Comments (4)
KramerChristian
commented on September 23, 2024
Hi Alice,
I am not sure whether I understand your issue: The 3rd and the 5th SMILES string in your question are exactly the same - if you start with
c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7
and apply a double-cut transformation, why would you expect to get
c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7?
Without knowing the details, I assume you the database you create indexes a double-cut transformation that replace one nitrogen heteorcycle with a single-fluorinated form of the other. The constant parts are one *F, and the large aromatic system. If you apply this transformation to yoru starting SMILES (e.g. the 3rd SMILES), you woudl expect to get exactly the fourth SMILES.
If this is not clear, please post the transformation SMILES that is applied to produce the molecule that surprises you.
Bests,
Christian
from mmpdb.
alicecapecchi
commented on September 23, 2024
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 has the correct transformation, but it is attached the wrong way around!
Sorry again and I hope this clarifies my question!
from mmpdb.
KramerChristian
commented on September 23, 2024
Hi Alice,
can you share the command you use to get the new compounds created and the full output if you run it with the --explain or --save-details option?
Thanks,
Christian
from mmpdb.
alicecapecchi
commented on September 23, 2024
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, enumeration_label='N', variable_num_heavies=6, variable_symmetry_class='1', variable_smiles='c1ccccc1', attachment_order='0', constant_num_heavies=29, constant_symmetry_class='1', constant_smiles='c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc12', constant_with_H_smiles='Fc1ccc2nc(CNc3cc(-c4ccccc4)cc4ccccc34)[nH]c2c1F')
variable 'c1ccccc1' not found as SMILES '[:1]c1ccccc1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=29, variable_symmetry_class='1', variable_smiles='c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc12', attachment_order='0', constant_num_heavies=6, constant_symmetry_class='1', constant_smiles='c1ccccc1', constant_with_H_smiles='c1ccccc1')
variable 'c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc12' not found as SMILES '[:1]c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=23, variable_symmetry_class='12', variable_smiles='c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1', attachment_order='01', constant_num_heavies=12, constant_symmetry_class='11', constant_smiles='c1ccccc1.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1' not found as SMILES '[:1]c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1[:2]'
variable 'c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1' not found as SMILES '[:2]c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=10, variable_symmetry_class='123', variable_smiles='c1cc()c2ccccc2c1', attachment_order='102', constant_num_heavies=25, constant_symmetry_class='122', constant_smiles='NCc1nc2ccc(F)c(F)c2[nH]1.c1ccccc1.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc()c2ccccc2c1' not found as SMILES '[:1]c1cc([:2])c2ccccc2c1[:3]'
variable 'c1cc()c2ccccc2c1*' not found as SMILES '[:1]c1cc([:3])c2ccccc2c1[:2]'
variable 'c1cc()c2ccccc2c1' not found as SMILES '[:2]c1cc([:1])c2ccccc2c1[:3]'
variable 'c1cc()c2ccccc2c1' not found as SMILES '[:2]c1cc([:3])c2ccccc2c1[:1]'
variable 'c1cc()c2ccccc2c1' not found as SMILES '[:3]c1cc([:1])c2ccccc2c1[:2]'
variable 'c1cc()c2ccccc2c1' not found as SMILES '[:3]c1cc([:2])c2ccccc2c1[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=11, variable_symmetry_class='123', variable_smiles='Nc1cc()c()c2ccccc12', attachment_order='012', constant_num_heavies=24, constant_symmetry_class='122', constant_smiles='Cc1nc2ccc(F)c(F)c2[nH]1.c1ccccc1.c1ccccc1', constant_with_H_smiles=None)
