On 24 June 2010 23:37, Rob Soe <kym3p...@gmail.com> wrote: > Hi all, > > I have two lists of molecules. The first list contains testing molecules > (test.sdf) and the second contains training molecules (train.sdf). > > I would like to compare each test molecule to all the training molecule and > calculate a corresponding Tanimoto similarity score. (I implemented it in my > code and it is super slow as it is O(n^2) ). I use GetFingerprint() and > Tanimoto() functions for such purpose. After the comparison, I picked up the > kth most similar molecules to the test molecule and predict something for > the test molecule. I am trying to make things a bit faster.
There is no way to speed this up - if it's O(N^2) it's O(N^2). > So I tried the following babel command: > > babel test_mol.smi train_mols.sdf -ofpt > > But the problem is that I have to manually replace each testing molecule > smile information for every time I run the command. In other words, the > script will only compare the first molecule in the 'test_mol.smi" to all the > molecules in 'train_mols.sdf'. So even if I have a list of testing molecules > in the 'test_mol.smi', the script will not compare them to the training > molecules except the first one in the list. > > Is there a way or trick I can use so that I can compare all my testing > molecules to the training molecules and get a list of Tc scores? > > > Thanks so much for your help! > Rob > > > > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
