Hello Wenhan Chen
I see that the slow part is optimizing the 3D geometry from JME
format, maybe from smiles too.
See my updated page
http://biomodel.uah.es/en/DIY/JSME/
Using the "diagnostics" you will see the difference.
I think MOL format is the fastest. I have managed to solve the
problem I had with tertiary carbons.
About your specific problme with charged atoms, you will have to test
which format is best understood.
> load SMILES "xxxxxxx" is what I am using. However what I found it,
> the smiles string is not sufficient to depict the original 2D
> structure.
Well, smiles is 1D, so there may be limitations. It works with normal
structures,. but yours seem to be special.
> Some of the molecules we tried to build lost the double bonds when
we
> get the result from the cactus.
MOL will be better at keeping the double bonds.
> conversion of the sdf
> file to other formats could be so troublesome. I thought it is
> straightforward in babel.
That's what Babel is made for -- format conversions. You should not
really need to convert formats, just use one that is best written by
JSME and read by JSmol
However now I am stuck at the adding
> correct number of H atoms
> to the charged atoms in sdf file which is kind of disturbing.
Anyway,
> I still am looking for ways to correct the number of H atoms.
I've drawn this
C+
/ \
C -- -C
and transferred as mol: I get cyclo CH2-CH2-CH
and the +1 charge is there:
label %[charge];
color label yellow;
font label 22;
Transfer as JME works too, and smiles too
Not for you?
------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