variable 'Nc1cc()c()c2ccccc12' not found as SMILES '[:1]Nc1cc([:2])c([:3])c2ccccc12'
variable 'Nc1cc()c()c2ccccc12' not found as SMILES '[:1]Nc1cc([:3])c([:2])c2ccccc12'
variable 'Nc1cc()c()c2ccccc12' not found as SMILES '[:2]Nc1cc([:1])c([:3])c2ccccc12'
variable 'Nc1cc()c()c2ccccc12' not found as SMILES '[:2]Nc1cc([:3])c([:1])c2ccccc12'
variable 'Nc1cc()c()c2ccccc12' not found as SMILES '[:3]Nc1cc([:1])c([:2])c2ccccc12'
variable 'Nc1cc()c()c2ccccc12' not found as SMILES '[:3]Nc1cc([:2])c([:1])c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=12, variable_symmetry_class='123', variable_smiles='CNc1cc()c()c2ccccc12', attachment_order='201', constant_num_heavies=23, constant_symmetry_class='112', constant_smiles='c1ccccc1.c1ccccc1.c1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles=None)
variable 'CNc1cc()c()c2ccccc12' not found as SMILES '[:1]CNc1cc([:2])c([:3])c2ccccc12'
variable 'CNc1cc()c()c2ccccc12' not found as SMILES '[:1]CNc1cc([:3])c([:2])c2ccccc12'
variable 'CNc1cc()c()c2ccccc12' not found as SMILES '[:2]CNc1cc([:1])c([:3])c2ccccc12'
variable 'CNc1cc()c()c2ccccc12' not found as SMILES '[:2]CNc1cc([:3])c([:1])c2ccccc12'
variable 'CNc1cc()c()c2ccccc12' not found as SMILES '[:3]CNc1cc([:1])c([:2])c2ccccc12'
variable 'CNc1cc()c()c2ccccc12' not found as SMILES '[:3]CNc1cc([:2])c([:1])c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=22, variable_symmetry_class='123', variable_smiles='c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1', attachment_order='102', constant_num_heavies=13, constant_symmetry_class='122', constant_smiles='F.c1ccccc1.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1' not found as SMILES '[:1]c1cc(NCc2nc3ccc([:2])c(F)c3[nH]2)c2ccccc2c1[:3]'
variable 'c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1' not found as SMILES '[:1]c1cc(NCc2nc3ccc([:3])c(F)c3[nH]2)c2ccccc2c1[:2]'
variable 'c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1' not found as SMILES '[:2]c1cc(NCc2nc3ccc([:1])c(F)c3[nH]2)c2ccccc2c1[:3]'
variable 'c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1' not found as SMILES '[:2]c1cc(NCc2nc3ccc([:3])c(F)c3[nH]2)c2ccccc2c1[:1]'
variable 'c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1' not found as SMILES '[:3]c1cc(NCc2nc3ccc([:1])c(F)c3[nH]2)c2ccccc2c1[:2]'
variable 'c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1' not found as SMILES '[:3]c1cc(NCc2nc3ccc([:2])c(F)c3[nH]2)c2ccccc2c1[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=22, variable_symmetry_class='123', variable_smiles='c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1', attachment_order='102', constant_num_heavies=13, constant_symmetry_class='122', constant_smiles='F.c1ccccc1.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1' not found as SMILES '[:1]c1cc(NCc2nc3ccc(F)c([:2])c3[nH]2)c2ccccc2c1[:3]'
variable 'c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1' not found as SMILES '[:1]c1cc(NCc2nc3ccc(F)c([:3])c3[nH]2)c2ccccc2c1[:2]'
variable 'c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1' not found as SMILES '[:2]c1cc(NCc2nc3ccc(F)c([:1])c3[nH]2)c2ccccc2c1[:3]'
variable 'c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1' not found as SMILES '[:2]c1cc(NCc2nc3ccc(F)c([:3])c3[nH]2)c2ccccc2c1[:1]'
variable 'c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1' not found as SMILES '[:3]c1cc(NCc2nc3ccc(F)c([:1])c3[nH]2)c2ccccc2c1[:2]'
variable 'c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1' not found as SMILES '[:3]c1cc(NCc2nc3ccc(F)c([:2])c3[nH]2)c2ccccc2c1[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=16, variable_symmetry_class='12', variable_smiles='c1cc(-c2ccccc2)c()c2ccccc12', attachment_order='01', constant_num_heavies=19, constant_symmetry_class='12', constant_smiles='NCc1nc2ccc(F)c(F)c2[nH]1.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc(-c2ccccc2)c()c2ccccc12' not found as SMILES '[:1]c1cc(-c2ccccc2)c([:2])c2ccccc12'
