Always write intra-residue bonds if available

[padix-key]

With the addition of NextGen PDBx files the include_bonds parameter was previously added to pdbx.set_structure(). This option had the advantage that both the 'classical' PDBx file (without chem_comp_bond category) and 'next-gen' PDBx file (with chem_comp_bond category) could be written.

However, in the meantime the 'next-gen' files have become the new standard files in the PDB, i.e. downloaded PDBx files always contain the chem_comp_bond category. Hence, this parameter does not make sense anymore and in my opinion rather leads to confusion: the struct_conn category (inter-residue bonds) is always written, if bonds are available, but the chem_comp_bond category (intra-residue bonds) is only written if include_bonds=True.

In consequence, this PR deprecates the include_bonds parameter in pdbx.set_structure(). It does not have an effect anymore, and chem_comp_bond is always written if AtomArray.bonds is available.

[codspeed-hq]

CodSpeed Performance Report

Merging #804 will degrade performances by 15.97%

_{Comparing padix-key:pdbx-next-gen (ad3fa31) with main (1d906ba)}

Summary

⚡ 1 improvements
❌ 3 (👁 3) regressions
✅ 55 untouched benchmarks

Benchmarks breakdown

	Benchmark	BASE	HEAD	Change
👁	benchmark_compress	570.4 ms	678.8 ms	-15.97%
👁	benchmark_deserialize_pdbx[cif]	92 ms	107.6 ms	-14.48%
👁	benchmark_serialize_pdbx[cif]	176.3 ms	203.5 ms	-13.36%
⚡	benchmark_set_structure[bcif-False]	11.6 ms	7.9 ms	+48.02%

[padix-key]

The performance decreased in some benchmarks as the newly downloaded PDBx files have more categories than before.