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Amons-based quantum machine learning for quantum chemistry

License: MIT License

Python 50.16% Fortran 3.87% Shell 0.03% Jupyter Notebook 44.43% C++ 0.45% Roff 0.08% DIGITAL Command Language 0.88% MATLAB 0.10%
quantum-chemistry machine-learning cheminformatics training-set-selection kernel-ridge-regression multi-fidelity-krr active-learning molecular-representation

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aqml's Issues

'RawMol' object has no attribute 'monomers'

When running the following command:

python gen_orca_jobs -loose -t optg -m b3lyp -b vdz -n 1 g7/*.sdf

I get the following output:

 ** set --maxit 60
 ** set --mem 1000
 ** set --calcfc 6
 first input file:  g7/frag_01_c00001.sdf
Traceback (most recent call last):
  File "gen_orca_jobs", line 152, in <module>
    mols = rawm.monomers
AttributeError: 'RawMol' object has no attribute 'monomers'

It seems the RawMol class is missing the monomers attribute. Is it possible for the repo to be updated with this? Or am I doing something wrong?

Problem with the demo example

Hi,

I've been trying to run the demo example from AQML, and the generation of amons works without any problems. However, when I run the train command it faces a problem with reading the xyz files from the demo. I am using the files that were provided with the tutorial, and I double checked their contents so everything should be fine. The error is below:

Running

aqml -train g7 -test target -p b3lypvdz 

gives

Traceback (most recent call last):
  File "/home/rafal/bin/anaconda3/lib/python3.9/site-packages/aqml/bin/aqml", line 190, in <module>
    obj.run()
  File "/home/rafal/bin/anaconda3/lib/python3.9/site-packages/cml/algo/aqml.py", line 582, in run
    obj = cc.molecules(fsk, [ag.p], unit=unit, isimple=isimple)
  File "/home/rafal/bin/anaconda3/lib/python3.9/site-packages/aqml/cheminfo/core.py", line 176, in __init__
    _nas, _zs, _coords, _nsheav, _props = obj2m(objs, property_names=property_names, idx=idx, isimple=isimple, unit=unit)
  File "/home/rafal/bin/anaconda3/lib/python3.9/site-packages/aqml/cheminfo/core.py", line 44, in obj2m
    _nas, _zs, _coords, _nsheav, _props = func(_obj, property_names=property_names, idx=idx)
  File "/home/rafal/bin/anaconda3/lib/python3.9/site-packages/aqml/cheminfo/rw/xyz.py", line 97, in read_xyz
    for i,mi in enumerate(rx.read_xyz(fileobj, index=index, properties_parser=rx.key_val_str_to_dict_regex)):
  File "/home/rafal/bin/anaconda3/lib/python3.9/site-packages/ase/io/extxyz.py", line 732, in read_xyz
    fileobj.seek(0)
ValueError: I/O operation on closed file.

I installed all the prerequisites and I'm using python 3.9. I would really appreciate your help and any ideas about the problem. Could it be python version incompatibility?

Best wishes,
Rafal

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