variable 'c1cc(-c2ccccc2)c()c2ccccc12' not found as SMILES '[:2]c1cc(-c2ccccc2)c([:1])c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=17, variable_symmetry_class='12', variable_smiles='Nc1cc(-c2ccccc2)c()c2ccccc12', attachment_order='01', constant_num_heavies=18, constant_symmetry_class='12', constant_smiles='Cc1nc2ccc(F)c(F)c2[nH]1.c1ccccc1', constant_with_H_smiles=None)
variable 'Nc1cc(-c2ccccc2)c()c2ccccc12' not found as SMILES '[:1]Nc1cc(-c2ccccc2)c([:2])c2ccccc12'
variable 'Nc1cc(-c2ccccc2)c()c2ccccc12' not found as SMILES '[:2]Nc1cc(-c2ccccc2)c([:1])c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=18, variable_symmetry_class='12', variable_smiles='CNc1cc(-c2ccccc2)c()c2ccccc12', attachment_order='10', constant_num_heavies=17, constant_symmetry_class='12', constant_smiles='c1ccccc1.c1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles=None)
variable 'CNc1cc(-c2ccccc2)c()c2ccccc12' not found as SMILES '[:1]CNc1cc(-c2ccccc2)c([:2])c2ccccc12'
variable 'CNc1cc(-c2ccccc2)c()c2ccccc12' not found as SMILES '[:2]CNc1cc(-c2ccccc2)c([:1])c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=28, variable_symmetry_class='12', variable_smiles='c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1F', attachment_order='01', constant_num_heavies=7, constant_symmetry_class='12', constant_smiles='F.c1ccccc1', constant_with_H_smiles=None)
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1F' not found as SMILES '[:1]c1ccc2nc(CNc3cc(-c4ccccc4)c([:2])c4ccccc34)[nH]c2c1F'
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1F' not found as SMILES '[:2]c1ccc2nc(CNc3cc(-c4ccccc4)c([:1])c4ccccc34)[nH]c2c1F'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=27, variable_symmetry_class='123', variable_smiles='c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1', attachment_order='021', constant_num_heavies=8, constant_symmetry_class='112', constant_smiles='F.F.c1ccccc1', constant_with_H_smiles=None)
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1' not found as SMILES '[:1]c1ccc2nc(CNc3cc(-c4ccccc4)c([:2])c4ccccc34)[nH]c2c1[:3]'
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1' not found as SMILES '[:1]c1ccc2nc(CNc3cc(-c4ccccc4)c([:3])c4ccccc34)[nH]c2c1[:2]'
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1' not found as SMILES '[:2]c1ccc2nc(CNc3cc(-c4ccccc4)c([:1])c4ccccc34)[nH]c2c1[:3]'
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1' not found as SMILES '[:2]c1ccc2nc(CNc3cc(-c4ccccc4)c([:3])c4ccccc34)[nH]c2c1[:1]'
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1' not found as SMILES '[:3]c1ccc2nc(CNc3cc(-c4ccccc4)c([:1])c4ccccc34)[nH]c2c1[:2]'
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c()c4ccccc34)[nH]c2c1' not found as SMILES '[:3]c1ccc2nc(CNc3cc(-c4ccccc4)c([:2])c4ccccc34)[nH]c2c1[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=28, variable_symmetry_class='12', variable_smiles='c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc12', attachment_order='10', constant_num_heavies=7, constant_symmetry_class='12', constant_smiles='F.c1ccccc1', constant_with_H_smiles=None)
variable 'c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc12' not found as SMILES '[:1]c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c([:2])c3[nH]2)c2ccccc12'
variable 'c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc12' not found as SMILES '[:2]c1c(-c2ccccc2)cc(NCc2nc3ccc(F)c([:1])c3[nH]2)c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=6, variable_symmetry_class='1', variable_smiles='c1ccccc1', attachment_order='0', constant_num_heavies=29, constant_symmetry_class='1', constant_smiles='c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1-c1ccccc1', constant_with_H_smiles='Fc1ccc2nc(CNc3ccc(-c4ccccc4)c4ccccc34)[nH]c2c1F')
