[BioPython] protein-ligand interactions

[mitlox]

Thank you very much for your solution.

Additionally It would be nice to have a structure object with the same 
information like in "near_ligand.pdb", that I do not need to read a new 
pdb file again:
structureMOD = Bio.PDB.PDBParser().get_structure("near", "near_ligand.pdb").

It is possible to have both a "near_ligand.pdb" and the same structure 
object?

Thank you in advance.

Best regards

Peter Cock wrote:
> Your structureCA object is just a python list, containing Residue objects.
> Instead you need to create a new object with the partial chain - which
> can be done by creating structure, model and chain objects manually.
>
> However, I suggest you re-read pages 5 and 6 of the Bio.PDB
> documentation for the recommend approach:
> http://biopython.org/DIST/docs/cookbook/biopdb_faq.pdf
> In your case, you'll want to write your own selection class using the
> residue distance to the ligand.  I recognise this might seem rather
> complicated for a python novice as you have to create your own
> class - so here is my solution:
>
> import Bio.PDB
> import numpy
>
> pdb_code = "1E8W"
> pdb_filename = "1E8W.pdb"
>
> structure = Bio.PDB.PDBParser().get_structure(pdb_code, pdb_filename)
> model = structure[0]
> chainA = model["A"]
>
> def residue_dist_to_ligand(protein_residue, ligand_residue) :
>     """Returns distance from the protein C-alpha to the closest ligand atom."""
>     distances = []
>     for atom in ligand_residue :
>         diff_vector  = protein_residue["CA"].coord - atom.coord
>         distances.append(numpy.sqrt(numpy.sum(diff_vector * diff_vector)))
>     return min(distances)
>
> class NearLigandSelect(Bio.PDB.Select):
>     def __init__(self, distance_threshold, ligand_residue) :
>         self.threshold = distance_threshold
>         self.ligand_res = ligand_residue
>
>     def accept_residue(self, residue):
>         if residue == self.ligand_res :
>             return True #change this to False if you don't want the ligand
>         else :
>             dist = residue_dist_to_ligand(residue, self.ligand_res)
>             return dist < self.threshold
>
> io=Bio.PDB.PDBIO()
> io.set_structure(structure)
> #From looking at the PDB file, ligand is last residue in chain A
> ligand_res = chainA.child_list[-1]
> #Going to use a distance theshold of 4A
> io.save("near_ligand.pdb", NearLigandSelect(4, ligand_res))
> print "Done"
>
> Peter
>
>