The approach used in Nick's solution - using reactions to put the molecules
together - will certainly work. It's very general and flexible.
For something this specific, you could also use Chem.CombineMols and an
RWMol. Here's a simple demonstration of that:
In [16]: m1 = Chem.MolFromSmiles('c1ccccc1[*:1]')
In [17]: m2 = Chem.MolFromSmiles('CCO[*:1]')
In [18]: m3 = Chem.CombineMols(m1,m2)
In [19]: em = Chem.RWMol(m3)
In [22]: em.AddBond(9,5,Chem.BondType.SINGLE)
Out[22]: 11
In [23]: em.RemoveAtom(10)
In [24]: em.RemoveAtom(6)
In [25]: Chem.SanitizeMol(em)
Out[25]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
In [26]: Chem.MolToSmiles(em)
OUT: 0
Out[26]: 'CCOc1ccccc1'
This requires, of course, a bit more code to identify where bonds should be
formed and the atoms that should be deleted (be sure you do this in order
of decreasing index).
Best,
-greg
On Fri, Jul 3, 2015 at 9:19 AM, Nicholas Firth <[email protected]>
wrote:
> 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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