variable 'c1ccccc1' not found as SMILES '[:1]c1ccccc1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=29, variable_symmetry_class='1', variable_smiles='c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1-c1ccccc1', attachment_order='0', constant_num_heavies=6, constant_symmetry_class='1', constant_smiles='c1ccccc1', constant_with_H_smiles='c1ccccc1')
variable 'c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:1]c1cc(NCc2nc3ccc(F)c(F)c3[nH]2)c2ccccc2c1-c1ccccc1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=16, variable_symmetry_class='12', variable_smiles='c1cc()c2ccccc2c1-c1ccccc1', attachment_order='10', constant_num_heavies=19, constant_symmetry_class='12', constant_smiles='NCc1nc2ccc(F)c(F)c2[nH]1.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc()c2ccccc2c1-c1ccccc1' not found as SMILES '[:1]c1cc([:2])c2ccccc2c1-c1ccccc1'
variable 'c1cc()c2ccccc2c1-c1ccccc1' not found as SMILES '[:2]c1cc([:1])c2ccccc2c1-c1ccccc1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=17, variable_symmetry_class='12', variable_smiles='Nc1cc()c(-c2ccccc2)c2ccccc12', attachment_order='01', constant_num_heavies=18, constant_symmetry_class='12', constant_smiles='Cc1nc2ccc(F)c(F)c2[nH]1.c1ccccc1', constant_with_H_smiles=None)
variable 'Nc1cc()c(-c2ccccc2)c2ccccc12' not found as SMILES '[:1]Nc1cc([:2])c(-c2ccccc2)c2ccccc12'
variable 'Nc1cc()c(-c2ccccc2)c2ccccc12' not found as SMILES '[:2]Nc1cc([:1])c(-c2ccccc2)c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=18, variable_symmetry_class='12', variable_smiles='CNc1cc()c(-c2ccccc2)c2ccccc12', attachment_order='10', constant_num_heavies=17, constant_symmetry_class='12', constant_smiles='c1ccccc1.c1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles=None)
variable 'CNc1cc()c(-c2ccccc2)c2ccccc12' not found as SMILES '[:1]CNc1cc([:2])c(-c2ccccc2)c2ccccc12'
variable 'CNc1cc()c(-c2ccccc2)c2ccccc12' not found as SMILES '[:2]CNc1cc([:1])c(-c2ccccc2)c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=28, variable_symmetry_class='12', variable_smiles='c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1-c1ccccc1', attachment_order='10', constant_num_heavies=7, constant_symmetry_class='12', constant_smiles='F.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:1]c1cc(NCc2nc3ccc([:2])c(F)c3[nH]2)c2ccccc2c1-c1ccccc1'
variable 'c1cc(NCc2nc3ccc()c(F)c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:2]c1cc(NCc2nc3ccc([:1])c(F)c3[nH]2)c2ccccc2c1-c1ccccc1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=27, variable_symmetry_class='123', variable_smiles='c1cc(NCc2nc3ccc()c()c3[nH]2)c2ccccc2c1-c1ccccc1', attachment_order='201', constant_num_heavies=8, constant_symmetry_class='112', constant_smiles='F.F.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc(NCc2nc3ccc()c()c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:1]c1cc(NCc2nc3ccc([:2])c([:3])c3[nH]2)c2ccccc2c1-c1ccccc1'
variable 'c1cc(NCc2nc3ccc()c()c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:1]c1cc(NCc2nc3ccc([:3])c([:2])c3[nH]2)c2ccccc2c1-c1ccccc1'
variable 'c1cc(NCc2nc3ccc()c()c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:2]c1cc(NCc2nc3ccc([:1])c([:3])c3[nH]2)c2ccccc2c1-c1ccccc1'
variable 'c1cc(NCc2nc3ccc()c()c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:2]c1cc(NCc2nc3ccc([:3])c([:1])c3[nH]2)c2ccccc2c1-c1ccccc1'
variable 'c1cc(NCc2nc3ccc()c()c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:3]c1cc(NCc2nc3ccc([:1])c([:2])c3[nH]2)c2ccccc2c1-c1ccccc1'
variable 'c1cc(NCc2nc3ccc()c()c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:3]c1cc(NCc2nc3ccc([:2])c([:1])c3[nH]2)c2ccccc2c1-c1ccccc1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=28, variable_symmetry_class='12', variable_smiles='c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1-c1ccccc1', attachment_order='10', constant_num_heavies=7, constant_symmetry_class='12', constant_smiles='F.c1ccccc1', constant_with_H_smiles=None)
