Fix residue matching when computing RMDSs

• Fix some bugs

• Updated compute_CapriClass conditions

• Added atom name selelction for lrmsd calculation
• Removed hardcoded chainIDs and added chainID selection in StructureSimilarity

• Added many2sql to support read multiple PDB files
• Added support for Path objects of input PDB files
• Added support for help(pdb2sql)
• Updated assignment of chain IDs in StructureSimilarity

• Added align to superpose a structure to a specific axis or plane
• Added superpose to superpose two structures based on selections
• Added fetch to download PDB file with given PDB ID
• Updated interface object to take pdb2sql object as input

1. add CITATION.cff
2. add .zenodo.json

Main updates:

1. Add unit tests
2. Add documentation

Update transform and add corresponding tests.

Update :
.* no extra was removed
.* init was updated
.* read not only pdb but list and numpy arrays