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efficiency

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This commit is contained in:
Greg Landrum
2013-10-15 07:00:04 +02:00
parent 1325a3d465
commit 54c9054ca9
2 changed files with 14 additions and 12 deletions
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24
Contrib/fraggle/FraggleLib.py
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@@ -297,7 +297,7 @@ def generate_fraggle_fragmentation(mol):
# If aliphatic turn to a Sc
#
# Return modified smiles
def atomContrib(subs,smi,options):
def atomContrib(subs,mol,options):
marked = {}
def partialFP(atomID):
@@ -316,7 +316,7 @@ def atomContrib(subs,smi,options):
#generate mol object & fp for input mol
aBits = [];
pMol = Chem.MolFromSmiles(smi)
pMol = Chem.Mol(mol.ToBinary())
pMolFp = Chem.RDKFingerprint(pMol, maxPath=5, fpSize=1024, nBitsPerHash=2, atomBits=aBits)
#generate fp of query_substructs
@@ -365,13 +365,13 @@ def atomContrib(subs,smi,options):
Chem.SanitizeMol(pMol)
except:
sys.stderr.write("Can't parse smiles: %s\n" % (Chem.MolToSmiles(pMol)))
pMol = Chem.MolFromSmiles(smi)
pMol = Chem.Mol(mol.ToBinary())
return Chem.MolToSmiles(pMol)
return pMol
modified_query_fps = {}
def compute_fraggle_similarity(inMol,inSmi,qMol,qSmi,qSubs,options):
def compute_fraggle_similarity(inMol,qMol,qSmi,qSubs,options):
qFP = Chem.RDKFingerprint(qMol, maxPath=5, fpSize=1024, nBitsPerHash=2)
iFP = Chem.RDKFingerprint(inMol, maxPath=5, fpSize=1024, nBitsPerHash=2)
@@ -381,14 +381,12 @@ def compute_fraggle_similarity(inMol,inSmi,qMol,qSmi,qSubs,options):
if qm_key in modified_query_fps:
qmMolFp = modified_query_fps[qm_key]
else:
query_modified = atomContrib(qSubs,qSmi,options)
qmMol = Chem.MolFromSmiles(query_modified)
qmMol = atomContrib(qSubs,qMol,options)
qmMolFp = Chem.RDKFingerprint(qmMol, maxPath=5, fpSize=1024, nBitsPerHash=2)
modified_query_fps[qm_key] = qmMolFp
retrieved_modified = atomContrib(qSubs,inSmi,options)
#print "%s.%s" % (query_modified,retrieved_modified)
rmMol = Chem.MolFromSmiles(retrieved_modified)
rmMol = atomContrib(qSubs,inMol,options)
#wrap in a try, catch
try:
rmMolFp = Chem.RDKFingerprint(rmMol, maxPath=5, fpSize=1024, nBitsPerHash=2)
@@ -403,4 +401,8 @@ def compute_fraggle_similarity(inMol,inSmi,qMol,qSmi,qSubs,options):
return rdkit_sim,fraggle_sim
# def GetFraggleSimilarity(queryMol,refMol):
# """ return the Fraggle similarity between two molecules
# """
# frags = generate_fraggle_fragmentation(mol)

2
Contrib/fraggle/atomcontrib.py
View File

@@ -114,7 +114,7 @@ if __name__ == '__main__':
continue;
#print '>>>',id_
rdkit_sim,fraggle_sim = FraggleLib.compute_fraggle_similarity(iMol,inSmi,query_mols[qID],qSmi,qSubs,options)
rdkit_sim,fraggle_sim = FraggleLib.compute_fraggle_similarity(iMol,query_mols[qID],qSmi,qSubs,options)
day_sim[qID][id_] = rdkit_sim
frag_sim[qID][id_] = max(frag_sim[qID][id_],fraggle_sim)