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View Code? Open in Web Editor NEWThe ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for organic molecules.
License: MIT License
The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for organic molecules.
License: MIT License
I see the scripts but where is the data?
How do I access the SMILES string for any molecule?
I notice some oxygen molecules appears in the ANI-1x dataset, such as the oxygen dimer below. I'd like to confirm what multiplicity these dimers are using during the Gaussian calculation, 1 or 5?
4
O 1.817700 0.308000 -0.269900
O 1.132200 -0.515000 0.285500
O -1.794600 -0.410600 -0.233300
O -1.155300 0.617600 0.217600
Hello!
Thank you so much for making the ANI-1x dataset available, it is a fantastic resource. I have a question regarding the availability of quadrupoles for molecules/conformers in the dataset. According to the paper, the 'wb97x_dz.quadrupole'
key should contain an array of size nan
. I ran the following code snippet:
ani1x_data = h5py.File('ani-1x/ani1x-release.h5')
frac_quads_li = []
for i in ani1x_data.keys():
all_quads = ani1x_data[i]['wb97x_dz.quadrupole']
all_quads_sub = np.unique(np.argwhere(~np.isnan(all_quads))[:,0])
frac_quads_li.append(float(len(all_quads_sub))/len(all_quads))
print(f'Avg Fraction Computed Quads: {round(np.average(frac_quads_li),3)}')
print(f'No Quad Count: {np.sum(np.array(frac_quads_li)==0.0)}/{len(frac_quads_li)}')
...and got the following result:
Avg Fraction Computed Quads: 0.215
No Quad Count: 1698/3114
So it appears that there are quite a few quadrupoles that are all nan, with more than half of molecules having no quadrupole information. When I run the same analysis on 'wb97x_dz.dipole'
, I found that 181 molecules have no dipole constants available for any conformers. I did not find anything in the publication or GH repo that mentioned these nan values (although I may have missed it). So I am just wondering what happened to the dipoles/quadrupoles in these cases, and whether there is a version of the ANI-1x dataset that contains these dipole/quadrupole values. If not, that is fine. Am happy to recalculate them, or omit the corresponding conformers for the analysis I am trying to do. But if a shareable version is available with these additional values I would appreciate it, as it would save me some time and compute.
Thank you for your time,
Marcus Schwarting
Where are the data?
What is the key of the energies on which the ANI models were trained on? And what the forces one?
Hello,
after using your example_loader file, it seems that the ccsd(t)_cbs.forces key is missing from the hd5 dump.
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