Removing All SMILES From Source List

[Dabacadabra]

Hello,

I am trying to use the lead optimization feature of AutoGrow4, following the instructions in the paper. However, with all of my SMILES, they fail the check in the test_source_smiles_convert command of the operations.py file, returning the following for every entry:

REMOVING SMILES FROM SOURCE LIST: Unformatted or blank entry in source compound list.
Removing: CompoundInfo(smiles='Nc1ncnc2c1n(cn2)[C@H]3OC@HC@@H[C@H]3O', name='ATP', short_id=None, docking_score=None, diversity_score=None, fitness_score=None)

I knew that ATP was a valid SMILES entry, so I decided to test with the authors' source .smi file, PARPI_BRICS_frags. I run into the same issue here, returning the following for every entry:

REMOVING SMILES FROM SOURCE LIST: Unformatted or blank entry in source compound list.
Removing: CompoundInfo(smiles='O=C(c1cc(Cc2n[nH]c(=O)c3ccccc23)ccc1F)N1CCN(C(=O)C2CC2)CC1', name='Olaparib', short_id=None, docking_score=None, diversity_score=None, fitness_score=None)

The JSON file I am using is attached as Test.json

Test.json

Here are the first couple lines of my .smi file:

Nc1ncnc2c1n(cn2)[C@H]3OC@HC@@H[C@H]3O ATP
O[C@@h]1COC[C@@h]1O frag_1
C frag_2
O=P(O)(O)OP(=O)(O)OP(=O)(O)O frag_4
[H]N carbon_frag_1
[H]NC carbon_frag_2
[H][N+]#[C-] carbon_frag_3
[H]N=O carbon_frag_4
[H]N=C carbon_frag_5
[H]NO carbon_frag_6
[H]NN carbon_frag_7
[H]N(C)C carbon_frag_8
[H]NCC carbon_frag_9
[H]NC=O carbon_frag_10
[H]NCO carbon_frag_11
[H]N=[N+]=[N-] carbon_frag_12
[H]NC#N carbon_frag_13

And here are the first couple lines of the .smi file by the authors:

O=C(c1cc(Cc2n[nH]c(=O)c3ccccc23)ccc1F)N1CCN(C(=O)C2CC2)CC1 Olaparib
O=CN1CCN(C(=O)c2cc(Cc3n[nH]c(=O)c4ccccc34)ccc2F)CC1 Olaparib_Frag_725627
Cc1n[nH]c(=O)c2ccccc12 Olaparib_Frag_497293
C1CNCCN1 Olaparib_Frag_137086
Cc1ccc(F)cc1 Olaparib_Frag_534618
Cc1ccc(F)c(C(=O)N2CCNCC2)c1 Olaparib_Frag_306774
O=c1[nH]ncc2ccccc12 Olaparib_Frag_127535
Cc1ccc(F)c(C(=O)N2CCN(C(=O)C3CC3)CC2)c1 Olaparib_Frag_903764
O=CN1CCN(C(=O)C2CC2)CC1 Olaparib_Frag_973255
O=CN1CCN(C(=O)c2ccccc2F)CC1 Olaparib_Frag_942416
O=C(c1cc(Cc2n[nH]c(=O)c3ccccc23)ccc1F)N1CCNCC1 Olaparib_Frag_652934

I understand that I used tab delineation and the .smi file by the author has 4 spaces, but I tried both delineations in my file and neither worked. Remember that the authors' .smi file didn't work either. Any help would be greatly appreciated. It may help to know that I am working in a WSL environment.

Thanks!