def PrintTanimoto(molA, molB, minb, maxb):
fpA = oegraphsim.OEFingerPrint()
fpB = oegraphsim.OEFingerPrint()
numbits = 2048
atype = oegraphsim.OEFPAtomType_DefaultPathAtom
btype = oegraphsim.OEFPBondType_DefaultPathBond
oegraphsim.OEMakePathFP(fpA, molA, numbits, minb, maxb, atype, btype)
oegraphsim.OEMakePathFP(fpB, molB, numbits, minb, maxb, atype, btype)
print("Tanimoto(A,B) = %.3f" % oegraphsim.OETanimoto(fpA, fpB))
def PrintTanimoto(molA, molB, atype, btype):
fpA = oegraphsim.OEFingerPrint()
fpB = oegraphsim.OEFingerPrint()
numbits = 2048
minb = 0
maxb = 5
oegraphsim.OEMakePathFP(fpA, molA, numbits, minb, maxb, atype, btype)
oegraphsim.OEMakePathFP(fpB, molB, numbits, minb, maxb, atype, btype)
print("Tanimoto(A,B) = %.3f" % oegraphsim.OETanimoto(fpA, fpB))
def calculate_mol_similarity(molA, molB):
"""
Function to calculate the similarity between two oemol objects
should be used to utils/openeye.py or openmoltools
:param molA: oemol object of molecule A
:param molB: oemol object of molecule B
:return: float, tanimoto score of the two molecules, between 0 and 1
"""
fpA = oegraphsim.OEFingerPrint()
fpB = oegraphsim.OEFingerPrint()
oegraphsim.OEMakeFP(fpA, molA, oegraphsim.OEFPType_MACCS166)
oegraphsim.OEMakeFP(fpB, molB, oegraphsim.OEFPType_MACCS166)
return oegraphsim.OETanimoto(fpA, fpB)
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
import sys
from openeye import oechem
from openeye import oegraphsim
# @ <SNIPPET-CALC-FROM-FILE>
if len(sys.argv) != 3:
oechem.OEThrow.Usage("%s <queryfile> <targetfile>" % sys.argv[0])
ifs = oechem.oemolistream()
if not ifs.open(sys.argv[1]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % sys.argv[1])
qmol = oechem.OEGraphMol()
if not oechem.OEReadMolecule(ifs, qmol):
oechem.OEThrow.Fatal("Unable to read query molecule")
qfp = oegraphsim.OEFingerPrint()
oegraphsim.OEMakeFP(qfp, qmol, oegraphsim.OEFPType_Path)
if not ifs.open(sys.argv[2]):
oechem.OEThrow.Fatal("Unable to open %s for reading" % sys.argv[2])
tfp = oegraphsim.OEFingerPrint()
for tmol in ifs.GetOEGraphMols():
oegraphsim.OEMakeFP(tfp, tmol, oegraphsim.OEFPType_Path)
print("%.3f" % oegraphsim.OETanimoto(qfp, tfp))
# @ </SNIPPET-CALC-FROM-FILE>
def cluster_similar_molecules(
smiles, fingerprint_type=oegraphsim.OEFPType_Tree, eps=0.5, min_samples=2
):
"""The method attempts to cluster a sets of molecules based on their
similarity using a Tanimoto distance metric and the `sklearn` DBSCAN
clustering code.
Notes
-----
This is based on the code by David Mobley:
https://github.com/openforcefield/release-1-benchmarking/blob/master/QM_molecule_selection/divide_sets.ipynb
Parameters
----------
smiles: list of str
The SMILES representations of the molecules to cluster.
fingerprint_type
The type of molecular fingerprint to use.
eps: float
The `eps` parameter to pass as an argument to DBSCAN while clustering.
min_samples: int
The `min_samples` parameter to pass as an argument to DBSCAN while
clustering.
Returns
-------
dict of str and list of str
The clustered SMILES patterns.
"""
assert isinstance(smiles, list)
# Build fingerprints
fingerprints = {}
for smiles_pattern in smiles:
oe_molecule = oechem.OEMol()
oechem.OEParseSmiles(oe_molecule, smiles_pattern)
fingerprint = oegraphsim.OEFingerPrint()
oegraphsim.OEMakeFP(fingerprint, oe_molecule, fingerprint_type)
fingerprints[smiles_pattern] = fingerprint
# Build a similarity matrix
distance_matrix = np.zeros((len(smiles), len(smiles)))
for i, smiles_i in enumerate(smiles):
for j, smiles_j in enumerate(smiles):
if i == j:
continue
distance_matrix[i, j] = 1.0 - oegraphsim.OETanimoto(
fingerprints[smiles_i], fingerprints[smiles_j]
)
# Cluster the data
clustering = DBSCAN(eps=eps, min_samples=min_samples, metric="precomputed")
clustered_smiles = clustering.fit(distance_matrix)
labels = clustered_smiles.labels_
smiles_by_cluster = {}
for label in set(labels):
smiles_by_cluster[label] = [
smiles[i] for i, x in enumerate(labels) if x == label
]
return smiles_by_cluster
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from openeye import oechem
from openeye import oegraphsim
# @ <SNIPPET-FP-TANIMOTO>
molA = oechem.OEGraphMol()
oechem.OESmilesToMol(molA, "c1ccc2c(c1)c(c(oc2=O)OCCSC(=N)N)Cl")
fpA = oegraphsim.OEFingerPrint()
oegraphsim.OEMakeFP(fpA, molA, oegraphsim.OEFPType_MACCS166)
molB = oechem.OEGraphMol()
oechem.OESmilesToMol(molB, "COc1cc2ccc(cc2c(=O)o1)NC(=N)N")
fpB = oegraphsim.OEFingerPrint()
oegraphsim.OEMakeFP(fpB, molB, oegraphsim.OEFPType_MACCS166)
molC = oechem.OEGraphMol()
oechem.OESmilesToMol(molC, "COc1c(c2ccc(cc2c(=O)o1)NC(=N)N)Cl")
fpC = oegraphsim.OEFingerPrint()
oegraphsim.OEMakeFP(fpC, molC, oegraphsim.OEFPType_MACCS166)
print("Tanimoto(A,B) = %.3f" % oegraphsim.OETanimoto(fpA, fpB))
print("Tanimoto(A,C) = %.3f" % oegraphsim.OETanimoto(fpA, fpC))
print("Tanimoto(B,C) = %.3f" % oegraphsim.OETanimoto(fpB, fpC))
# @ </SNIPPET-FP-TANIMOTO>
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from __future__ import print_function
from openeye import oechem
from openeye import oegraphsim
mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "c1ccccc1")
# @ <SNIPPET-PATH-FP-TYPE>
fpA = oegraphsim.OEFingerPrint()
numbits = 1024
minbonds = 0
maxbonds = 5
oegraphsim.OEMakePathFP(fpA, mol, numbits, minbonds, maxbonds,
oegraphsim.OEFPAtomType_DefaultPathAtom,
oegraphsim.OEFPBondType_DefaultPathBond)
fpB = oegraphsim.OEFingerPrint()
numbits = 2048
oegraphsim.OEMakePathFP(fpB, mol, numbits, minbonds, maxbonds,
oegraphsim.OEFPAtomType_DefaultPathAtom,
oegraphsim.OEFPBondType_DefaultPathBond)
print("same fingerprint types = %r" % oegraphsim.OEIsSameFPType(fpA, fpB))
print(oegraphsim.OETanimoto(fpA, fpB))
# @ </SNIPPET-PATH-FP-TYPE>
