If you working in python this should help you.
I wrote these scripts when using obspectrophores. "get_spectrophore.py"
will get you a compound spectrophore (tested with sdf but should work with
other obabel supported format).The second one will compute their euclidean
distances.
def get_spectrophore(ligand):
import subprocess
import numpy as np
"""
:param : ligand
:return: obspectrophore in python dictionary form {compound : spectrophore}.
"""
executable = "obspectrophore" #path to obspectrophore executable
cmd = [ executable, '-i', ligand]
try:
output = subprocess.check_output(cmd, stderr=
subprocess.STDOUT).decode('ascii') #check_output
output = [e for e in output.split("Angstrom")[-1].split("\n")][2:-1]
output = [e.split("\t")[:-1] for e in output]
out_dict = {}
for e in output:
out_dict[e[0]] = np.array([ float(e) for e in e[1:]])
output = out_dict
except subprocess.CalledProcessError as e:
sys.stderr.write(e.output.decode('ascii'))
return output
ligands = "test.sdf"
print(get_spectrophore(ligands))def obspectrophores_euclidean(ligand1, ligand2):
import numpy as np
"""
:param ligand1
:param ligand2
:return:euclidean distance of their obspectrophores.
"""
score = ""
ligand1_spectrophore = get_spectrophore(ligand1)
ligand2_spectrophore = get_spectrophore(ligand2)
scores =[] #{('ZINC000000000221', 'ZINC000000000221'): 0.0 key: tuple of
ligand, value: euclidean distance
for lig2 in ligand2_spectrophore:
for lig1 in ligand1_spectrophore:
spec_euc_dist = np.linalg.norm((ligand1_spectrophore[lig1] -
ligand2_spectrophore[lig2]))
scores.append((lig1, lig2, spec_euc_dist))
return scores
test_ligand = "test.sdf"
print(obspectrophores_euclidean(test_ligand, test_ligand)) #should return zero_______________________________________________
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