Hi Axel,
I was sure there was something in the core that did this but I can't seem to
find it now! I have a function that uses isotope labelled dummy atoms to attach
fragments if it's of any use? As with most the code I write, it doesn't have
the greatest error handling, or rational use of deepcopy.
def connectAllFragsIsomeric(molList):
numFrags = len(molList)
isotopeList = []
allIsos = []
# This loop is to make a list of molecules along with which isotopes they
contain
# so I can keep track of where which R-Groups are later
for i in range(numFrags):
molList[i] = processToIsomericMol(molList[i])
for atom in molList[i].GetAtoms():
isotope = atom.GetIsotope()
if(isotope):
isotopeList.append(isotope)
allIsos.append(isotope)
molList[i] = [molList[i], deepcopy(isotopeList)]
del isotopeList[:]
allIsos.sort()
allIsos = list(set(allIsos))
for i in allIsos:
reactantIdx = []
# Find two fragments with the labeled R-group
for j in range(len(molList)):
if(i in molList[j][1]):
reactantIdx.append(j)
# Sanity check that there are only two frags with the same R-group
if(len(reactantIdx) != 2):
print 'Too many fragments with a R-groups numbered with %i' % i
exit()
rxn =
AllChem.ReactionFromSmarts('[a,A:1]-[%i*:2].[a,A:3]-[%i*:4]>>[a,A:1]-[a,A:3].[%i*:2][%i*:4]'
% (i, i, i, i))
ps = rxn.RunReactants((molList[reactantIdx[0]][0],
molList[reactantIdx[1]][0]))
newMol = ps[0][0]
newIsos = list(set(molList[reactantIdx[0]][1]) |
set(molList[reactantIdx[1]][1]))
newIsos.remove(i)
molList.append([newMol, newIsos])
del molList[reactantIdx[1]]
del molList[reactantIdx[0]]
return molList
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E [email protected] | W www.icr.ac.uk | Twitter
@ICRnews
________________________________________
From: Axel Pahl [[email protected]]
Sent: 03 July 2015 07:27
To: RDKit Discuss
Subject: [Rdkit-discuss] create a mol from core and mol fragments
Dear fellow RDKitters,
I use ReplaceCore and GetMolFrags to create a 2D SAR table:
tmp = Chem.ReplaceCore(mol, core_mol, labelByIndex=True)
frag_mols = list(Chem.GetMolFrags(tmp, asMols=True))
Is it also possible to do the reverse? Create a new molecule from the core and
two fragments?
I would like to fill the gaps in the SAR table and calculate some properties
for these molecules.
Kind regards,
Axel
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
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