fix: avoid increasing the model number to match the one from the pdb

[PabloNA97]

Hi!

As always, I hope I didn't misunderstood something - I know you are very busy :)

I was trying to use the 5.0.0 version of extract_residues to find 3 residues from a PDB file. (find the PDB attached). This is the residue selection:

step_extract_residues:
  tool: extract_residues
  paths:
    input_structure_path: receptor.pdb 
    output_residues_path: pocket_residues.pdb
  properties:
    residues: [{'res_id': '37', 'model':'0'}, {'res_id': '49', 'model':'0'}, {'res_id': '112', 'model':'0'}]                            

The std err yields the following:

ExtractResidues: The residues given by user were not found in input structure

The fact is that the biobb sums 1 to the model number when building the structure residues to compare with the user selection. We do this in line 179 of common.py:

"model": str(residue.get_parent().get_parent().get_id()+1),

If I change the model of my selection to 1 then the biobb finds the residues (meaning new_structure is not empty, see line 120 in extract_residues.py) but the corresponding output_residues_path is empty. This is because it tries to write residues of model 1 when the only existing model in the input structure is 0.

I'm not sure of the original reason to add 1 to the model of the residues built using create_biopython_residue(). But applying this change the biobb works as expected and finds the residues from model 0.