variable 'c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:1]c1cc(NCc2nc3ccc(F)c([:2])c3[nH]2)c2ccccc2c1-c1ccccc1'
variable 'c1cc(NCc2nc3ccc(F)c()c3[nH]2)c2ccccc2c1-c1ccccc1' not found as SMILES '[:2]c1cc(NCc2nc3ccc(F)c([:1])c3[nH]2)c2ccccc2c1-c1ccccc1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=13, variable_symmetry_class='1', variable_smiles='NCc1nc2ccc(F)c(F)c2[nH]1', attachment_order='0', constant_num_heavies=22, constant_symmetry_class='1', constant_smiles='c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles='c1ccc(-c2ccc3ccccc3c2-c2ccccc2)cc1')
variable 'NCc1nc2ccc(F)c(F)c2[nH]1' not found as SMILES '[:1]NCc1nc2ccc(F)c(F)c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=22, variable_symmetry_class='1', variable_smiles='c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', attachment_order='0', constant_num_heavies=13, constant_symmetry_class='1', constant_smiles='NCc1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles='NCc1nc2ccc(F)c(F)c2[nH]1')
variable 'c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12' not found as SMILES '[:1]c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=1, variable_symmetry_class='11', variable_smiles='N', attachment_order='01', constant_num_heavies=34, constant_symmetry_class='12', constant_smiles='Cc1nc2ccc(F)c(F)c2[nH]1.c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles=None)
variable 'N' not found as SMILES '[:1]N[:2]'
variable 'N' not found as SMILES '[:2]N[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=2, variable_symmetry_class='12', variable_smiles='CN', attachment_order='10', constant_num_heavies=33, constant_symmetry_class='12', constant_smiles='c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.c1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles=None)
variable 'CN' not found as SMILES '[:1]CN[:2]'
variable 'CN' not found as SMILES '[:2]CN[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=12, variable_symmetry_class='12', variable_smiles='NCc1nc2ccc()c(F)c2[nH]1', attachment_order='10', constant_num_heavies=23, constant_symmetry_class='12', constant_smiles='F.c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles=None)
variable 'NCc1nc2ccc()c(F)c2[nH]1' not found as SMILES '[:1]NCc1nc2ccc([:2])c(F)c2[nH]1'
variable 'NCc1nc2ccc()c(F)c2[nH]1' not found as SMILES '[:2]NCc1nc2ccc([:1])c(F)c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=11, variable_symmetry_class='123', variable_smiles='NCc1nc2ccc()c()c2[nH]1', attachment_order='201', constant_num_heavies=24, constant_symmetry_class='112', constant_smiles='F.F.c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles=None)
variable 'NCc1nc2ccc()c()c2[nH]1' not found as SMILES '[:1]NCc1nc2ccc([:2])c([:3])c2[nH]1'
variable 'NCc1nc2ccc()c()c2[nH]1' not found as SMILES '[:1]NCc1nc2ccc([:3])c([:2])c2[nH]1'
variable 'NCc1nc2ccc()c()c2[nH]1' not found as SMILES '[:2]NCc1nc2ccc([:1])c([:3])c2[nH]1'
variable 'NCc1nc2ccc()c()c2[nH]1' not found as SMILES '[:2]NCc1nc2ccc([:3])c([:1])c2[nH]1'
variable 'NCc1nc2ccc()c()c2[nH]1' not found as SMILES '[:3]NCc1nc2ccc([:1])c([:2])c2[nH]1'
variable 'NCc1nc2ccc()c()c2[nH]1' not found as SMILES '[:3]NCc1nc2ccc([:2])c([:1])c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=12, variable_symmetry_class='12', variable_smiles='NCc1nc2ccc(F)c()c2[nH]1', attachment_order='10', constant_num_heavies=23, constant_symmetry_class='12', constant_smiles='F.c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles=None)
variable 'NCc1nc2ccc(F)c()c2[nH]1' not found as SMILES '[:1]NCc1nc2ccc(F)c([:2])c2[nH]1'
