Expansion of port-bonding

[timbernat]

Several refinements and additions planned for the rdutils.bonding module:

• Considering making part of rdutils directly
• Need to test and verify that saturated structures generate (under normal usage) valid RDKit Mols
• Add support for labeling newly-created ports (as commented out here by decrease_bond_order uniquely via int_complement
• Re-implement increase_bond_order to change bond in "one-shot" (rather than by iterating single-order upconversions). This would remove the need to relocate atom IDs by map number after each upconversion and would simplify sanitization
• Canonicalize alternate implementation of _increase_bond_order backend method
• Revisit implementations of dissolve_bond and saturate_ports
• bonding.permutation :
  • add support for Cycle-based bond remap input (either via dict or directly via maths.cominbatorics.permutations.Cycle/Permutation) to reduce redundancy in current notation
  • add option to pass custom arrow delimiters for atom bond change (rather than just "----->" and "--x-->"
  • Have bond changes be logged, rather than printed
• bonding.substitution : implement capping such that newly-inserted atoms in cap groups are appended to the list of atom ids, rather than mixed in (i.e. reimplement hydrogenate_mol_ports and saturate_ports to preserve initial atom order via Chem.rdmolops.RenumberAtoms)