update function to write PDB from chorizo, and fix a bug that ignored input H positions

[diogomart]

Minor changes with regards to LinkedRDKitChorizo.to_pdb(), just keeping up to date with all the recent refactoring.

H position on link atoms, which are atoms that have bonds to adjacent residues, were being replaced by RDKit calculated positions. This is now fixed.

[diogomart]

Thanks :)