variable 'NCc1nc2ccc(F)c()c2[nH]1' not found as SMILES '[:2]NCc1nc2ccc(F)c([:1])c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=12, variable_symmetry_class='1', variable_smiles='Cc1nc2ccc(F)c(F)c2[nH]1', attachment_order='0', constant_num_heavies=23, constant_symmetry_class='1', constant_smiles='Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles='Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12')
variable 'Cc1nc2ccc(F)c(F)c2[nH]1' not found as SMILES '[:1]Cc1nc2ccc(F)c(F)c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=23, variable_symmetry_class='1', variable_smiles='Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', attachment_order='0', constant_num_heavies=12, constant_symmetry_class='1', constant_smiles='Cc1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles='Cc1nc2ccc(F)c(F)c2[nH]1')
variable 'Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12' not found as SMILES '[:1]Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=1, variable_symmetry_class='11', variable_smiles='C', attachment_order='01', constant_num_heavies=34, constant_symmetry_class='12', constant_smiles='Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.c1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles=None)
variable 'C' not found as SMILES '[:1]C[:2]'
variable 'C' not found as SMILES '[:2]C[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=11, variable_symmetry_class='12', variable_smiles='Cc1nc2ccc()c(F)c2[nH]1', attachment_order='10', constant_num_heavies=24, constant_symmetry_class='12', constant_smiles='F.Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles=None)
variable 'Cc1nc2ccc()c(F)c2[nH]1' not found as SMILES '[:1]Cc1nc2ccc([:2])c(F)c2[nH]1'
variable 'Cc1nc2ccc()c(F)c2[nH]1' not found as SMILES '[:2]Cc1nc2ccc([:1])c(F)c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=10, variable_symmetry_class='123', variable_smiles='Cc1nc2ccc()c()c2[nH]1', attachment_order='201', constant_num_heavies=25, constant_symmetry_class='112', constant_smiles='F.F.Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles=None)
variable 'Cc1nc2ccc()c()c2[nH]1' not found as SMILES '[:1]Cc1nc2ccc([:2])c([:3])c2[nH]1'
variable 'Cc1nc2ccc()c()c2[nH]1' not found as SMILES '[:1]Cc1nc2ccc([:3])c([:2])c2[nH]1'
variable 'Cc1nc2ccc()c()c2[nH]1' not found as SMILES '[:2]Cc1nc2ccc([:1])c([:3])c2[nH]1'
variable 'Cc1nc2ccc()c()c2[nH]1' not found as SMILES '[:2]Cc1nc2ccc([:3])c([:1])c2[nH]1'
variable 'Cc1nc2ccc()c()c2[nH]1' not found as SMILES '[:3]Cc1nc2ccc([:1])c([:2])c2[nH]1'
variable 'Cc1nc2ccc()c()c2[nH]1' not found as SMILES '[:3]Cc1nc2ccc([:2])c([:1])c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=11, variable_symmetry_class='12', variable_smiles='Cc1nc2ccc(F)c()c2[nH]1', attachment_order='10', constant_num_heavies=24, constant_symmetry_class='12', constant_smiles='F.Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles=None)
variable 'Cc1nc2ccc(F)c()c2[nH]1' not found as SMILES '[:1]Cc1nc2ccc(F)c([:2])c2[nH]1'
variable 'Cc1nc2ccc(F)c()c2[nH]1' not found as SMILES '[:2]Cc1nc2ccc(F)c([:1])c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=11, variable_symmetry_class='1', variable_smiles='c1nc2ccc(F)c(F)c2[nH]1', attachment_order='0', constant_num_heavies=24, constant_symmetry_class='1', constant_smiles='CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles='CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12')
variable 'c1nc2ccc(F)c(F)c2[nH]1' not found as SMILES '[:1]c1nc2ccc(F)c(F)c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=24, variable_symmetry_class='1', variable_smiles='CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', attachment_order='0', constant_num_heavies=11, constant_symmetry_class='1', constant_smiles='c1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles='Fc1ccc2nc[nH]c2c1F')
