pdb2sql selects one alternative location for atoms

[FarzanehParizi]

Better pdb2sql has an option to select one alternative location for atoms of a residue

Description of problem While checking the similarity of two PDBs (decoy & ref) when there are alternative locations of atoms for a PDB, it fails to calculate RMSD, as one has more atoms for a residue.

Suggested solution pdb2sql can have a feature that the user selects which of the alternative locations to select (e.g. altloc= "A") while generating a pdb2sql object (not using only occ value on PDB column)

Alternative solution While checking the similarity of two pdb2sql objects, selects one alternative location

Additional context If letting the user defines based on occ value on PDB column, it happens in some PDBs that the occ value is around 50 and that would not be that much helpful

[FarzanehParizi]

You can use the following PDB files for this issue for PDB ID: 5KSA (change the extension from txt to pdb)

BL00060001_decoy.txt BL00060001_ref.txt

[FarzanehParizi]

The previous case had an alternative location in the Receptor region. The following case has an alternative location in the Ligand region. PDB ID: 6DFS

6DFS_6BLX_BL00140001_decoy.txt 6DFS_6BLX_BL00140001_ref.txt

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