Fix hydrogen mask mismatch in check_intermolecular_distance

[SergeiNikolenko]

Summary

• Bug: check_intermolecular_distance() filters hydrogen atoms from torch tensors (coords_protein, atoms_protein_all) but does not filter the corresponding numpy arrays (atom_names_cond, pos_cond). A downstream boolean mask (ids_cond) derived from the filtered tensor is then used to index the unfiltered numpy arrays, causing an IndexError whenever the protein PDB contains explicit hydrogen atoms.
• Fix: Apply the same H-filtering mask to atom_names_cond and pos_cond so all arrays stay in sync.
• Test: Added regression test that verifies the function works with protein atoms containing explicit hydrogens.

Reproduction

This occurs with any prepared protein PDB that contains explicit H atoms (common in MD/docking pipelines). For example, loading with Chem.MolFromPDBFile(path, removeHs=True) often retains explicit H from prepared structures.

# Minimal reproduction
import numpy as np
from posebench_fast.filters.fast_filters import check_intermolecular_distance

atom_names_cond = np.array(["C", "N", "O", "C", "N", "H", "H", "H"])  # 5 heavy + 3 H
pos_cond = np.random.randn(8, 3).astype(np.float32)
# ... set up mol, pos_pred, atom_names_pred ...
# Raises: IndexError: boolean index did not match indexed array along axis 0;
#         size of axis is 8 but size of corresponding boolean axis is 5

Error traceback

fast_filters.py:295: in check_intermolecular_distance
    atom_names_cond[ids_cond], pos_cond[ids_cond]
    ^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: boolean index did not match indexed array along axis 0;
            size of axis is 8 but size of corresponding boolean axis is 5

Test plan

• New test test_check_intermolecular_distance_with_protein_hydrogens passes with fix, fails without
• Existing test suite (test_rmsd.py) continues to pass
• Verified on real docking data (324 molecules, PDB with 2668 atoms including 1322 H)