update make_fixed_size to accomodate numpy arrays

[dingquanyu]

1. added desired_num_res to np_example_to_features function to accommodate the need of padding when modelling multimeric models
2. moved the itpm, ptm prediction from alphafold.model.ModelRunner to AlphaPulldown's alphafold_backend in order to remove padded residues before calculating iptm, iptm+ptm scores.
3. update data_transform pipeline according to the needs of padding

[dingquanyu]

@jkosinski @DimaMolod quite some changes in this PR to support padding in AlphaPulldown but not that divergent from AlphaFold's repo. Rebase from AlphaFold is still doable and without conflicts.