Hi James,
some time ago I implemented a filter function during a pdb mining
campaign. The Idea was to exclude compounds to far away from drug like
chemical matter.
The function I wrote is not the prettiest one, but it is somehow
complementary to your substructure matching. The filter function uses
typical descriptors you might want to have in a filter routine, so
maybe this can give some inspiration. I added the import statement and
some print statements in order to make cut and paste play-arounds
easier:
----Snip------------------------
from Chem import Descriptors, Crippen, Lipinski, AvailDescriptors
#For more Descriptors try AvailDescriptors.descList
def DLfilter(mol):
try:
if Descriptors.MolWt(mol) <= 100 or Descriptors.MolWt(mol)
>=800:
print 'Failed in filter function
MolWt:',Descriptors.MolWt(mol)
return False
if Lipinski.NumHDonors(mol) >= 5:
print 'Failed in filter function
NumHDonors:',Lipinski.NumHDonors(mol)
return False
if Lipinski.NumHAcceptors(mol) >= 10:
print 'Failed in filter function
NumHAcceptors:',Lipinski.NumHAcceptors(mol)
return False
if Crippen.MolLogP(mol) <= -4 or Crippen.MolLogP(mol) >=
6:
print 'Failed in filter function LogP:',Crippen.MolLogP(mol)
return False
if Lipinski.NumRotatableBonds(mol) >= 15:
print 'Failed in filter function
NumRotatableBonds:',Lipinski.NumRotatableBonds(mol)
return False
else:
return True
except:
print "D'oh"
return False
----Snip------------------------
Kind regards,
Markus
James Davidson wrote:
Hi Greg,
Thanks for the reply.
1. In RDKit, has the 'cleaning / washing / salt-stripping' of
molecules already been formalised based on a set of rules, etc?
Not that I'm aware of on the open-source side of things. All
of the functionality required to do this is, I believe,
present in the RDKit though.
Great - I certainly found all the functionality I was looking for, but just wanted to make sure I wasn't missing any short-cuts!
2. When identifying compounds that contain a non-allowed
atom-type,
why do I find the SMARTS def [!H;!C;!N;!O;!F;!S;!Cl;!Br;!I] gives
unexpected results, but [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53]
works as I would expect?
This is a fairly common SMARTS "gotcha": in SMARTS the query "[C]"
means "aliphatic C". This leads to the following behavior:
[3]>>>
Chem.MolFromSmiles('c1ccccc1').GetSubstructMatches(Chem.MolFro
mSmarts('[!C]'))
Out[3] ((0,), (1,), (2,), (3,), (4,), (5,)) If you want to be
sure that your SMARTS will capture aliphatic or aromatic
atoms, you need to provide the atomic numbers, as in your
second query:
[4]>>>
Chem.MolFromSmiles('c1ccccc1').GetSubstructMatches(Chem.MolFro
mSmarts('[!#6]'))
Out[4] ()
Wow - I really was having some sort of mental block yesterday! (goes-off to look for some sort of embarrassed + dunce smiley...)
Kind regards
James
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