There isn't great documentation for this, but the way the current code
works is reasonably simple.
If your reaction has two products (i.e. two molecules separated by a dot),
you will get two products (i.e. two separate molecules) when you call
RunReactants(); that's what you asked for.
Here's a very simple illustration of that with some silly isotope labels to
make it easier to see what's happening:
In [33]: rxn = AllChem.ReactionFromSmarts("[CH:1][O:2]>>[C:1].[O:2]")
In [34]: ps =
rxn.RunReactants((Chem.MolFromSmiles('[13CH2]1[12CH2][14CH2]O[15CH]1N'),))
In [35]: len(ps)
Out[35]: 1
In [36]: len(ps[0])
Out[36]: 2
In [37]: Chem.MolToSmiles(ps[0][0],True)
Out[37]: '[14CH2][12CH2][13CH2][15CH2]N'
In [39]: Chem.MolToSmiles(ps[0][1],True)
Out[39]: '[13CH2][12CH2][14CH2]O'
If you draw the molecule and the products, I think you'll see what's going
on.
If you are just interested in breaking a bond, you need to use "component
level grouping", like this:
In [40]: rxn = AllChem.ReactionFromSmarts("[CH:1][O:2]>>([C:1].[O:2])")
In [41]: ps =
rxn.RunReactants((Chem.MolFromSmiles('[13CH2]1[12CH2][14CH2]O[15CH]1N'),))
In [42]: len(ps)
Out[42]: 1
In [43]: len(ps[0])
Out[43]: 1
In [44]: Chem.MolToSmiles(ps[0][0],True)
Out[44]: 'N[15CH2][13CH2][12CH2][14CH2]O'
That formulation says, in effect, "[C:1] and [O:2] should be in the same
product molecule, but there should be no bond between them".
I should probably do a blog post on this and then incorporate it into the
documentation.
I hope this helps clear things up,
-greg
On Fri, Apr 22, 2016 at 11:31 AM, 吴玲 <monicacul...@126.com> wrote:
> Hi Grégori,
>
> Maybe I don't have a clear understanding of this function, I know the dot
> represent disconncction of two fragments ,and I suppose changes just
> occurs in mapped molecular fragment, the remaining part of reactant is
> invariable, in other words, if mapped molecular fragment breaks based on
> input pattern, the rest of the reactant is maintained.
> So I still expect one site breaks, both ends would be connected by
> in-between atons .Maybe I shoud deep study the documentation of rdkit and
> SMARTS definition.
> Thank for your helps!
>
> Monica
>
>
>
>
>
> At 2016-04-22 16:32:39, greg...@gerebtzoff.com wrote:
> >Hi Monica,
> >
> >As Greg stated, why do you expect your product not to be fragmented?
> >I suggest you to have a careful look at the SMARTS definition (for
> >instance from Daylight:
> >http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html)
> >In SMARTS patterns, the dot indicates disconnected fragments. Thus you
> >obtain in your product... disconnected fragments.
> >
> >Best,
> >
> >Grégori
> >
> >
> >Le 2016-04-22 10:13, 吴玲 a écrit :
> >> Greg,
> >>
> >> After changing the pattern into
> >> "[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11]
> >> , I get the same result .A ring structure just like you said is broken
> >> into pieces.
> >> pattern:[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:8]=[C:7]=[O:9].[N+:4].[C:6][C:5]=[O:11]
> >>
> >> output:[O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=[O-].[NH4+].CCC=O
> >>
> >> The input reactant ([O-]C(=O)C1=CNC(=O)CC1) if mapped with
> >> pattern'reactants ,it should be "
> >> [O-:8][C:7](=[O:9])[C:6]1=[C:5][N:4][C:2](=[O:3])[C:1][C:*]1,
> >>
> >> what I mean is that the input reactant with a ring that CARBON6
> >> connect with CARBON1 by CARBON* ,why the CARBON6 AND CARBON1 IN THE
> >> product is not connected by the CARBON* ?
> >>
> >> Thanks a lot,
> >>
> >> -Monica
> >>
> >> At 2016-04-20 12:43:36, "Greg Landrum" <greg.land...@gmail.com> wrote:
> >>
> >>> Monica,
> >>>
> >>> Why do you think you should get a single chain from the ring
> >>> structure?
> >>> If you look at the atom mapping in your input reaction:
> >>>
> >>>
> >> [C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11]
> >>>
> >>> You've told it to put:
> >>> - carbons 1 and 2 from the reactant into product 1
> >>> - carbon 8 into product 2, carbon 7 into product 2 but converted
> >>> into an oxygen first.
> >>> - carbon 5 and 6 into product 4. In other words: you requested that
> >>> the input molecule be broken into pieces.
> >>>
> >>> The atom mapping tells you which atoms in the reactants correspond
> >>> to which atoms in the products.
> >>>
> >>> I would suggest that you look carefully at your reaction
> >>> definitions, in particular the atom mapping numbers, in Marvin and
> >>> make sure that you think that what you're asking for makes sense.
> >>>
> >>> -greg
> >>>
> >>> On Wed, Apr 20, 2016 at 6:04 AM, 吴玲 <monicacul...@126.com>
> >>> wrote:
> >>>
> >>>> Hi Greg,
> >>>>
> >>>> Thanks a lot for previous help! There is another question in
> >>>> RunReactants I want to ask for some help.
> >>>>
> >>>> when I input the pattern as
> >>>>
> >>>
> >> “[C:1][C:2](=[O:3])[N+0:4][C:5]=[C:6][C:7]([O-:8])=[O:9].[OH2:10].[OH2:11]>>[C:1][C:2]([O-:10])=[O:3].[O:7]=[C:8]=[O:9].[N+:4].[C:6][C:5]=[O:11]”
> >>>> and give the reactants rs1 =
> >>>>
> >>>
> >> ["[O-]C(=O)C1=CNC(=O)CC1","CC(=O)NC=C(CC([O-])=O)C([O-])=O","CC(=O)NC=C(C(CO)C([O-])=O)C([O-])=O"]
> >>>> ,rs2 = ['O'] , rs3 = ['O'],
> >>>> when I check the output product, I find that the first reactants
> >>>> with a ring structure divided into four sections instead of three
> >>>> parts containing a NH4+,a CO2,and a long chain composed by the
> >>>> remained two fragments.In other words , I think that the product
> >>>> should be like this:
> >>>>
> >>>> what's the matter with this pattern? why this reaction predicted
> >>>> is wrong and the other is correct?(output result attached below).
> >>>>
> >>>> pattern:
> >>>>
> >>>> 1 [O-]C(=O)C1=CNC(=O)CC1.O.O>>CCC(=O)[O-].O=C=O.[NH4+].CCC=O
> >>>>
> >>>> 2
> >>>>
> >>>
> >> CC(=O)NC=C(CC([O-])=O)C([O-])=O.O.O>>CC(=O)[O-].O=C=O.[NH4+].O=CCCC(=O)[O-]
> >>>>
> >>>> 3
> >>>>
> >>>
> >> CC(=O)NC=C(C(CO)C([O-])=O)C([O-])=O.O.O>>CC(=O)[O-].O=C=O.[NH4+].O=CCC(CO)C(=O)[O-]
> >>>>
> >>>> best wishes,
> >>>>
> >>>> monica
> >>>>
> >>>>
> >>>
> >> ------------------------------------------------------------------------------
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> >>
> >>
> >>
> >> Links:
> >> ------
> >> [1] https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> >> [2] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >>
> >> ------------------------------------------------------------------------------
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