auto-detect same entity for non-ligands

[arogozhnikov]

Description / Motivation

ihm does not like when complex has identical entities, even with different names (and we for simplicity created single entity per asym_id).

Here is their test: https://github.com/ihmwg/python-ihm/blob/cc4aaded6f705cd3e22de48c0ca9865b05f955da/test/test_dumper.py#L507

this commit introduces automated detection of same entity, entity is named after the first entity replica (e.g. Entity example-peptide-copy1 for example below).

Test plan

run with FASTA input:

>protein|name=peptide-1
AGSHSMR
>protein|name=peptide-2
AGSHSMR
>protein|name=peptide-3
AGSHSMRAA
>protein|name=peptide-4
AGSHSMRAA
>ligand|name=ligand-1
C
>ligand|name=ligand-2
C
>ligand|name=ligand-3
CC
>ligand|name=ligand-4
CC