Hi,? ??Supposing I'd like to matching 100 substructures with 1000 compounds
represented as smiles.What I did is:
suppl = AllChem.SmilesMolSupplier('allmoleculenew.smi',delimiter='\t')l =
len(suppl)for j in range(ll): ?# I have to make substructures in the first
loop.? ??for i in range(l):
? ??? ??suppl[i].GetSubstructMatches(s[j])?and found the performance is not
good.
Then I did a comparison and found that it was because the conformation of the
compounds where not initiated.If I use MolFromSmiles，the performance will
improve a lot.start = time.clock()suppl =
AllChem.SmilesMolSupplier('allmoleculenew.smi',delimiter='\t')
l=len(suppl)?print time.clock()-start ? # >>>?0.0373735355168 ?indicating that
the molecules were not initiated.
for i in range(l):
? ??suppl[i].GetSubstructMatches(sa)
? ??suppl[i].GetSubstructMatches(sa2)
print time.clock()-start ? # >>>?11.1884715172
start = time.clock()
f = open('allmoleculenew.smi')
for i in range(l):
? ??mol = Chem.MolFromSmiles(f.next().split('\t')[0])
? ??mol.GetSubstructMatches(sa)
? ??mol.GetSubstructMatches(sa2)print time.clock()-start # >>>?5.44030582111
The second method was double faster than the first, indicating that the "init"
is more time consuming compared to matching.I think?SmilesMolSupplier is a good
API to load multiple compounds but it didnot parse the smiles immediately,
which adds the?time complexity to the further application. So is it possible to
manually initiate the compounds?
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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