def combine_score(pdbfile,
recepChain,
ligChain,
statpotrun=True,
vdwrun=True,
electrorun=True,
shaperun=True,
pH=True,
depth="msms",
dist=8.6):
combined_dict = {}
my_struct = pdbtools.read_pdb(pdbfile)
depth_dict = pdb_resdepth.calculate_resdepth(structure=my_struct,
pdb_filename=pdbfile,
method=depth)
distmat = matrice_distances.calc_distance_matrix(structure=my_struct,
depth=depth_dict,
chain_R=recepChain,
chain_L=ligChain,
dist_max=dist,
method=depth)
combined_dict["pdb"] = pdbfile.split("/")[-1]
if statpotrun == True:
statpot = knowledge.parse_distance_mat(distmat, method=["glaser"])
combined_dict["statpot"] = statpot
if vdwrun == True:
vdw = Lennard_Jones.lennard_jones(dist_matrix=distmat)
combined_dict["vdw"] = vdw
if electrorun == True:
electro = electrostatic.electrostatic(inter_resid_dict=distmat, pH=pH)
combined_dict["electro"] = electro
if shaperun == True:
shape = shape_complement.runshape(structure=my_struct,
recepChain=recepChain,
depth_dict=depth_dict,
ligChain=ligChain,
method=depth)
combined_dict["shape"] = shape
# foldx = TOADD
return (combined_dict)
input2 (BioPDB Structure): Complex's structure
OUPUT:
result(List): atom coordinates
"""
chain = aa[0]
code = aa[1]
position = aa[2]
coord = None
if code == 'GLY':
atom = structure[0][chain][int(position)]['CA']
return atom.get_coord()
elif code in [
'PRO', 'ALA', 'VAL', 'LEU', 'ILE', 'MET', 'CYS', 'PHE', 'TYR',
'TRP', 'HIS', 'LYS', 'ARG', 'GLN', 'ASN', 'GLU', 'ASP', 'SER',
'THR'
]:
atom = structure[0][chain][position]['CB']
return atom.get_coord()
return 'Error'
if __name__ == '__main__':
structure = pdbt.read_pdb("2za4_modified.pdb")
depth = resd.calculate_resdepth(structure, "2za4_modified.pdb")
dist_matrix = calc_distance_matrix(structure, depth, ["A"], ["B"])
parse_distance_mat(dist_matrix, ['glaser', 'pons_surf'])
'''
Calculating Lennard-Jones potential
INPUT:
input1(Dictionary): Distances dictionary. Output of calc_distance_matrix() function
input2 (Float): sigma value for Lennard-Jones function. Default value: 3.9
input3 (Int): epsilon value for Lennard-Jones function. Default value: 10
OUPUT:
result(Float): Lennard-Jones energy value for the complex
'''
energy = 0
for dist in dist_matrix.values():
frac = pow((sigma / dist), 6)
part_energy = 4 * epsilon * (pow(frac, 2) - frac)
energy += part_energy
return energy
if __name__ == "__main__":
filename = sys.argv[1]
structure = pdbt.read_pdb(filename)
depth = resd.calculate_resdepth(structure, filename)
dist_matrix = distm.calc_distance_matrix(structure, depth, chain_recp,
chain_lig)
lennard_jones(dist_matrix)
rec_grid = dict_to_mat(grid_dict=rec_grid_dict,
L=grid_parameters[0],
resolution=resolution)
lig_grid = dict_to_mat(grid_dict=lig_grid_dict,
L=grid_parameters[0],
resolution=resolution)
result = multi_mat(rec_grid=rec_grid, lig_grid=lig_grid)
return (result)
if __name__ == "__main__":
"""
Usage for testing
shape_complement.py path/to/complex.pdb recepChain1,recepChainN ligChain1,ligChainN
"""
myfile = sys.argv[1]
recepChain = sys.argv[2].split(",")
ligChain = sys.argv[3].split(",")
my_struct = pdbtools.read_pdb(myfile)
depth_dict = pdb_resdepth.calculate_resdepth(structure=my_struct,
pdb_filename=myfile)
tmp = runshape(structure=my_struct,
recepChain=recepChain,
ligChain=ligChain,
depth_dict=depth_dict,
resolution=2,
depthCutoff=4,
resScale="atom")
print(tmp)