variable 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12' not found as SMILES '[:1]CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=10, variable_symmetry_class='12', variable_smiles='c1nc2ccc()c(F)c2[nH]1', attachment_order='01', constant_num_heavies=25, constant_symmetry_class='12', constant_smiles='CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F', constant_with_H_smiles=None)
variable 'c1nc2ccc()c(F)c2[nH]1' not found as SMILES '[:1]c1nc2ccc([:2])c(F)c2[nH]1'
variable 'c1nc2ccc()c(F)c2[nH]1' matches SMILES '[:2]c1nc2ccc([:1])c(F)c2[nH]1' (id 2)
Evaluating 1 possible rule SMILES: ['21']
Evaluate constant 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' with permutation '21' against rules using SMILES [:2]c1nc2ccc([:1])c(F)c2[nH]1 (2)
Processing fragment Fragmentation(num_cuts=3, enumeration_label='N', variable_num_heavies=9, variable_symmetry_class='123', variable_smiles='c1nc2ccc()c()c2[nH]1', attachment_order='012', constant_num_heavies=26, constant_symmetry_class='122', constant_smiles='CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F.F', constant_with_H_smiles=None)
variable 'c1nc2ccc()c()c2[nH]1' not found as SMILES '[:1]c1nc2ccc([:2])c([:3])c2[nH]1'
variable 'c1nc2ccc()c()c2[nH]1' not found as SMILES '[:1]c1nc2ccc([:3])c([:2])c2[nH]1'
variable 'c1nc2ccc()c()c2[nH]1' not found as SMILES '[:2]c1nc2ccc([:1])c([:3])c2[nH]1'
variable 'c1nc2ccc()c()c2[nH]1' not found as SMILES '[:2]c1nc2ccc([:3])c([:1])c2[nH]1'
variable 'c1nc2ccc()c()c2[nH]1' not found as SMILES '[:3]c1nc2ccc([:1])c([:2])c2[nH]1'
variable 'c1nc2ccc()c()c2[nH]1' not found as SMILES '[:3]c1nc2ccc([:2])c([:1])c2[nH]1'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=10, variable_symmetry_class='12', variable_smiles='c1nc2ccc(F)c()c2[nH]1', attachment_order='01', constant_num_heavies=25, constant_symmetry_class='12', constant_smiles='CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F', constant_with_H_smiles=None)
variable 'c1nc2ccc(F)c()c2[nH]1' not found as SMILES '[:1]c1nc2ccc(F)c([:2])c2[nH]1'
variable 'c1nc2ccc(F)c()c2[nH]1' matches SMILES '[:2]c1nc2ccc(F)c([*:1])c2[nH]1' (id 3)
Evaluating 1 possible rule SMILES: ['21']
Evaluate constant 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' with permutation '21' against rules using SMILES [:2]c1nc2ccc(F)c([:1])c2[nH]1 (3)
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=1, variable_symmetry_class='1', variable_smiles='*F', attachment_order='0', constant_num_heavies=34, constant_symmetry_class='1', constant_smiles='*c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1F', constant_with_H_smiles='Fc1cccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c12')
variable 'F' not found as SMILES '[:1]F'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=34, variable_symmetry_class='1', variable_smiles='c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1F', attachment_order='0', constant_num_heavies=1, constant_symmetry_class='1', constant_smiles='F', constant_with_H_smiles='F')
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1F' not found as SMILES '[:1]c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1F'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=33, variable_symmetry_class='12', variable_smiles='c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1', attachment_order='01', constant_num_heavies=2, constant_symmetry_class='11', constant_smiles='F.F', constant_with_H_smiles=None)
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1' not found as SMILES '[:1]c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1[:2]'
variable 'c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1' not found as SMILES '[:2]c1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=1, variable_symmetry_class='1', variable_smiles='F', attachment_order='0', constant_num_heavies=34, constant_symmetry_class='1', constant_smiles='c1c(F)ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c12', constant_with_H_smiles='Fc1ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c2c1')
