OBAtom::GetType() ??

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OBAtom::GetType() ??

B.W.H. van Beest
Hi,

Can somebody explain to me what the "OBAtom::GetType()" method returns?
I don't understand what OpenBabel intends to do here.

For example, when I have a file in the Tripos mol2 format (see fragment
below), the atoms read
have the type "C.3" for the first and the last atom, and "C.2" for the
atoms 2-9. (column 6 below)

When I read the mol2-file into an OBMol, then, when I ask for the type
then the result is always "C3", for all 10 atoms.
When I set the type to e.g. "foo", then I get an error message that the
type "foo" is not valid. Fair enough,
but is there a way that I can set the type (in the mol2 file) to any
string I like, and then get the same string back
when I ask fot the OBAtomM::GetType()?


@<TRIPOS>ATOM
      1 C1        3.690   2.630   2.480    C.3   0 aap1 0.12
      2 C2        4.940   1.840   2.810    C.2   0 aap2 1.23
      3 C3        6.130   2.710   2.420    C.2   0 aap3 1.23
      4 C4        7.420   1.980   2.740    C.2   0 aap4 1.23
      5 C5        8.590   2.860   2.340    C.2   0 aap5 1.23
      6 C6        9.890   2.140   2.660    C.2   0 aap6 1.23
      7 C7       11.060   3.030   2.250    C.2   0 aap7 1.23
      8 C8       12.320   2.270   2.580    C.2   0 aap8 1.23
      9 C9       13.550   3.060   2.180    C.2   0 aap9 1.23
     10 C10      14.690   2.130   2.510    C.3   0 aap0 0.34


Kind Regards,
Bertwim

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Re: OBAtom::GetType() ??

Noel O'Boyle
Administrator
GetType returns the internal OpenBabel atom type. If you want to
translate this to Sybyl atom types, see the example code at
http://baoilleach.blogspot.com/2008/07/calculate-circular-fingerprints-with.html
.

Does this answer your question?

- Noel

2009/10/21 B.W.H. van Beest <[hidden email]>:

> Hi,
>
> Can somebody explain to me what the "OBAtom::GetType()" method returns?
> I don't understand what OpenBabel intends to do here.
>
> For example, when I have a file in the Tripos mol2 format (see fragment
> below), the atoms read
> have the type "C.3" for the first and the last atom, and "C.2" for the
> atoms 2-9. (column 6 below)
>
> When I read the mol2-file into an OBMol, then, when I ask for the type
> then the result is always "C3", for all 10 atoms.
> When I set the type to e.g. "foo", then I get an error message that the
> type "foo" is not valid. Fair enough,
> but is there a way that I can set the type (in the mol2 file) to any
> string I like, and then get the same string back
> when I ask fot the OBAtomM::GetType()?
>
>
> @<TRIPOS>ATOM
>      1 C1        3.690   2.630   2.480    C.3   0 aap1 0.12
>      2 C2        4.940   1.840   2.810    C.2   0 aap2 1.23
>      3 C3        6.130   2.710   2.420    C.2   0 aap3 1.23
>      4 C4        7.420   1.980   2.740    C.2   0 aap4 1.23
>      5 C5        8.590   2.860   2.340    C.2   0 aap5 1.23
>      6 C6        9.890   2.140   2.660    C.2   0 aap6 1.23
>      7 C7       11.060   3.030   2.250    C.2   0 aap7 1.23
>      8 C8       12.320   2.270   2.580    C.2   0 aap8 1.23
>      9 C9       13.550   3.060   2.180    C.2   0 aap9 1.23
>     10 C10      14.690   2.130   2.510    C.3   0 aap0 0.34
>
>
> Kind Regards,
> Bertwim
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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