BUG: Different features was cropped separately

[huangbinapple]

There is a bug.

Different feature was cropped separately in the dataloader, causing the final cropped features not align with each other.

        for k, v in example.items():
            if k in FEATURES_1D:
                fixed_size_example[k], seq_mask = make_fixed_size_1d(
                    v, fixed_size=self.fixed_size, start_idx=start_idx
                )

In the function make_fixed_size_1d, there is a random function to sample a fixed piece from the whole pdb sample. As it in the loop for k, v in example.items(), different features such as "aatype" and "chain_index" may be cropped as different pieces from the whole sample.

@alexechu @duerrsimon @gelnesr @zhkim216