Alice Capecchi

Hi Helen, are you using Windows? I am asking because unfortunately tmap (and therefore map4) does not work in Windows. Cheers, Alice

Hi Amir, I am not sure I understand what you mean with pointing it to another library. If you want to find analogs of a query molecule within a library...

Hi Amir, You cannot do it directly using map4.py. You would need to calculate the MAP4 fingerprint (for example using "map4.py") for your three compounds and for your 100k library....

Hi Mohammad, No, I am sorry, this is not possible in the current implementation of MAP4. It would be a very welcomed contribution. Cheers, Alice

C1=CC=C(C=C1)C2=C3C=CC=CC3=C(C4=CC=CC=C42)C5=CC=CC6=C5C(=CC=C6)C7=CC=CC8=CC=CC=C87

Hi Christian, I must have copy pasted the same molecules twice by mistake, sorry for the confusion! the expected molecules would be Fc1cnc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cn2c1. And I agree that the 4th smiles...

Sure :) mmpdb fragment example_dataset_double_cut.smi -o test_double_cut.fragments (where example_dataset_double_cut.smi are the SMILES: c1ccc(cc1)c2ccc3c(c2)c(c(cc3NCc4cn5cc(cnc5n4)F)c6ccccc6)c7ccccc7 test1 c1ccc(cc1)c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7 test2) mmpdb index test_double_cut.fragments -o test_double_cut.mmpdb mmpdb transform --smiles 'c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7' test_double_cut.mmpdb --explain Processing fragment Fragmentation(num_cuts=1,...