[BioPython] Trying to extract a (single) ligand from a PDB file (dimere)

[Florian Koelling]

Hi folks!
I'm new to biopython and tried to write a parser to extract a Ligand
from it 's PDB file. It even works - but I've got a dimer with two
ligands  and  I'd like to have a new PDB file containing only one
ligand.
My trials to acces the residue(the ligand) via the residue id failed...

Hope you can Help me.

My code so far :-((((

#### LIGAND DETECTION

import Bio.PDB
from Bio.PDB import*
import Numeric


parser = PDBParser()                                    
structure = parser.get_structure('s', '2F1G.pdb')
print  "\n"
print "structure_object_created"

requirement_id_list = []                
requirement_names_list = []                                     

residue = structure.get_residues()



for i in residue:       
        residue_id = i.get_id()                                         
                        
        if residue_id[0]
!='W':                                         #parsing water
                
                        if residue_id[0] !='
':                         #parsing
                                resname=(residue_id[0]).strip('H_')     #remove
het_flag                                
                                        
                                requirement_names_list.append(resname)          #RES
NAME
                                requirement_id_list.append
(residue_id[1])      #RES ID

###Req_lists: requirements for writing

print '\n'
print requirement_names_list, 'ligands_Names-> Hetatms '
print requirement_id_list, 'ligands_IDs-> Hetatms '
print '\n'

if len(requirement_names_list) == 0:
        print 'no_hetatms found!'
        assert()



class HetatmSelect(Select):                             
                def accept_residue(self, residue):
                                                                
                        if residue.get_resname()  in
requirement_names_list[0] : #writing 1st_element
        
                                                        
                                return 1
                        else:
                                return 0        


io=PDBIO()                                              ###WRITING
io.set_structure(structure)
io.save('ligand_parsed.pdb', HetatmSelect())
print "writing parsed pdb file .... Done"


Thanx alot!

Floran