Delete Clashes between water and protein

Delete_Clashes.py

## Using BioPython Doing All the Manipulations
## 
import numpy as np
from Bio.PDB import *
from Bio.KDTree import KDTree


parser_p = PDBParser()
parser_m = PDBParser()
#3eiy_stripped.pdb LSD_POPE.pdb 
prot = parser_p.get_structure('CXCR4-A','./3eiy_stripped.pdb')
memb = parser_p.get_structure('POPE-M' ,'./onlyWater.pdb')

prot_atoms = [at for at  in prot.get_atoms() ] 
memb_atoms = [at for at  in memb.get_atoms()] 
prot_coos = np.array([at.coord for at  in prot_atoms],np.float)
memb_coos = np.array([at.coord for at  in memb_atoms],np.float)
clashes = [] 
atom_kdtree = KDTree(3)
atom_kdtree.set_coords(memb_coos)
for p in range(len(prot_coos)): 
    atom_kdtree.search(prot_coos[p], 1.500)
    res = list(atom_kdtree.get_indices()) 
    clashes = clashes + res 
del_res = [memb_atoms[c].get_parent().get_id()[1] for c in clashes]
del_res = list(set(del_res))
for chain in memb[0]: [chain.detach_child((' ', ids, ' ')) for ids in del_res]
io = PDBIO()
io.set_structure(memb)
#io.save('Cropped_MembranePOPE_wProtein.pdb')
io.save('watercropped.pdb')