When I want to replicate one of RDKit’s python functions in C++, I go to the
source. RDKit has very readable wrappers that make this a surprisingly nice
approach (many other pieces of software have pretty ugly wrappers, so this is a
major compliment to RDKit).
For this, I think the source is:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Wrap/MolOps.cpp#L483
There is a nice if-else that shows you how to get the behaviors of asMols =
False, then asMols=True. There is obviously a little bit of manipulation to get
the output into python, but hopefully it is clear how one might make a similar
pure C++ function.
-David
> On Apr 11, 2016, at 8:24 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
>
> lgor,
>
> Yes, this version looks good. But, I am wondering whether I can specify
> asMols. I specify asMols in the python version of my tool, so I want to do
> the same thing for getting the same result in my C++ code. Or could you help
> me to confirm that the version you mentioned actually has the same effect as
> asMols = true?
>
> Thanks.
> Yingfeng
>
> On Sun, Apr 10, 2016 at 11:35 PM, Igor Filippov <igor.v.filip...@gmail.com
> <mailto:igor.v.filip...@gmail.com>> wrote:
> Did you want
> std::vector<boost::shared_ptr<ROMol
> <http://rdkit.org/docs/cppapi/classRDKit_1_1ROMol.html>> >
> RDKit::MolOps::getMolFrags ( const ROMol
> <http://rdkit.org/docs/cppapi/classRDKit_1_1ROMol.html> & mol, bool
> sanitizeFrags = true,
> by any chance? This will return a vector of ROMol's which correspond to the
> contiguous fragments.
>
> Igor
>
>
> On Sun, Apr 10, 2016 at 11:04 PM, Yingfeng Wang <ywang...@gmail.com
> <mailto:ywang...@gmail.com>> wrote:
> Greg,
>
> Thanks. In python, I am using GetMolFrags by the following way,
>
> Chem.GetMolFrags(current_modified_mol, asMols=True, sanitizeFrags=False)
>
> However, there is not a version at the link you mentioned allows me to
> specify asMols. Could you please give me more hints?
>
> Thanks.
> Yingfeng
>
> On Sun, Apr 10, 2016 at 10:49 PM, Greg Landrum <greg.land...@gmail.com
> <mailto:greg.land...@gmail.com>> wrote:
>
>
> On Mon, Apr 11, 2016 at 1:35 AM, Yingfeng Wang <ywang...@gmail.com
> <mailto:ywang...@gmail.com>> wrote:
>
> Thanks. Say, the current RWMol object has 10 bonds, so ids of these bonds
> should be from 1-10. Now, I remove one bond. How do I reset all nine bonds
> with ids from 1-9 (if one or two atoms are gone with this bond, I also want
> to reset the ids of these atoms).
>
> You don't need to do that, it happens automatically
>
> In addition, say, there are two fragments after one bond is removed. How do I
> get these two fragments as mols. In python, I can use Chem.GetMolFrags. But
> how do I get my job done in C++?
>
> There are a number of different versions of MolOps::getMolFrags(), pick the
> on that does what you like:
> http://rdkit.org/docs/cppapi/namespaceRDKit_1_1MolOps.html#ad8100d785d32fb3c173b83949766b87b
>
> <http://rdkit.org/docs/cppapi/namespaceRDKit_1_1MolOps.html#ad8100d785d32fb3c173b83949766b87b>
>
> Since the Python and C++ function/method names are often similar to each
> other, a good way to find answers like this is to google for the name of the
> Python function you are looking for and look for the link to the C++
> documentation in the results.
>
> Best,
> -greg
>
>
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