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kvkarandashev / bmapqml

Machine learning for target property optimization.
MIT License
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from bmapqml.chemxpl.utils import xyz_list2mols_extgraph output = xyz_list2mols_extgraph(["/home/jan/projects/MOLOPT/molopt/examples/chemxpl/MC_minimization/t.xyz"]) #4

Closed janweinreich closed 2 years ago

janweinreich commented 2 years ago

t.xyz is a simple asperin molecule but for

from bmapqml.chemxpl.utils import xyz_list2mols_extgraph output = xyz_list2mols_extgraph(["/home/jan/projects/MOLOPT/molopt/examples/chemxpl/MC_minimization/t.xyz"])

output is None.

This is because unfiltered_list=Parallel(n_jobs=default_num_procs(), backend=default_parallel_backend)(delayed(try_xyz2mol_extgraph)(None, read_xyz=read_xyz) for read_xyz in read_xyzs) returns None but i don't understand why

kvkarandashev commented 2 years ago

Could you check whether this works with updated code? If it does not please append the xyz file.

janweinreich commented 2 years ago

tested this with the code you pushed this afternoon

21 Generated with https://api.leruli.com/latest/references/BEG2019,BCE2020,rdkit/bibtex C -3.294 -1.175 0.235 C -1.96 -0.803 -0.336 O -1.767 -0.246 -1.381 O -0.968 -1.205 0.491 C 0.324 -0.784 0.255 C 1.317 -1.75 0.178 C 2.631 -1.377 -0.036 C 2.959 -0.04 -0.193 C 1.974 0.925 -0.119 C 0.647 0.57 0.117 C -0.39 1.62 0.261 O -1.408 1.513 0.899 O -0.065 2.752 -0.373 H -4.029 -1.256 -0.559 H -3.221 -2.1 0.8 H -3.586 -0.374 0.913 H 1.04 -2.787 0.287 H 3.399 -2.135 -0.089 H 3.983 0.249 -0.371 H 2.218 1.969 -0.231 H -0.776 3.403 -0.269

kvkarandashev commented 2 years ago

Are you sure you are using the newest version? Import seems to work just fine for me.

janweinreich commented 2 years ago

indeed after your most recent commit it works -> init_ncharges=[17, 17] (Pdb) output [heavy atoms: [C:6,V:4,H:3, C:6,V:4,H:0, C:8,V:2,H:0, C:8,V:2,H:0, C:6,V:4,H:0, C:6,V:4,H:1, C:6,V:4,H:1, C:6,V:4,H:1, C:6,V:4,H:1, C:6,V:4,H:0, C:6,V:4,H:0, C:8,V:2,H:0, C:8,V:2,H:1] , bonds&orders: {(0, 1): 1, (1, 2): 2, (1, 3): 1, (3, 4): 1, (4, 5): 1, (5, 6): 2, (6, 7): 1, (7, 8): 2, (4, 9): 2, (8, 9): 1, (9, 10): 1, (10, 11): 2, (10, 12): 1}]