A supplier is random access, so your call to supp[I] here is probably quite
expensive:
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])
I highly suggest using the python iteration as opposed to using an index
such as:
for mol in suppl:
for pat in s:
mol.GetSubstructMatches(pat)
I expect this will help quite a bit. You may also consider using the
FilterCatalog which is designed to handle larger data sets and may help in
your case.
On Tue, Nov 1, 2016 at 4:22 AM, 杨弘宾 <yanyangh...@163.com> wrote:
> 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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