Jan H. Jensen

param_gfn0-xtb.txt not findable in conda install

2

`conda install -q -y -c conda-forge xtb` works fine (i.e. GFN1 and GNF2) except that gfn0 calculations fail: [ERROR] Program stopped due to fatal error -3- Could not setup parameterisation...

pdbbind_nn.py no longer working.

3

https://github.com/deepchem/DeepLearningLifeSciences/blob/master/Chapter05/pdbbind_nn.py throws this error RuntimeError: expected scalar type Float but found Char

GetSubstructMatches with dative bonds

1

The following finds no matches: m = Chem.MolFromSmiles('C1P->[Zr+3][Zr+3][Zr+3]’)) m = Chem.MolFromSmiles('C1P-[Zr+3]-1') m.GetSubstructMatches(Chem.MolFromSmarts('C1P-[Zr+3]-1’))

The new version gives a surface area of 156 A^2 for NH4+, while the legacy version gives 42 Å^2. The latter is correct