variable 'F' not found as SMILES '[:1]F'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=1, enumeration_label='N', variable_num_heavies=34, variable_symmetry_class='1', variable_smiles='c1c(F)ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c12', attachment_order='0', constant_num_heavies=1, constant_symmetry_class='1', constant_smiles='F', constant_with_H_smiles='F')
variable 'c1c(F)ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c12' not found as SMILES '[:1]c1c(F)ccc2nc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)[nH]c12'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=1, variable_symmetry_class='11', variable_smiles='N', attachment_order='01', constant_num_heavies=34, constant_symmetry_class='12', constant_smiles='c1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.Cc1nc2ccc(F)c(F)c2[nH]1', constant_with_H_smiles=None)
variable 'N' not found as SMILES '[:1]N[:2]'
variable 'N' not found as SMILES '[:2]N[:1]'
No matching rule SMILES found. Skipping fragment.
Processing fragment Fragmentation(num_cuts=2, enumeration_label='N', variable_num_heavies=1, variable_symmetry_class='11', variable_smiles='C', attachment_order='01', constant_num_heavies=34, constant_symmetry_class='12', constant_smiles='c1nc2ccc(F)c(F)c2[nH]1.Nc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12', constant_with_H_smiles=None)
variable 'C' not found as SMILES '[:1]C[:2]'
variable 'C' not found as SMILES '[:2]C[:1]'
No matching rule SMILES found. Skipping fragment.
Rule 1: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 1: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 1: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 1: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 1: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 1: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 2: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 2: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 2: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 2: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 2: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
Rule 2: 'CNc1cc(-c2ccccc2)c(-c2ccccc2)c2ccccc12.F' + '[:1]c1cnc2nc([:2])cn2c1' -> 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
== Product SMILES in database: 1 ==
Evaluating the 12 rule environments for 'Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1'
ID SMILES
1 Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1
Thanks for your help!
Alice
from mmpdb.
Related Issues (20)
- To increase the max_rotatable_bonds? HOT 2
- How to get environment smiles? HOT 3
- How to build mmpdb with large data set HOT 4
- cannot fix the AttributeError: module '__main__' has no attribute '__spec__' HOT 2
- store fragments in a SQLite db instead of JSON-Lines HOT 2
- Use SQLAlchemy to work with the database HOT 1
- organize command-line processing and move to click HOT 4
- Remove vendered use of peewee HOT 1
- Use importlib.resources instead of __file__ HOT 1
- Can we specify the environmental radius when generating the mmpdb? HOT 11
- Which "cut-smarts" patterns (i.e. fragmentation parameters) are used by default for Transform function? HOT 1
- mmpdb transform behaves unexpectedly HOT 5
- Error when using "--out mmpa" HOT 4
- [docs] README.md: create installation guide HOT 5
- AttributeError: module '__main__' has no attribute '__spec__'
- Support for CXSMILES HOT 4
- Obtain list of matched pairs with common core from an ID. HOT 4
- Automatically get MMPs for a given data set HOT 4
- Turning on --property flag leading to a smaller number of transformed structures
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from mmpdb.