r0][$([NX3+](=[OX1])([O-])),$([NX3](=O)=O)]".
>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
>>> a=pybel.readstring('smi','c1c1[N+](=O)[O-]')
>>> s.findall(a)
[(6, 7, 8, 9)]
It is a pity that rdkit can calculate the topological distance between
two atoms while it cannot match the fragments... Is there any better
API which I didn't find?
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology
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[Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as expected
Hi,? ? I tryied using rdkit to match fragments with compounds only to find that
rdkit performed not well in SMARTS. The following is the notebook I worked.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FragmentMatcher
from rdkit.Chem.Draw import IPythonConsole
In?[49]:p = FragmentMatcher.FragmentMatcher()
p.Init('[a!r0][NX3+](=[OX1])([O-])')
In?[50]:mol = Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
mol
Out[50]:In?[51]:p.HasMatch(mol)
Out[51]:0In?[52]:print Chem.MolFromSmarts('[a!r0][NX3+](=[OX1])([O-])')
None
However, openbabel worked well in matching the substrcutre. Even "or operator"
was avaiable such as "[a!r0][$([NX3+](=[OX1])([O-])),$([NX3](=O)=O)]".?
>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
>>> a=pybel.readstring('smi','c1c1[N+](=O)[O-]')
>>> s.findall(a)
[(6, 7, 8, 9)]
It is a pity that rdkit can calculate the topological distance between two
atoms while it cannot match the fragments... Is there any better API which I
didn't find?
Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology?
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