Hi,
I am using openbabel C++ API to develope a atom mapping program, and I find
> two problems. And my question is can I customize or create a new
> element/atom by my own.
>
> *(1) Not chemically interpreted groups*
> For example, if I have the following .mol file, R cannot be recognized,
> because I do not have detail information about what R is as a functional
> group. Can I store R as a new element? How can I do that by C++.
>
I had to deal with something like that, and I converted R to deuterium...
Not exactly what you want, but it may help.
>
> *(2) change one atom in a molecular to another atom*
> In the code, I sometimes need to change one atom to a new one, say I want
> to
> change one Carbon (C) to another atom (C1). Can I define a new atom, which
> is totally different from any atoms I will encounter in this .mol file.
>
Same answer, you could use an isotope, even unreal isotope. See e.g.
http://forums.openbabel.org/generate-a-smarts-with-explicit-H-tp3236309p3237233.html
Regards,
Pascal
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